mm9_v1_chr9_+_120058842_120058868	48.487	SOX2.p2	AK013799|Mobp|17433|myelin-associated oligodendrocytic basic protein	AK019323|Mobp|17433|myelin-associated oligodendrocytic basic protein	AK028057|Mobp|17433|myelin-associated oligodendrocytic basic protein	AK083103|Mobp|17433|myelin-associated oligodendrocytic basic protein	AK140055|Mobp|17433|myelin-associated oligodendrocytic basic protein	BC048492|Mobp|17433|myelin-associated oligodendrocytic basic protein	NM_001039364|Mobp|17433|myelin-associated oligodendrocytic basic protein	NM_001039365|Mobp|17433|myelin-associated oligodendrocytic basic protein	NM_008614|Mobp|17433|myelin-associated oligodendrocytic basic protein
mm9_v1_chr17_-_51878720_51878731	30.3017	SOX2.p2	AK081385|Satb1|20230|special AT-rich sequence binding protein 1
mm9_v1_chr12_-_73337534_73337705	27.8609	SOX2.p2	AK013731|Rtn1|104001|reticulon 1	AK014358|Rtn1|104001|reticulon 1
mm9_v1_chr18_-_43219062_43219124	23.5657	SOX2.p2	BC026686|Ppp2r2b|72930|protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), beta isoform	AK148956|Ppp2r2b|72930|protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), beta isoform	AK013600|Ppp2r2b|72930|protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), beta isoform	NM_028392|Ppp2r2b|72930|protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), beta isoform
mm9_v1_chr18_+_37157533_37157533	20.8734	SOX2.p2	AY013767|Pcdha9|192161|protocadherin alpha 9	NM_138661|Pcdha9|192161|protocadherin alpha 9
mm9_v1_chrX_+_155897136_155897153	20.3707	SOX2.p2	AK005554|Mtap7d2|78283|MAP7 domain containing 2	AK030316|Mtap7d2|78283|MAP7 domain containing 2
mm9_v1_chrX_+_132424640_132424733	19.898	SOX2.p2	AK214737|Bhlhb9|70237|basic helix-loop-helix domain containing, class B9
mm9_v1_chr17_-_90436488_90436574	19.0587	SOX2.p2	AJ006802|Nrxn1|18189|neurexin I
mm9_v1_chr2_-_170232008_170232013	17.5175	SOX2.p2	AK008957|Bcas1|76960|breast carcinoma amplified sequence 1	AK031825|Bcas1|76960|breast carcinoma amplified sequence 1
mm9_v1_chr18_-_23197156_23197163	17.0836	SOX2.p2	BC056377|Nol4|319211|nucleolar protein 4	NM_001161483|Nol4|319211|nucleolar protein 4
mm9_v1_chrX_+_155897056_155897081	16.7171	SOX2.p2	AK019929|Mtap7d2|78283|MAP7 domain containing 2	AK031868|Mtap7d2|78283|MAP7 domain containing 2	AK043342|Mtap7d2|78283|MAP7 domain containing 2
mm9_v1_chrX_-_149078963_149079085	16.2144	SOX2.p2	AK029338|Shroom2|110380|shroom family member 2	AK032256|Shroom2|110380|shroom family member 2	AK049850|Shroom2|110380|shroom family member 2	BC092373|Shroom2|110380|shroom family member 2
mm9_v1_chr18_+_37120093_37120209	16.0749	SOX2.p2	AY013763|Pcdha5|12941|protocadherin alpha 5	NM_009959|Pcdha5|12941|protocadherin alpha 5	AB008181|Pcdha5|12941|protocadherin alpha 5
mm9_v1_chr12_+_91570569_91570694	15.4542	SOX2.p2	AJ006804|Nrxn3|18191|neurexin III
mm9_v1_chr5_+_67067477_67067482	14.8096	SOX2.p2	AK004066|Uchl1|22223|ubiquitin carboxy-terminal hydrolase L1	AK013729|Uchl1|22223|ubiquitin carboxy-terminal hydrolase L1
mm9_v1_chr18_+_82723920_82724127	14.7548	SOX2.p2	AK005129|Mbp|17196|myelin basic protein	M15060|Mbp|17196|myelin basic protein	BC004704|Mbp|17196|myelin basic protein	DQ887821|Mbp|17196|myelin basic protein	M15062|Mbp|17196|myelin basic protein	AK189263|Mbp|17196|myelin basic protein	AK190490|Mbp|17196|myelin basic protein	AK191010|Mbp|17196|myelin basic protein	AK195158|Mbp|17196|myelin basic protein	AK197274|Mbp|17196|myelin basic protein	AK199946|Mbp|17196|myelin basic protein
mm9_v1_chr9_-_49311823_49311910	14.7045	SOX2.p2	X07233|Ncam1|17967|neural cell adhesion molecule 1
mm9_v1_chr18_+_37112301_37112419	14.4598	SOX2.p2	AK149282|Pcdha4|12936|protocadherin alpha 4	AK048980|Pcdha4|12936|protocadherin alpha 4	BC060211|Pcdha4|12936|protocadherin alpha 4	D86916|Pcdha4|12936|protocadherin alpha 4	NM_007766|Pcdha4|12936|protocadherin alpha 4	AF464180|Pcdha4-g|100384868|protocadherin alpha 4-gamma	NM_001174154|Pcdha4-g|100384868|protocadherin alpha 4-gamma	AY013762|Pcdha4|12936|protocadherin alpha 4
mm9_v1_chr10_-_30375572_30375672	14.2877	SOX2.p2	BC080742|Ncoa7|211329|nuclear receptor coactivator 7	AK033503|Ncoa7|211329|nuclear receptor coactivator 7	AK171679|Ncoa7|211329|nuclear receptor coactivator 7	BC058572|Ncoa7|211329|nuclear receptor coactivator 7	BC080670|Ncoa7|211329|nuclear receptor coactivator 7	BC049997|Ncoa7|211329|nuclear receptor coactivator 7	AK165098|Ncoa7|211329|nuclear receptor coactivator 7	AK042369|Ncoa7|211329|nuclear receptor coactivator 7	EF602028|Ncoa7|211329|nuclear receptor coactivator 7	NM_001111267|Ncoa7|211329|nuclear receptor coactivator 7
mm9_v1_chr18_+_37127284_37127409	14.0933	SOX2.p2	D86917|Pcdha6|12937|protocadherin alpha 6	BC150815|Pcdha6|12937|protocadherin alpha 6	BC150816|Pcdha6|12937|protocadherin alpha 6	BC054813|Pcdha6|12937|protocadherin alpha 6	AY013764|Pcdha6|12937|protocadherin alpha 6	NM_007767|Pcdha6|12937|protocadherin alpha 6
mm9_v1_chr5_+_89012596_89012599	13.4188	SOX2.p2	BC049127|Rufy3|52822|RUN and FYVE domain containing 3	NM_027530|Rufy3|52822|RUN and FYVE domain containing 3
mm9_v1_chr10_+_20760625_20760625	13.2725	SOX2.p2	AK161335|Ahi1|52906|Abelson helper integration site 1	NM_001177776|Ahi1|52906|Abelson helper integration site 1
mm9_v1_chr9_+_109905895_109906037	12.984	SOX2.p2	
mm9_v1_chr10_+_119256444_119256567	12.8794	SOX2.p2	BC067398|Grip1|74053|glutamate receptor interacting protein 1	AK039673|Grip1|74053|glutamate receptor interacting protein 1	AB051560|Grip1|74053|glutamate receptor interacting protein 1	AB051561|Grip1|74053|glutamate receptor interacting protein 1	NM_028736|Grip1|74053|glutamate receptor interacting protein 1	NM_130891|Grip1|74053|glutamate receptor interacting protein 1
mm9_v1_chr18_+_37133455_37133703	12.8734	SOX2.p2	BC080863|Pcdha7|12939|protocadherin alpha 7	AY013765|Pcdha7|12939|protocadherin alpha 7	NM_009957|Pcdha7|12939|protocadherin alpha 7	AB008179|Pcdha7|12939|protocadherin alpha 7	EU854476|Pcdha7|12939|protocadherin alpha 7
mm9_v1_chr10_+_28863801_28863929	12.8098	SOX2.p2	NM_026138|6330407J23Rik|67412|RIKEN cDNA 6330407J23 gene	AK030682|6330407J23Rik|67412|RIKEN cDNA 6330407J23 gene
mm9_v1_chr11_+_87574041_87574047	12.5757	SOX2.p2	AK043747|Bzrap1|207777|benzodiazepine receptor associated protein 1	NM_172449|Bzrap1|207777|benzodiazepine receptor associated protein 1
mm9_v1_chr15_+_98465328_98465599	12.1588	SOX2.p2	U20372|Cacnb3|12297|calcium channel, voltage-dependent, beta 3 subunit	AF498245|Cacnb3|12297|calcium channel, voltage-dependent, beta 3 subunit	AF498246|Cacnb3|12297|calcium channel, voltage-dependent, beta 3 subunit
mm9_v1_chr5_+_19413335_19413335	12.1562	SOX2.p2	AK147530|Magi2|50791|membrane associated guanylate kinase, WW and PDZ domain containing 2	NM_001170745|Magi2|50791|membrane associated guanylate kinase, WW and PDZ domain containing 2	NM_015823|Magi2|50791|membrane associated guanylate kinase, WW and PDZ domain containing 2
mm9_v1_chr2_-_165709697_165709718	12.1145	SOX2.p2	AK003657|Zmynd8|228880|zinc finger, MYND-type containing 8
mm9_v1_chrX_+_162782484_162782852	11.8678	SOX2.p2	NM_001177955|Gpm6b|14758|glycoprotein m6b	NM_001177956|Gpm6b|14758|glycoprotein m6b	NM_001177957|Gpm6b|14758|glycoprotein m6b	NM_001177958|Gpm6b|14758|glycoprotein m6b	NM_001177959|Gpm6b|14758|glycoprotein m6b	NM_001177960|Gpm6b|14758|glycoprotein m6b	AF254869|Gpm6b|14758|glycoprotein m6b	AF254870|Gpm6b|14758|glycoprotein m6b	AF254872|Gpm6b|14758|glycoprotein m6b	AF254873|Gpm6b|14758|glycoprotein m6b	AF254874|Gpm6b|14758|glycoprotein m6b	AF254875|Gpm6b|14758|glycoprotein m6b	AF254878|Gpm6b|14758|glycoprotein m6b	AF254879|Gpm6b|14758|glycoprotein m6b	AK013660|Gpm6b|14758|glycoprotein m6b	AK140714|Gpm6b|14758|glycoprotein m6b	S65737|Gpm6b|14758|glycoprotein m6b
mm9_v1_chr12_-_73337707_73337756	11.7175	SOX2.p2	AK002997|Rtn1|104001|reticulon 1	NM_001007596|Rtn1|104001|reticulon 1
mm9_v1_chr5_+_37637027_37637257	11.667	SOX2.p2	Y09080|Crmp1|12933|collapsin response mediator protein 1	AB006714|Crmp1|12933|collapsin response mediator protein 1	NM_007765|Crmp1|12933|collapsin response mediator protein 1	BC031738|Crmp1|12933|collapsin response mediator protein 1	U72875|Crmp1|12933|collapsin response mediator protein 1
mm9_v1_chr5_+_67067497_67067526	11.5575	SOX2.p2	BC039177|Uchl1|22223|ubiquitin carboxy-terminal hydrolase L1	AB025313|Uchl1|22223|ubiquitin carboxy-terminal hydrolase L1	AF172334|Uchl1|22223|ubiquitin carboxy-terminal hydrolase L1
mm9_v1_chr11_-_97372344_97372370	11.4057	SOX2.p2	AK051643|Srcin1|56013|SRC kinase signaling inhibitor 1
mm9_v1_chr7_-_38554642_38554770	11.3638	SOX2.p2	AK122270|Zfp536|243937|zinc finger protein 536	AK030633|Zfp536|243937|zinc finger protein 536	NM_172385|Zfp536|243937|zinc finger protein 536
mm9_v1_chrX_+_130829929_130829942	11.226	SOX2.p2	AK005180|Tmem35|67564|transmembrane protein 35	AK018535|Tmem35|67564|transmembrane protein 35	AK043881|Tmem35|67564|transmembrane protein 35	AK042538|Tmem35|67564|transmembrane protein 35
mm9_v1_chr4_-_91042997_91043190	11.1844	SOX2.p2	AK149201|Elavl2|15569|ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)	AK141919|Elavl2|15569|ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)	NM_001177883|Elavl2|15569|ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)
mm9_v1_chr5_+_27231234_27231317	11.0655	SOX2.p2	AK051708|Dpp6|13483|dipeptidylpeptidase 6	BC085154|Dpp6|13483|dipeptidylpeptidase 6	NM_001198886|Dpp6|13483|dipeptidylpeptidase 6
mm9_v1_chr18_+_37644674_37644812	11.0462	SOX2.p2	BC017149|Pcdhb17|93888|protocadherin beta 17	NM_053142|Pcdhb17|93888|protocadherin beta 17	AK077255|Pcdhb17|93888|protocadherin beta 17	AF326310|Pcdhb17|93888|protocadherin beta 17	AY013778|Pcdhb17|93888|protocadherin beta 17
mm9_v1_chr18_+_37098858_37098971	11.0401	SOX2.p2	BC030897|Pcdha2|353234|protocadherin alpha 2	NM_198117|Pcdha2|353234|protocadherin alpha 2	BC141390|Pcdha2|353234|protocadherin alpha 2	AY013760|Pcdha2|353234|protocadherin alpha 2
mm9_v1_chr1_-_42749940_42749978	10.8756	SOX2.p2	BC059892|2610017I09Rik|66297|RIKEN cDNA 2610017I09 gene	BC058417|2610017I09Rik|66297|RIKEN cDNA 2610017I09 gene
mm9_v1_chr8_+_125935470_125935482	10.7687	SOX2.p2	AF312873|Tubb3|22152|tubulin, beta 3
mm9_v1_chr10_-_70055559_70055571	10.7357	SOX2.p2	NM_001162846|Phyhipl|70911|phytanoyl-CoA hydroxylase interacting protein-like	AK014946|Phyhipl|70911|phytanoyl-CoA hydroxylase interacting protein-like
mm9_v1_chr16_-_18622083_18622120	10.7209	SOX2.p2	
mm9_v1_chr18_+_37152024_37152120	10.5588	SOX2.p2	BC139424|Pcdha8|353235|protocadherin alpha 8	BC139426|Pcdha8|353235|protocadherin alpha 8	AY013766|Pcdha8|353235|protocadherin alpha 8	NM_201243|Pcdha8|353235|protocadherin alpha 8
mm9_v1_chr18_+_82723854_82723899	10.5558	SOX2.p2	NM_001025251|Mbp|17196|myelin basic protein	NM_001025255|Mbp|17196|myelin basic protein	NM_001025256|Mbp|17196|myelin basic protein	NM_001025258|Mbp|17196|myelin basic protein	NM_001025259|Mbp|17196|myelin basic protein	AK079621|Mbp|17196|myelin basic protein	NM_001025254|Mbp|17196|myelin basic protein
mm9_v1_chr1_+_160292470_160292548	10.554	SOX2.p2	AK164117|Astn1|11899|astrotactin 1	NM_007495|Astn1|11899|astrotactin 1	BC094666|Astn1|11899|astrotactin 1
mm9_v1_chr15_+_98465193_98465247	10.4686	SOX2.p2	NM_007581|Cacnb3|12297|calcium channel, voltage-dependent, beta 3 subunit	AK148088|Cacnb3|12297|calcium channel, voltage-dependent, beta 3 subunit
mm9_v1_chr18_+_82723907_82723917	10.3615	SOX2.p2	AK147966|Mbp|17196|myelin basic protein
mm9_v1_chr12_+_30213224_30213265	10.2391	SOX2.p2	AK012660|Myt1l|17933|myelin transcription factor 1-like	AK139366|Myt1l|17933|myelin transcription factor 1-like	NM_001093775|Myt1l|17933|myelin transcription factor 1-like	NM_001093778|Myt1l|17933|myelin transcription factor 1-like	NM_008666|Myt1l|17933|myelin transcription factor 1-like
mm9_v1_chr5_+_89012547_89012592	10.2059	SOX2.p2	AK018184|Rufy3|52822|RUN and FYVE domain containing 3
mm9_v1_chr4_-_109960078_109960115	10.1385	SOX2.p2	BC052451|Elavl4|15572|ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	AF041342|Elavl4|15572|ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	AK079088|Elavl4|15572|ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	NM_001038698|Elavl4|15572|ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)
mm9_v1_chr2_+_143371807_143372226	10.1307	SOX2.p2	AK158598|Pcsk2|18549|proprotein convertase subtilisin/kexin type 2	AK133620|Pcsk2|18549|proprotein convertase subtilisin/kexin type 2	NM_008792|Pcsk2|18549|proprotein convertase subtilisin/kexin type 2	BC057348|Pcsk2|18549|proprotein convertase subtilisin/kexin type 2	AK158493|Pcsk2|18549|proprotein convertase subtilisin/kexin type 2	AK161585|Pcsk2|18549|proprotein convertase subtilisin/kexin type 2	BC052013|Pcsk2|18549|proprotein convertase subtilisin/kexin type 2	AK039783|Pcsk2|18549|proprotein convertase subtilisin/kexin type 2	M55669|Pcsk2|18549|proprotein convertase subtilisin/kexin type 2	AF483512|Pcsk2|18549|proprotein convertase subtilisin/kexin type 2	AF483513|Pcsk2|18549|proprotein convertase subtilisin/kexin type 2
mm9_v1_chrX_+_130829763_130829919	10.0186	SOX2.p2	BC042623|Tmem35|67564|transmembrane protein 35	NM_026239|Tmem35|67564|transmembrane protein 35	BC050880|Tmem35|67564|transmembrane protein 35
mm9_v1_chr9_-_75531734_75531890	9.9697	SOX2.p2	AK158315|Scg3|20255|secretogranin III	AK133655|Scg3|20255|secretogranin III	AK139140|Scg3|20255|secretogranin III	AK164089|Scg3|20255|secretogranin III	BC024785|Scg3|20255|secretogranin III	U02982|Scg3|20255|secretogranin III	AK148498|Scg3|20255|secretogranin III	NM_001164790|Scg3|20255|secretogranin III	NM_009130|Scg3|20255|secretogranin III
mm9_v1_chr16_-_46120221_46120363	9.93409	SOX2.p2	AY029156|Cd96|84544|CD96 antigen	AK040329|Cd96|84544|CD96 antigen	BC052865|Cd96|84544|CD96 antigen	AK154076|Cd96|84544|CD96 antigen	AK156470|Cd96|84544|CD96 antigen	NM_032465|Cd96|84544|CD96 antigen	AK040539|Cd96|84544|CD96 antigen
mm9_v1_chr3_+_8509479_8509599	9.83511	SOX2.p2	AK149212|Stmn2|20257|stathmin-like 2	AK043202|Stmn2|20257|stathmin-like 2	AK003659|Stmn2|20257|stathmin-like 2	AK013020|Stmn2|20257|stathmin-like 2	NM_025285|Stmn2|20257|stathmin-like 2	BC026538|Stmn2|20257|stathmin-like 2
mm9_v1_chr14_+_60997104_60997126	9.76486	SOX2.p2	NM_001164705|Fam123a|72125|family with sequence similarity 123, member A	NM_028113|Fam123a|72125|family with sequence similarity 123, member A
mm9_v1_chr5_-_23012407_23012525	9.63336	SOX2.p2	AK044922|Srpk2|20817|serine/arginine-rich protein specific kinase 2	AK201776|Srpk2|20817|serine/arginine-rich protein specific kinase 2
mm9_v1_chr13_-_111070225_111070335	9.55421	SOX2.p2	AB232589|Rab3c|67295|RAB3C, member RAS oncogene family	AF312037|Rab3c|67295|RAB3C, member RAS oncogene family	AJ310532|Rab3c|67295|RAB3C, member RAS oncogene family	BC114335|Rab3c|67295|RAB3C, member RAS oncogene family	AY026947|Rab3c|67295|RAB3C, member RAS oncogene family	AK079574|Rab3c|67295|RAB3C, member RAS oncogene family	AK148904|Rab3c|67295|RAB3C, member RAS oncogene family	AK014132|Rab3c|67295|RAB3C, member RAS oncogene family
mm9_v1_chr6_+_54222814_54222856	9.43396	SOX2.p2	BC051139|Chn2|69993|chimerin (chimaerin) 2	NM_023543|Chn2|69993|chimerin (chimaerin) 2	BC141060|Chn2|69993|chimerin (chimaerin) 2
mm9_v1_chr7_-_82453166_82453213	9.32403	SOX2.p2	AK139478|Sv2b|64176|synaptic vesicle glycoprotein 2 b	AK140104|Sv2b|64176|synaptic vesicle glycoprotein 2 b	AK035927|Sv2b|64176|synaptic vesicle glycoprotein 2 b	AK043830|Sv2b|64176|synaptic vesicle glycoprotein 2 b
mm9_v1_chr19_-_42160732_42160861	9.31593	SOX2.p2	AK180979|Morn4|226123|MORN repeat containing 4	AK214121|Morn4|226123|MORN repeat containing 4	BC023055|Morn4|226123|MORN repeat containing 4	AK159230|Morn4|226123|MORN repeat containing 4	AK154147|Morn4|226123|MORN repeat containing 4	NM_198108|Morn4|226123|MORN repeat containing 4
mm9_v1_chr8_+_65430028_65430291	9.24188	SOX2.p2	AJ278998|Spock3|72902|sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3	AK049843|Spock3|72902|sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3	AK220280|Spock3|72902|sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3	AK013644|Spock3|72902|sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3	BC017601|Spock3|72902|sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3	NM_023689|Spock3|72902|sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3	AK164338|Spock3|72902|sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3	BC053334|Spock3|72902|sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3
mm9_v1_chr5_+_112684838_112684856	9.23855	SOX2.p2	AK014012|Crybb1|12960|crystallin, beta B1	AF106853|Crybb1|12960|crystallin, beta B1	AK053869|Crybb1|12960|crystallin, beta B1	NM_023695|Crybb1|12960|crystallin, beta B1	BC029012|Crybb1|12960|crystallin, beta B1
mm9_v1_chr2_+_14310024_14310041	9.21063	SOX2.p2	NM_001012305|Slc39a12|277468|solute carrier family 39 (zinc transporter), member 12	AK134622|Slc39a12|277468|solute carrier family 39 (zinc transporter), member 12	BC089362|Slc39a12|277468|solute carrier family 39 (zinc transporter), member 12	BC113764|Slc39a12|277468|solute carrier family 39 (zinc transporter), member 12	BC113765|Slc39a12|277468|solute carrier family 39 (zinc transporter), member 12
mm9_v1_chr7_+_89319681_89319705	9.18792	SOX2.p2	BC027096|Sh3gl3|20408|SH3-domain GRB2-like 3
mm9_v1_chr9_-_21820860_21820861	9.1428	SOX2.p2	AK134781|Elavl3|15571|ELAV (embryonic lethal, abnormal vision, Drosophila)-like 3 (Hu antigen C)
mm9_v1_chr10_+_61245998_61246044	9.12404	SOX2.p2	
mm9_v1_chr7_+_89319717_89319836	9.06853	SOX2.p2	NM_017400|Sh3gl3|20408|SH3-domain GRB2-like 3	AK012114|Sh3gl3|20408|SH3-domain GRB2-like 3	BC100453|Sh3gl3|20408|SH3-domain GRB2-like 3
mm9_v1_chr1_+_160292665_160292848	9.06493	SOX2.p2	AK147450|Astn1|11899|astrotactin 1	AK138576|Astn1|11899|astrotactin 1	AK045561|Astn1|11899|astrotactin 1	AK165200|Astn1|11899|astrotactin 1	U48797|Astn1|11899|astrotactin 1	AB093222|Astn1|11899|astrotactin 1
mm9_v1_chr3_-_80606500_80606592	8.90934	SOX2.p2	BC066193|Gria2|14800|glutamate receptor, ionotropic, AMPA2 (alpha 2)	X57498|Gria2|14800|glutamate receptor, ionotropic, AMPA2 (alpha 2)	BC048248|Gria2|14800|glutamate receptor, ionotropic, AMPA2 (alpha 2)
mm9_v1_chr11_-_77538789_77538794	8.8483	SOX2.p2	AJ239052|Cryba1|12957|crystallin, beta A1	BC107342|Cryba1|12957|crystallin, beta A1	NM_009965|Cryba1|12957|crystallin, beta A1
mm9_v1_chr9_+_46721685_46721730	8.79883	SOX2.p2	AK038437|2900052N01Rik|73040|RIKEN cDNA 2900052N01 gene	AK049847|2900052N01Rik|73040|RIKEN cDNA 2900052N01 gene	AK013669|2900052N01Rik|73040|RIKEN cDNA 2900052N01 gene	BC054400|2900052N01Rik|73040|RIKEN cDNA 2900052N01 gene	AK140089|2900052N01Rik|73040|RIKEN cDNA 2900052N01 gene
mm9_v1_chr12_+_30219769_30219800	8.6624	SOX2.p2	AK036205|Myt1l|17933|myelin transcription factor 1-like	NM_001093776|Myt1l|17933|myelin transcription factor 1-like	BC079651|Myt1l|17933|myelin transcription factor 1-like
mm9_v1_chr12_+_3365295_3365555	8.6388	SOX2.p2	AK147572|Kif3c|16570|kinesin family member 3C	BC062648|Kif3c|16570|kinesin family member 3C	AF013116|Kif3c|16570|kinesin family member 3C
mm9_v1_chr14_-_9142289_9142295	8.61144	SOX2.p2	BC055107|Fam107a|268709|family with sequence similarity 107, member A	NM_183187|Fam107a|268709|family with sequence similarity 107, member A	AK165722|Fam107a|268709|family with sequence similarity 107, member A
mm9_v1_chr14_+_60997156_60997209	8.52409	SOX2.p2	BC056350|Fam123a|72125|family with sequence similarity 123, member A	AK139177|Fam123a|72125|family with sequence similarity 123, member A	AK032651|Fam123a|72125|family with sequence similarity 123, member A	AK011185|Fam123a|72125|family with sequence similarity 123, member A
mm9_v1_chr10_-_115910911_115910982	8.4796	SOX2.p2	AK013647|Kcnmb4|58802|potassium large conductance calcium-activated channel, subfamily M, beta member 4
mm9_v1_chr4_-_91066674_91066674	8.43553	SOX2.p2	BC049125|Elavl2|15569|ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)	BC058393|Elavl2|15569|ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)	NM_207685|Elavl2|15569|ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)
mm9_v1_chr15_-_88808967_88808984	8.36751	SOX2.p2	AK030396|Mlc1|170790|megalencephalic leukoencephalopathy with subcortical cysts 1 homolog (human)	AK043757|Mlc1|170790|megalencephalic leukoencephalopathy with subcortical cysts 1 homolog (human)	BC024719|Mlc1|170790|megalencephalic leukoencephalopathy with subcortical cysts 1 homolog (human)	NM_133241|Mlc1|170790|megalencephalic leukoencephalopathy with subcortical cysts 1 homolog (human)
mm9_v1_chr3_+_34548916_34548976	8.33902	SOX2.p2	NM_011443|Sox2|20674|SRY-box containing gene 2	U31967|Sox2|20674|SRY-box containing gene 2
mm9_v1_chr12_+_3365147_3365223	8.33834	SOX2.p2	AK133649|Kif3c|16570|kinesin family member 3C	BC053053|Kif3c|16570|kinesin family member 3C
mm9_v1_chr5_+_67067359_67067456	8.2828	SOX2.p2	NM_011670|Uchl1|22223|ubiquitin carboxy-terminal hydrolase L1
mm9_v1_chr9_-_52484889_52484906	8.21646	SOX2.p2	AK053489|AI593442|330941|expressed sequence AI593442
mm9_v1_chr14_-_122097583_122097657	8.21162	SOX2.p2	BC157964|Dock9|105445|dedicator of cytokinesis 9	NM_001081039|Dock9|105445|dedicator of cytokinesis 9
mm9_v1_chr6_-_18464737_18464763	8.13543	SOX2.p2	BC068156|Cttnbp2|30785|cortactin binding protein 2	AK021092|Cttnbp2|30785|cortactin binding protein 2
mm9_v1_chr9_-_29219306_29219337	8.11383	SOX2.p2	AF282980|Ntm|235106|neurotrimin	BC023307|Ntm|235106|neurotrimin
mm9_v1_chrX_+_10173557_10173565	8.11368	SOX2.p2	
mm9_v1_chr6_+_86354212_86354404	8.09898	SOX2.p2	NM_001164078|Tia1|21841|cytotoxic granule-associated RNA binding protein 1	NM_001164079|Tia1|21841|cytotoxic granule-associated RNA binding protein 1	NM_011585|Tia1|21841|cytotoxic granule-associated RNA binding protein 1	AK144222|Tia1|21841|cytotoxic granule-associated RNA binding protein 1	AK088486|Tia1|21841|cytotoxic granule-associated RNA binding protein 1	BC023813|Tia1|21841|cytotoxic granule-associated RNA binding protein 1	BC046812|Tia1|21841|cytotoxic granule-associated RNA binding protein 1	BC027826|Tia1|21841|cytotoxic granule-associated RNA binding protein 1	U55862|Tia1|21841|cytotoxic granule-associated RNA binding protein 1
mm9_v1_chr9_-_49607164_49607185	8.02927	SOX2.p2	NM_001081445|Ncam1|17967|neural cell adhesion molecule 1	NM_001113204|Ncam1|17967|neural cell adhesion molecule 1	NM_010875|Ncam1|17967|neural cell adhesion molecule 1
mm9_v1_chr9_-_75458865_75458907	7.95527	SOX2.p2	AF237629|Tmod2|50876|tropomodulin 2
mm9_v1_chr8_+_56040553_56040581	7.93176	SOX2.p2	BC024759|Gpm6a|234267|glycoprotein m6a	BC033394|Gpm6a|234267|glycoprotein m6a	S65735|Gpm6a|234267|glycoprotein m6a	BC029711|Gpm6a|234267|glycoprotein m6a
mm9_v1_chr14_-_80171003_80171120	7.89202	SOX2.p2	AK140407|Pcdh8|18530|protocadherin 8	AF231125|Pcdh8|18530|protocadherin 8	BC052388|Pcdh8|18530|protocadherin 8	BC053008|Pcdh8|18530|protocadherin 8	AK048638|Pcdh8|18530|protocadherin 8	AK049982|Pcdh8|18530|protocadherin 8	NM_001042726|Pcdh8|18530|protocadherin 8	NM_021543|Pcdh8|18530|protocadherin 8
mm9_v1_chr8_+_10153910_10154187	7.77518	SOX2.p2	BC072580|Myo16|244281|myosin XVI	NM_001081397|Myo16|244281|myosin XVI	BC151049|Myo16|244281|myosin XVI	BC151051|Myo16|244281|myosin XVI	BC157966|Myo16|244281|myosin XVI	BC172122|Myo16|244281|myosin XVI	BC082311|Myo16|244281|myosin XVI	AK082350|Myo16|244281|myosin XVI
mm9_v1_chr18_-_77870871_77870990	7.75591	SOX2.p2	AK009215|2310007O11Rik|74177|RIKEN cDNA 2310007O11 gene
mm9_v1_chr1_+_129702056_129702170	7.74199	SOX2.p2	AK033697|Ccnt2|72949|cyclin T2
mm9_v1_chr10_-_115910578_115910595	7.7371	SOX2.p2	AF215892|Kcnmb4|58802|potassium large conductance calcium-activated channel, subfamily M, beta member 4	BC117779|Kcnmb4|58802|potassium large conductance calcium-activated channel, subfamily M, beta member 4	NM_021452|Kcnmb4|58802|potassium large conductance calcium-activated channel, subfamily M, beta member 4	BC048471|Kcnmb4|58802|potassium large conductance calcium-activated channel, subfamily M, beta member 4
mm9_v1_chr6_-_135664978_135664993	7.69551	SOX2.p2	
mm9_v1_chr2_+_179777363_179777404	7.67199	SOX2.p2	BC053087|Ss18l1|269397|synovial sarcoma translocation gene on chromosome 18-like 1
mm9_v1_chr7_-_107475377_107475426	7.63296	SOX2.p2	
mm9_v1_chr12_-_36768992_36769002	7.61811	SOX2.p2	AK008175|Tspan13|66109|tetraspanin 13
mm9_v1_chr9_-_60497537_60497561	7.61064	SOX2.p2	AK082406|Lrrc49|102747|leucine rich repeat containing 49
mm9_v1_chrX_+_139952975_139953253	7.59925	SOX2.p2	AK158893|Pak3|18481|p21 protein (Cdc42/Rac)-activated kinase 3	NM_001195048|Pak3|18481|p21 protein (Cdc42/Rac)-activated kinase 3	AK031853|Pak3|18481|p21 protein (Cdc42/Rac)-activated kinase 3
mm9_v1_chr7_-_89079168_89079313	7.58682	SOX2.p2	AK014849|Hdgfrp3|29877|hepatoma-derived growth factor, related protein 3	AK044858|Hdgfrp3|29877|hepatoma-derived growth factor, related protein 3	AK051401|Hdgfrp3|29877|hepatoma-derived growth factor, related protein 3	AK135495|Hdgfrp3|29877|hepatoma-derived growth factor, related protein 3
mm9_v1_chr9_-_29219382_29219527	7.57706	SOX2.p2	AK158752|Ntm|235106|neurotrimin
mm9_v1_chr9_+_111277323_111277357	7.57262	SOX2.p2	BC086653|Trank1|320429|tetratricopeptide repeat and ankyrin repeat containing 1
mm9_v1_chr18_-_43847367_43847426	7.50951	SOX2.p2	AK133750|Jakmip2|76217|janus kinase and microtubule interacting protein 2	NM_001163637|Jakmip2|76217|janus kinase and microtubule interacting protein 2
mm9_v1_chr17_-_51951378_51951378	7.47687	SOX2.p2	AK158518|Satb1|20230|special AT-rich sequence binding protein 1	NM_001163630|Satb1|20230|special AT-rich sequence binding protein 1
mm9_v1_chr4_-_151235861_151235879	7.4396	SOX2.p2	AK158710|Camta1|100072|calmodulin binding transcription activator 1	NM_001081557|Camta1|100072|calmodulin binding transcription activator 1	NM_001195565|Camta1|100072|calmodulin binding transcription activator 1
mm9_v1_chr18_+_59222034_59222186	7.41908	SOX2.p2	NM_001167925|A730017C20Rik|225583|RIKEN cDNA A730017C20 gene	NM_173759|A730017C20Rik|225583|RIKEN cDNA A730017C20 gene	AK080452|A730017C20Rik|225583|RIKEN cDNA A730017C20 gene	AK048493|A730017C20Rik|225583|RIKEN cDNA A730017C20 gene	BC075669|A730017C20Rik|225583|RIKEN cDNA A730017C20 gene
mm9_v1_chr4_+_43521765_43521777	7.41424	SOX2.p2	AK166403|Car9|230099|carbonic anhydrase 9
mm9_v1_chr14_-_20796199_20796254	7.41207	SOX2.p2	AK075698|Gng2|14702|guanine nucleotide binding protein (G protein), gamma 2	AK160396|Gng2|14702|guanine nucleotide binding protein (G protein), gamma 2	AK012405|Gng2|14702|guanine nucleotide binding protein (G protein), gamma 2
mm9_v1_chr1_+_17135421_17135611	7.39697	SOX2.p2	AK149281|Gdap1|14545|ganglioside-induced differentiation-associated-protein 1	AK083814|Gdap1|14545|ganglioside-induced differentiation-associated-protein 1	NM_010267|Gdap1|14545|ganglioside-induced differentiation-associated-protein 1	AK045460|Gdap1|14545|ganglioside-induced differentiation-associated-protein 1	Y17850|Gdap1|14545|ganglioside-induced differentiation-associated-protein 1	AK020988|Gdap1|14545|ganglioside-induced differentiation-associated-protein 1	BC048177|Gdap1|14545|ganglioside-induced differentiation-associated-protein 1	BC060212|Gdap1|14545|ganglioside-induced differentiation-associated-protein 1	AK049655|Gdap1|14545|ganglioside-induced differentiation-associated-protein 1	BC051135|Gdap1|14545|ganglioside-induced differentiation-associated-protein 1	AK139057|Gdap1|14545|ganglioside-induced differentiation-associated-protein 1
mm9_v1_chr12_-_36769054_36769127	7.33111	SOX2.p2	BC018317|Tspan13|66109|tetraspanin 13	NM_025359|Tspan13|66109|tetraspanin 13	AK158761|Tspan13|66109|tetraspanin 13	AK167979|Tspan13|66109|tetraspanin 13	AK012571|Tspan13|66109|tetraspanin 13	AK090217|Tspan13|66109|tetraspanin 13	AK090322|Tspan13|66109|tetraspanin 13	AK165768|Tspan13|66109|tetraspanin 13	AK167495|Tspan13|66109|tetraspanin 13
mm9_v1_chr3_+_13471681_13471721	7.31087	SOX2.p2	AK079659|Ralyl|76897|RALY RNA binding protein-like	AK032086|Ralyl|76897|RALY RNA binding protein-like
mm9_v1_chr8_+_98226914_98226962	7.30519	SOX2.p2	NM_001195006|Ndrg4|234593|N-myc downstream regulated gene 4	NM_145602|Ndrg4|234593|N-myc downstream regulated gene 4	AK168873|Ndrg4|234593|N-myc downstream regulated gene 4	AK090374|Ndrg4|234593|N-myc downstream regulated gene 4	AK144294|Ndrg4|234593|N-myc downstream regulated gene 4	BC006595|Ndrg4|234593|N-myc downstream regulated gene 4
mm9_v1_chr1_-_75250520_75250549	7.26772	SOX2.p2	BC064020|Ptprn|19275|protein tyrosine phosphatase, receptor type, N
mm9_v1_chr2_+_121134843_121134847	7.21351	SOX2.p2	AK018185|Mtap1a|17754|microtubule-associated protein 1 A
mm9_v1_chr7_+_97535516_97535523	7.16412	SOX2.p2	AB057756|Sytl2|83671|synaptotagmin-like 2
mm9_v1_chr18_-_43552694_43552984	7.15164	SOX2.p2	BC023003|Dpysl3|22240|dihydropyrimidinase-like 3	NM_009468|Dpysl3|22240|dihydropyrimidinase-like 3	X87817|Dpysl3|22240|dihydropyrimidinase-like 3
mm9_v1_chr8_+_56040445_56040534	7.08382	SOX2.p2	BC029683|Gpm6a|234267|glycoprotein m6a	BC033357|Gpm6a|234267|glycoprotein m6a	AK053538|Gpm6a|234267|glycoprotein m6a
mm9_v1_chr7_-_89079335_89079355	7.00442	SOX2.p2	AK045542|Hdgfrp3|29877|hepatoma-derived growth factor, related protein 3	NM_013886|Hdgfrp3|29877|hepatoma-derived growth factor, related protein 3
mm9_v1_chr2_-_65405546_65405588	6.93191	SOX2.p2	AK148881|Scn3a|20269|sodium channel, voltage-gated, type III, alpha	NM_018732|Scn3a|20269|sodium channel, voltage-gated, type III, alpha
mm9_v1_chr14_+_84933363_84933455	6.91781	SOX2.p2	AK045478|Pcdh17|219228|protocadherin 17	AK079626|Pcdh17|219228|protocadherin 17	AK046505|Pcdh17|219228|protocadherin 17	AK047338|Pcdh17|219228|protocadherin 17
mm9_v1_chr14_-_109313333_109313374	6.85721	SOX2.p2	AK173296|Slitrk1|76965|SLIT and NTRK-like family, member 1
mm9_v1_chr9_+_107948476_107948586	6.82851	SOX2.p2	AK004808|Ip6k1|27399|inositol hexaphosphate kinase 1	AK208826|Ip6k1|27399|inositol hexaphosphate kinase 1
mm9_v1_chr14_-_109313298_109313300	6.82365	SOX2.p2	AK144290|Slitrk1|76965|SLIT and NTRK-like family, member 1
mm9_v1_chr9_-_49607017_49607038	6.71806	SOX2.p2	AK011804|Ncam1|17967|neural cell adhesion molecule 1	AK011905|Ncam1|17967|neural cell adhesion molecule 1	AK082621|Ncam1|17967|neural cell adhesion molecule 1	AK051197|Ncam1|17967|neural cell adhesion molecule 1
mm9_v1_chr7_+_69493148_69493265	6.66706	SOX2.p2	NM_010882|Ndn|17984|necdin	BC147249|Ndn|17984|necdin	BC147250|Ndn|17984|necdin	AK005078|Ndn|17984|necdin	AK075729|Ndn|17984|necdin	AK076025|Ndn|17984|necdin	AK078129|Ndn|17984|necdin	AK135444|Ndn|17984|necdin	AK149086|Ndn|17984|necdin	AK075735|Ndn|17984|necdin	M80840|Ndn|17984|necdin
mm9_v1_chr7_+_98239427_98239516	6.63343	SOX2.p2	AF388675|Dlg2|23859|discs, large homolog 2 (Drosophila)
mm9_v1_chr14_-_49282546_49282546	6.57438	SOX2.p2	BC017609|Otx2|18424|orthodenticle homolog 2 (Drosophila)	NM_144841|Otx2|18424|orthodenticle homolog 2 (Drosophila)
mm9_v1_chrX_+_90900201_90900217	6.51415	SOX2.p2	AK149304|Pcyt1b|236899|phosphate cytidylyltransferase 1, choline, beta isoform	AY189950|Pcyt1b|236899|phosphate cytidylyltransferase 1, choline, beta isoform	NM_177546|Pcyt1b|236899|phosphate cytidylyltransferase 1, choline, beta isoform	AK053577|Pcyt1b|236899|phosphate cytidylyltransferase 1, choline, beta isoform
mm9_v1_chr8_-_87461251_87461273	6.51062	SOX2.p2	BC054524|Mast1|56527|microtubule associated serine/threonine kinase 1	NM_019945|Mast1|56527|microtubule associated serine/threonine kinase 1	AK141034|Mast1|56527|microtubule associated serine/threonine kinase 1
mm9_v1_chr6_+_143156520_143156614	6.48826	SOX2.p2	AK004338|Etnk1|75320|ethanolamine kinase 1
mm9_v1_chr4_+_109650629_109650657	6.4805	SOX2.p2	NM_172296|Dmrta2|242620|doublesex and mab-3 related transcription factor like family A2	AK080774|Dmrta2|242620|doublesex and mab-3 related transcription factor like family A2	AY145837|Dmrta2|242620|doublesex and mab-3 related transcription factor like family A2
mm9_v1_chr15_-_98783909_98783984	6.47023	SOX2.p2	M13445|Tuba1a|22142|tubulin, alpha 1A	NM_011653|Tuba1a|22142|tubulin, alpha 1A	AK077529|Tuba1a|22142|tubulin, alpha 1A	BC056169|Tuba1a|22142|tubulin, alpha 1A	BC083344|Tuba1a|22142|tubulin, alpha 1A	BC083343|Tuba1a|22142|tubulin, alpha 1A	BC085256|Tuba1a|22142|tubulin, alpha 1A	BC083345|Tuba1a|22142|tubulin, alpha 1A	AK145404|Tuba1a|22142|tubulin, alpha 1A	AK146983|Tuba1a|22142|tubulin, alpha 1A	AK167687|Tuba1a|22142|tubulin, alpha 1A	AK168762|Tuba1a|22142|tubulin, alpha 1A	AK169610|Tuba1a|22142|tubulin, alpha 1A	AK164335|Tuba1a|22142|tubulin, alpha 1A
mm9_v1_chr10_-_115922360_115922443	6.4018	SOX2.p2	AK019295|Cnot2|72068|CCR4-NOT transcription complex, subunit 2
mm9_v1_chr9_-_21822333_21822348	6.39657	SOX2.p2	AK078068|Elavl3|15571|ELAV (embryonic lethal, abnormal vision, Drosophila)-like 3 (Hu antigen C)
mm9_v1_chr11_-_79317471_79317554	6.3887	SOX2.p2	BC024757|Omg|18377|oligodendrocyte myelin glycoprotein
mm9_v1_chr3_+_105776628_105776733	6.37659	SOX2.p2	BC137995|Ovgp1|12659|oviductal glycoprotein 1	AK054141|Ovgp1|12659|oviductal glycoprotein 1	D32137|Ovgp1|12659|oviductal glycoprotein 1	NM_007696|Ovgp1|12659|oviductal glycoprotein 1	AY521455|Ovgp1|12659|oviductal glycoprotein 1
mm9_v1_chr7_+_97535490_97535508	6.31785	SOX2.p2	AK051653|Sytl2|83671|synaptotagmin-like 2	NM_001040087|Sytl2|83671|synaptotagmin-like 2	NM_001040088|Sytl2|83671|synaptotagmin-like 2	AK162921|Sytl2|83671|synaptotagmin-like 2	AK027924|Sytl2|83671|synaptotagmin-like 2
mm9_v1_chr15_+_91958558_91958558	6.31096	SOX2.p2	NM_007727|Cntn1|12805|contactin 1
mm9_v1_chr1_-_195196423_195196475	6.29193	SOX2.p2	AF428262|Camk1g|215303|calcium/calmodulin-dependent protein kinase I gamma	BC021840|Camk1g|215303|calcium/calmodulin-dependent protein kinase I gamma	NM_144817|Camk1g|215303|calcium/calmodulin-dependent protein kinase I gamma
mm9_v1_chr18_+_37901716_37901894	6.28239	SOX2.p2	BC054556|Pcdhgb6|93703|protocadherin gamma subfamily B, 6	NM_033578|Pcdhgb6|93703|protocadherin gamma subfamily B, 6	AY013808|Pcdhgb6|93703|protocadherin gamma subfamily B, 6
mm9_v1_chr15_+_4325490_4325644	6.27108	SOX2.p2	AK038575|Plcxd3|239318|phosphatidylinositol-specific phospholipase C, X domain containing 3	NM_177355|Plcxd3|239318|phosphatidylinositol-specific phospholipase C, X domain containing 3	BC137637|Plcxd3|239318|phosphatidylinositol-specific phospholipase C, X domain containing 3	BC137639|Plcxd3|239318|phosphatidylinositol-specific phospholipase C, X domain containing 3	AK044972|Plcxd3|239318|phosphatidylinositol-specific phospholipase C, X domain containing 3
mm9_v1_chr6_+_141472906_141473070	6.24948	SOX2.p2	AK045782|Slco1c1|58807|solute carrier organic anion transporter family, member 1c1	NM_001177772|Slco1c1|58807|solute carrier organic anion transporter family, member 1c1	NM_021471|Slco1c1|58807|solute carrier organic anion transporter family, member 1c1	AK048926|Slco1c1|58807|solute carrier organic anion transporter family, member 1c1	AK161010|Slco1c1|58807|solute carrier organic anion transporter family, member 1c1	BC078456|Slco1c1|58807|solute carrier organic anion transporter family, member 1c1	AY007379|Slco1c1|58807|solute carrier organic anion transporter family, member 1c1
mm9_v1_chr11_+_54128404_54128494	6.23567	SOX2.p2	NM_001033599|Acsl6|216739|acyl-CoA synthetase long-chain family member 6	AY786360|Acsl6|216739|acyl-CoA synthetase long-chain family member 6	AY786362|Acsl6|216739|acyl-CoA synthetase long-chain family member 6	AK032479|Acsl6|216739|acyl-CoA synthetase long-chain family member 6	AK039380|Acsl6|216739|acyl-CoA synthetase long-chain family member 6
mm9_v1_chr7_+_90015842_90015842	6.20763	SOX2.p2	NM_175366|Mex3b|108797|mex3 homolog B (C. elegans)
mm9_v1_chr2_+_157385835_157385932	6.18298	SOX2.p2	AK003004|Nnat|18111|neuronatin	AK077465|Nnat|18111|neuronatin	AK160626|Nnat|18111|neuronatin	NM_010923|Nnat|18111|neuronatin	NM_180960|Nnat|18111|neuronatin	X83569|Nnat|18111|neuronatin	X83570|Nnat|18111|neuronatin	BC036984|Nnat|18111|neuronatin	AB004048|Nnat|18111|neuronatin	X83568|Nnat|18111|neuronatin
mm9_v1_chr18_+_37089837_37089938	6.17881	SOX2.p2	BC082326|Pcdha1|116731|protocadherin alpha 1	AY013756|Pcdha1|116731|protocadherin alpha 1	NM_054072|Pcdha1|116731|protocadherin alpha 1
mm9_v1_chr10_+_90292388_90292441	6.1727	SOX2.p2	AK032061|Anks1b|77531|ankyrin repeat and sterile alpha motif domain containing 1B
mm9_v1_chr1_-_175297624_175297771	6.16493	SOX2.p2	AY059393|Cadm3|94332|cell adhesion molecule 3	BC115417|Cadm3|94332|cell adhesion molecule 3	BC115418|Cadm3|94332|cell adhesion molecule 3	BC079837|Cadm3|94332|cell adhesion molecule 3	AF195662|Cadm3|94332|cell adhesion molecule 3
mm9_v1_chr5_+_72091188_72091254	6.13672	SOX2.p2	BC157920|Gabrb1|14400|gamma-aminobutyric acid (GABA) A receptor, subunit beta 1	BC130258|Gabrb1|14400|gamma-aminobutyric acid (GABA) A receptor, subunit beta 1	NM_008069|Gabrb1|14400|gamma-aminobutyric acid (GABA) A receptor, subunit beta 1
mm9_v1_chr10_+_69388242_69388279	6.13518	SOX2.p2	L40631|Ank3|11735|ankyrin 3, epithelial	NM_009670|Ank3|11735|ankyrin 3, epithelial	NM_170687|Ank3|11735|ankyrin 3, epithelial
mm9_v1_chr4_-_120781830_120781830	6.12559	SOX2.p2	AK006456|Tmco2|69469|transmembrane and coiled-coil domains 2	NM_001081312|Tmco2|69469|transmembrane and coiled-coil domains 2
mm9_v1_chr1_+_40082201_40082235	6.11313	SOX2.p2	AK020498|Map4k4|26921|mitogen-activated protein kinase kinase kinase kinase 4	AK167747|Map4k4|26921|mitogen-activated protein kinase kinase kinase kinase 4	AK004047|Map4k4|26921|mitogen-activated protein kinase kinase kinase kinase 4
mm9_v1_chr7_-_34926055_34926067	6.10122	SOX2.p2	AK213025|Uba2|50995|ubiquitin-like modifier activating enzyme 2
mm9_v1_chr4_+_129190877_129190896	6.09784	SOX2.p2	AK079390|Marcksl1|17357|MARCKS-like 1	AK150261|Marcksl1|17357|MARCKS-like 1	AK152990|Marcksl1|17357|MARCKS-like 1	AK169355|Marcksl1|17357|MARCKS-like 1	X61399|Marcksl1|17357|MARCKS-like 1	BC006757|Marcksl1|17357|MARCKS-like 1
mm9_v1_chr10_+_53316720_53316974	6.07099	SOX2.p2	AK010210|Asf1a|66403|ASF1 anti-silencing function 1 homolog A (S. cerevisiae)	NM_025541|Asf1a|66403|ASF1 anti-silencing function 1 homolog A (S. cerevisiae)	AK012376|Asf1a|66403|ASF1 anti-silencing function 1 homolog A (S. cerevisiae)	AK031513|Asf1a|66403|ASF1 anti-silencing function 1 homolog A (S. cerevisiae)	AK088618|Asf1a|66403|ASF1 anti-silencing function 1 homolog A (S. cerevisiae)	AK007804|Asf1a|66403|ASF1 anti-silencing function 1 homolog A (S. cerevisiae)	BC027628|Asf1a|66403|ASF1 anti-silencing function 1 homolog A (S. cerevisiae)
mm9_v1_chr1_-_175297778_175297829	6.06499	SOX2.p2	AK036352|Cadm3|94332|cell adhesion molecule 3	AK053077|Cadm3|94332|cell adhesion molecule 3	AK038917|Cadm3|94332|cell adhesion molecule 3	NM_053199|Cadm3|94332|cell adhesion molecule 3
mm9_v1_chr4_+_126850123_126850181	6.01859	SOX2.p2	AK158868|Dlgap3|242667|discs, large (Drosophila) homolog-associated protein 3
mm9_v1_chr16_+_7409879_7410026	5.98779	SOX2.p2	AK034297|Rbfox1|268859|RNA binding protein, fox-1 homolog (C. elegans) 1
mm9_v1_chr7_+_107423813_107423829	5.98149	SOX2.p2	AK164085|Pgm2l1|70974|phosphoglucomutase 2-like 1
mm9_v1_chr6_+_107479719_107479841	5.97309	SOX2.p2	AK139965|Lrrn1|16979|leucine rich repeat protein 1, neuronal	AK139355|Lrrn1|16979|leucine rich repeat protein 1, neuronal	AK164849|Lrrn1|16979|leucine rich repeat protein 1, neuronal	D45913|Lrrn1|16979|leucine rich repeat protein 1, neuronal	NM_008516|Lrrn1|16979|leucine rich repeat protein 1, neuronal	BC058701|Lrrn1|16979|leucine rich repeat protein 1, neuronal	AK160841|Lrrn1|16979|leucine rich repeat protein 1, neuronal
mm9_v1_chr19_+_38339167_38339370	5.97164	SOX2.p2	AK045443|Lgi1|56839|leucine-rich repeat LGI family, member 1	BC066090|Lgi1|56839|leucine-rich repeat LGI family, member 1	NM_020278|Lgi1|56839|leucine-rich repeat LGI family, member 1	AF246818|Lgi1|56839|leucine-rich repeat LGI family, member 1	AK035873|Lgi1|56839|leucine-rich repeat LGI family, member 1	AK031996|Lgi1|56839|leucine-rich repeat LGI family, member 1
mm9_v1_chr16_+_13986691_13986753	5.94085	SOX2.p2	AK049997|2900011O08Rik|67254|RIKEN cDNA 2900011O08 gene	AK076136|2900011O08Rik|67254|RIKEN cDNA 2900011O08 gene	AK139470|2900011O08Rik|67254|RIKEN cDNA 2900011O08 gene	AK136859|2900011O08Rik|67254|RIKEN cDNA 2900011O08 gene	NM_144518|2900011O08Rik|67254|RIKEN cDNA 2900011O08 gene	AK019307|2900011O08Rik|67254|RIKEN cDNA 2900011O08 gene	BC022741|2900011O08Rik|67254|RIKEN cDNA 2900011O08 gene	AK035868|2900011O08Rik|67254|RIKEN cDNA 2900011O08 gene
mm9_v1_chr7_+_114514258_114514338	5.92917	SOX2.p2	AK089115|Syt9|60510|synaptotagmin IX	NM_021889|Syt9|60510|synaptotagmin IX	AK156631|Syt9|60510|synaptotagmin IX	BC132495|Syt9|60510|synaptotagmin IX	BC137904|Syt9|60510|synaptotagmin IX	BC145024|Syt9|60510|synaptotagmin IX
mm9_v1_chr17_+_70871444_70871503	5.91539	SOX2.p2	NM_001128180|Dlgap1|224997|discs, large (Drosophila) homolog-associated protein 1	AK161941|Dlgap1|224997|discs, large (Drosophila) homolog-associated protein 1	AK163689|Dlgap1|224997|discs, large (Drosophila) homolog-associated protein 1
mm9_v1_chr17_-_35975075_35975143	5.88632	SOX2.p2	X04663|Tubb5|22154|tubulin, beta 5
mm9_v1_chr10_+_89336253_89336253	5.88034	SOX2.p2	NM_001128086|Anks1b|77531|ankyrin repeat and sterile alpha motif domain containing 1B
mm9_v1_chr9_-_103664100_103664222	5.85992	SOX2.p2	BC052085|Tmem108|81907|transmembrane protein 108	AK077586|Tmem108|81907|transmembrane protein 108	AK044989|Tmem108|81907|transmembrane protein 108	AK047474|Tmem108|81907|transmembrane protein 108	AK086266|Tmem108|81907|transmembrane protein 108	AK141589|Tmem108|81907|transmembrane protein 108	AK052330|Tmem108|81907|transmembrane protein 108	NM_178638|Tmem108|81907|transmembrane protein 108
mm9_v1_chr3_-_80606641_80606686	5.81827	SOX2.p2	AK044574|Gria2|14800|glutamate receptor, ionotropic, AMPA2 (alpha 2)	AK134572|Gria2|14800|glutamate receptor, ionotropic, AMPA2 (alpha 2)	AK086614|Gria2|14800|glutamate receptor, ionotropic, AMPA2 (alpha 2)	AK043490|Gria2|14800|glutamate receptor, ionotropic, AMPA2 (alpha 2)	AK141525|Gria2|14800|glutamate receptor, ionotropic, AMPA2 (alpha 2)
mm9_v1_chrX_+_133527693_133527841	5.79481	SOX2.p2	NM_001035509|Zcchc18|66995|zinc finger, CCHC domain containing 18	NM_001035510|Zcchc18|66995|zinc finger, CCHC domain containing 18	NM_025893|Zcchc18|66995|zinc finger, CCHC domain containing 18	AK005317|Zcchc18|66995|zinc finger, CCHC domain containing 18	BC017627|Zcchc18|66995|zinc finger, CCHC domain containing 18	AK134856|Zcchc18|66995|zinc finger, CCHC domain containing 18
mm9_v1_chr18_+_37644390_37644448	5.7938	SOX2.p2	AK122533|Pcdhb17|93888|protocadherin beta 17
mm9_v1_chr4_+_129190872_129190875	5.79062	SOX2.p2	AK083913|Marcksl1|17357|MARCKS-like 1
mm9_v1_chr6_+_30758582_30758676	5.77144	SOX2.p2	AK014219|Copg2as2|100044236|coatomer protein complex, subunit gamma 2, antisense 2
mm9_v1_chr9_-_75458954_75458978	5.76034	SOX2.p2	AK079077|Tmod2|50876|tropomodulin 2	AK164178|Tmod2|50876|tropomodulin 2
mm9_v1_chr8_-_87461220_87461246	5.75536	SOX2.p2	AF077818|Mast1|56527|microtubule associated serine/threonine kinase 1
mm9_v1_chr11_+_3230733_3230843	5.74986	SOX2.p2	NM_178149|Pik3ip1|216505|phosphoinositide-3-kinase interacting protein 1	AK028419|Pik3ip1|216505|phosphoinositide-3-kinase interacting protein 1	AK029304|Pik3ip1|216505|phosphoinositide-3-kinase interacting protein 1	AK154842|Pik3ip1|216505|phosphoinositide-3-kinase interacting protein 1	AK005141|Pik3ip1|216505|phosphoinositide-3-kinase interacting protein 1	AK160300|Pik3ip1|216505|phosphoinositide-3-kinase interacting protein 1	AF528081|Pik3ip1|216505|phosphoinositide-3-kinase interacting protein 1	BC055920|Pik3ip1|216505|phosphoinositide-3-kinase interacting protein 1	BC079641|Pik3ip1|216505|phosphoinositide-3-kinase interacting protein 1	AF528078|Pik3ip1|216505|phosphoinositide-3-kinase interacting protein 1	BC028479|Pik3ip1|216505|phosphoinositide-3-kinase interacting protein 1
mm9_v1_chr6_-_12699189_12699252	5.74864	SOX2.p2	NM_001164805|Thsd7a|330267|thrombospondin, type I, domain containing 7A
mm9_v1_chr10_-_80693488_80693567	5.7284	SOX2.p2	AY349150|Atcay|16467|ataxia, cerebellar, Cayman type homolog (human)	BC048903|Atcay|16467|ataxia, cerebellar, Cayman type homolog (human)	AK038990|Atcay|16467|ataxia, cerebellar, Cayman type homolog (human)	NM_178662|Atcay|16467|ataxia, cerebellar, Cayman type homolog (human)	AK039411|Atcay|16467|ataxia, cerebellar, Cayman type homolog (human)	AK028298|Atcay|16467|ataxia, cerebellar, Cayman type homolog (human)	AK038483|Atcay|16467|ataxia, cerebellar, Cayman type homolog (human)	AK162959|Atcay|16467|ataxia, cerebellar, Cayman type homolog (human)	AK086723|Atcay|16467|ataxia, cerebellar, Cayman type homolog (human)
mm9_v1_chr18_+_35750071_35750097	5.71053	SOX2.p2	AK166063|Matr3|17184|matrin 3
mm9_v1_chr11_-_79317583_79317590	5.70374	SOX2.p2	NM_019409|Omg|18377|oligodendrocyte myelin glycoprotein	AK136910|Omg|18377|oligodendrocyte myelin glycoprotein
mm9_v1_chr7_-_34926107_34926132	5.6936	SOX2.p2	AK218279|Uba2|50995|ubiquitin-like modifier activating enzyme 2	AK208593|Uba2|50995|ubiquitin-like modifier activating enzyme 2
mm9_v1_chr4_+_98213324_98213424	5.684	SOX2.p2	NM_001005787|Inadl|12695|InaD-like (Drosophila)	NM_007704|Inadl|12695|InaD-like (Drosophila)	AF060539|Inadl|12695|InaD-like (Drosophila)
mm9_v1_chr15_+_99532787_99532913	5.68314	SOX2.p2	BC026783|Smarcd1|83797|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1
mm9_v1_chr1_+_9591550_9591585	5.65356	SOX2.p2	BC066997|3110035E14Rik|76982|RIKEN cDNA 3110035E14 gene
mm9_v1_chr2_+_112124767_112124844	5.6489	SOX2.p2	AF211855|Slc12a6|107723|solute carrier family 12, member 6	NM_133648|Slc12a6|107723|solute carrier family 12, member 6
mm9_v1_chr5_+_135526788_135526925	5.63835	SOX2.p2	
mm9_v1_chr6_-_128531620_128531628	5.63156	SOX2.p2	AK138836|BC048546|232400|cDNA sequence BC048546	NM_001001179|BC048546|232400|cDNA sequence BC048546	AK161184|BC048546|232400|cDNA sequence BC048546
mm9_v1_chr1_-_42724504_42724516	5.59949	SOX2.p2	BC049671|2610017I09Rik|66297|RIKEN cDNA 2610017I09 gene
mm9_v1_chr9_-_108363229_108363406	5.59405	SOX2.p2	AK157991|Klhdc8b|78267|kelch domain containing 8B	AK087143|Klhdc8b|78267|kelch domain containing 8B	AK154428|Klhdc8b|78267|kelch domain containing 8B
mm9_v1_chr19_+_22767272_22767282	5.58531	SOX2.p2	AK053673|Trpm3|226025|transient receptor potential cation channel, subfamily M, member 3	AK046908|Trpm3|226025|transient receptor potential cation channel, subfamily M, member 3	AK077331|Trpm3|226025|transient receptor potential cation channel, subfamily M, member 3	AK082141|Trpm3|226025|transient receptor potential cation channel, subfamily M, member 3	AK142504|Trpm3|226025|transient receptor potential cation channel, subfamily M, member 3	AK161909|Trpm3|226025|transient receptor potential cation channel, subfamily M, member 3	AK163890|Trpm3|226025|transient receptor potential cation channel, subfamily M, member 3
mm9_v1_chr12_+_25516433_25516564	5.57018	SOX2.p2	NM_001083341|Mboat2|67216|membrane bound O-acyltransferase domain containing 2	NM_026037|Mboat2|67216|membrane bound O-acyltransferase domain containing 2	AK076045|Mboat2|67216|membrane bound O-acyltransferase domain containing 2	AK012931|Mboat2|67216|membrane bound O-acyltransferase domain containing 2	AK031682|Mboat2|67216|membrane bound O-acyltransferase domain containing 2	AK031824|Mboat2|67216|membrane bound O-acyltransferase domain containing 2	AK033106|Mboat2|67216|membrane bound O-acyltransferase domain containing 2	AK034873|Mboat2|67216|membrane bound O-acyltransferase domain containing 2	BC025020|Mboat2|67216|membrane bound O-acyltransferase domain containing 2	AK215458|Mboat2|67216|membrane bound O-acyltransferase domain containing 2	AB297383|Mboat2|67216|membrane bound O-acyltransferase domain containing 2	AB305046|Mboat2|67216|membrane bound O-acyltransferase domain containing 2
mm9_v1_chr7_+_25266986_25267120	5.5641	SOX2.p2	AK143204|Cadm4|260299|cell adhesion molecule 4	NM_153112|Cadm4|260299|cell adhesion molecule 4	AY059394|Cadm4|260299|cell adhesion molecule 4
mm9_v1_chr11_-_69635657_69635766	5.56081	SOX2.p2	BC100505|Spem1|74288|sperm maturation 1	BC048760|Spem1|74288|sperm maturation 1	EF120626|Spem1|74288|sperm maturation 1	NM_028855|Spem1|74288|sperm maturation 1	AK007080|Spem1|74288|sperm maturation 1
mm9_v1_chr13_-_111070344_111070365	5.54084	SOX2.p2	AK164316|Rab3c|67295|RAB3C, member RAS oncogene family
mm9_v1_chr3_-_95032039_95032230	5.47009	SOX2.p2	BC022963|Mllt11|56772|myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 11	AK046005|Mllt11|56772|myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 11	U95498|Mllt11|56772|myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 11	AB000733|Mllt11|56772|myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 11	AK158495|Mllt11|56772|myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 11
mm9_v1_chr9_+_108728650_108728650	5.45771	SOX2.p2	AF427498|Celsr3|107934|cadherin, EGF LAG seven-pass G-type receptor 3 (flamingo homolog, Drosophila)	NM_080437|Celsr3|107934|cadherin, EGF LAG seven-pass G-type receptor 3 (flamingo homolog, Drosophila)
mm9_v1_chr11_-_119878383_119878471	5.42979	SOX2.p2	AK147239|Aatk|11302|apoptosis-associated tyrosine kinase
mm9_v1_chr5_+_89012537_89012542	5.41875	SOX2.p2	AK013185|Rufy3|52822|RUN and FYVE domain containing 3
mm9_v1_chr18_-_35374531_35374610	5.41787	SOX2.p2	AK043173|Lrrtm2|107065|leucine rich repeat transmembrane neuronal 2	AK046818|Lrrtm2|107065|leucine rich repeat transmembrane neuronal 2	AK049920|Lrrtm2|107065|leucine rich repeat transmembrane neuronal 2	AK043784|Lrrtm2|107065|leucine rich repeat transmembrane neuronal 2
mm9_v1_chr14_-_21437545_21437583	5.40866	SOX2.p2	AK047620|Usp54|78787|ubiquitin specific peptidase 54	NM_030180|Usp54|78787|ubiquitin specific peptidase 54
mm9_v1_chr9_+_122832164_122832215	5.38796	SOX2.p2	AK147198|Zfp105|22646|zinc finger protein 105	BC052165|Zfp105|22646|zinc finger protein 105	NM_009544|Zfp105|22646|zinc finger protein 105	AF045565|Zfp105|22646|zinc finger protein 105
mm9_v1_chrX_+_102695110_102695127	5.37817	SOX2.p2	BC060953|Cypt2-ps|245566|cysteine-rich perinuclear theca 2, pseudogene	NM_173436|Cypt2-ps|245566|cysteine-rich perinuclear theca 2, pseudogene	AF463499|Cypt2-ps|245566|cysteine-rich perinuclear theca 2, pseudogene
mm9_v1_chr12_+_41172669_41172674	5.34751	SOX2.p2	AK030653|Dock4|238130|dedicator of cytokinesis 4	AK031713|Dock4|238130|dedicator of cytokinesis 4
mm9_v1_chr7_+_98239230_98239295	5.31636	SOX2.p2	NM_011807|Dlg2|23859|discs, large homolog 2 (Drosophila)
mm9_v1_chr14_-_71018208_71018377	5.30351	SOX2.p2	AF079846|Epb4.9|13829|erythrocyte protein band 4.9	AF155547|Epb4.9|13829|erythrocyte protein band 4.9	BC037021|Epb4.9|13829|erythrocyte protein band 4.9
mm9_v1_chr12_+_110798661_110798666	5.30291	SOX2.p2	AK019916|Meg3|17263|maternally expressed 3
mm9_v1_chr3_+_17695743_17695745	5.27934	SOX2.p2	AK046405|6430547I21Rik|320521|RIKEN cDNA 6430547I21 gene	AK032443|6430547I21Rik|320521|RIKEN cDNA 6430547I21 gene
mm9_v1_chr3_-_141645214_141645214	5.27819	SOX2.p2	BC065143|Bmpr1b|12167|bone morphogenetic protein receptor, type 1B	NM_007560|Bmpr1b|12167|bone morphogenetic protein receptor, type 1B
mm9_v1_chr6_-_36759929_36760219	5.27691	SOX2.p2	BC002064|Ptn|19242|pleiotrophin	BC048363|Ptn|19242|pleiotrophin	AK161964|Ptn|19242|pleiotrophin	D90225|Ptn|19242|pleiotrophin	AK161847|Ptn|19242|pleiotrophin	AK011699|Ptn|19242|pleiotrophin	AK133835|Ptn|19242|pleiotrophin	BC061695|Ptn|19242|pleiotrophin	AK017768|Ptn|19242|pleiotrophin	AK011346|Ptn|19242|pleiotrophin
mm9_v1_chr7_-_67149962_67150045	5.25946	SOX2.p2	BC069894|Snrpn|20646|small nuclear ribonucleoprotein N	BC024880|Snrpn|20646|small nuclear ribonucleoprotein N	BC019589|Snrpn|20646|small nuclear ribonucleoprotein N	BC132082|Snurf|84704|SNRPN upstream reading frame	BC132084|Snurf|84704|SNRPN upstream reading frame	AK013607|Snrpn|20646|small nuclear ribonucleoprotein N	AK144386|Snrpn|20646|small nuclear ribonucleoprotein N	AF101042|Snurf|84704|SNRPN upstream reading frame	NM_013670|Snrpn|20646|small nuclear ribonucleoprotein N	NM_033174|Snurf|84704|SNRPN upstream reading frame
mm9_v1_chr3_-_57651621_57651757	5.24473	SOX2.p2	NM_019410|Pfn2|18645|profilin 2
mm9_v1_chr10_+_69488049_69488073	5.22909	SOX2.p2	AK013684|Ank3|11735|ankyrin 3, epithelial
mm9_v1_chr17_+_17539635_17539669	5.22521	SOX2.p2	BC049574|Lix1|66643|limb expression 1 homolog (chicken)	NM_025681|Lix1|66643|limb expression 1 homolog (chicken)
mm9_v1_chr3_-_84024766_84024812	5.20162	SOX2.p2	BC058668|Trim2|80890|tripartite motif-containing 2	AB043550|Trim2|80890|tripartite motif-containing 2	AK046887|Trim2|80890|tripartite motif-containing 2	AK147395|Trim2|80890|tripartite motif-containing 2	AK039741|Trim2|80890|tripartite motif-containing 2	AK045410|Trim2|80890|tripartite motif-containing 2	AK083057|Trim2|80890|tripartite motif-containing 2	NM_030706|Trim2|80890|tripartite motif-containing 2
mm9_v1_chr5_+_89012600_89012641	5.18738	SOX2.p2	AK045610|Rufy3|52822|RUN and FYVE domain containing 3	AK083242|Rufy3|52822|RUN and FYVE domain containing 3
mm9_v1_chr8_+_26750755_26750755	5.17828	SOX2.p2	NM_001081269|Whsc1l1|234135|Wolf-Hirschhorn syndrome candidate 1-like 1 (human)
mm9_v1_chr1_-_191167231_191167231	5.15796	SOX2.p2	NM_001159850|Kcnk2|16526|potassium channel, subfamily K, member 2
mm9_v1_chr17_+_17539832_17539856	5.1575	SOX2.p2	AK017685|Lix1|66643|limb expression 1 homolog (chicken)	AK012220|Lix1|66643|limb expression 1 homolog (chicken)	BC052700|Lix1|66643|limb expression 1 homolog (chicken)	BC063057|Lix1|66643|limb expression 1 homolog (chicken)
mm9_v1_chr19_-_46401618_46401645	5.14464	SOX2.p2	BC057353|Psd|73728|pleckstrin and Sec7 domain containing	NM_028627|Psd|73728|pleckstrin and Sec7 domain containing
mm9_v1_chr15_-_84388113_84388233	5.11534	SOX2.p2	AK083881|Ldoc1l|223732|leucine zipper, down-regulated in cancer 1-like
mm9_v1_chr6_+_121586190_121586250	5.04696	SOX2.p2	NM_175628|A2m|232345|alpha-2-macroglobulin	AY185125|A2m|232345|alpha-2-macroglobulin	BC072642|A2m|232345|alpha-2-macroglobulin
mm9_v1_chr15_-_44584003_44584003	5.0453	SOX2.p2	AB232449|Sybu|319613|syntabulin (syntaxin-interacting)	BC065045|Sybu|319613|syntabulin (syntaxin-interacting)	NM_178765|Sybu|319613|syntabulin (syntaxin-interacting)
mm9_v1_chr10_-_31410391_31410392	5.04165	SOX2.p2	AK018248|Nkain2|432450|Na+/K+ transporting ATPase interacting 2
mm9_v1_chr8_-_4259126_4259300	5.03898	SOX2.p2	AK158759|Ctxn1|330695|cortexin 1	BC028881|Ctxn1|330695|cortexin 1	AK154120|Ctxn1|330695|cortexin 1	NM_183315|Ctxn1|330695|cortexin 1
mm9_v1_chr1_-_42751652_42751673	4.96505	SOX2.p2	BC094545|2610017I09Rik|66297|RIKEN cDNA 2610017I09 gene	AK011437|2610017I09Rik|66297|RIKEN cDNA 2610017I09 gene	AK019154|2610017I09Rik|66297|RIKEN cDNA 2610017I09 gene	AK048630|2610017I09Rik|66297|RIKEN cDNA 2610017I09 gene
mm9_v1_chr2_+_179777187_179777250	4.93973	SOX2.p2	NM_178750|Ss18l1|269397|synovial sarcoma translocation gene on chromosome 18-like 1	BC054730|Ss18l1|269397|synovial sarcoma translocation gene on chromosome 18-like 1	AK133944|Ss18l1|269397|synovial sarcoma translocation gene on chromosome 18-like 1
mm9_v1_chr9_-_83040061_83040223	4.93242	SOX2.p2	AK002970|Hmgn3|94353|high mobility group nucleosomal binding domain 3	BC005693|Hmgn3|94353|high mobility group nucleosomal binding domain 3	AK003272|Hmgn3|94353|high mobility group nucleosomal binding domain 3	AK153223|Hmgn3|94353|high mobility group nucleosomal binding domain 3	NM_026122|Hmgn3|94353|high mobility group nucleosomal binding domain 3	NM_175074|Hmgn3|94353|high mobility group nucleosomal binding domain 3
mm9_v1_chr15_-_100325669_100325697	4.91489	SOX2.p2	BC035295|Csrnp2|207785|cysteine-serine-rich nuclear protein 2	NM_153407|Csrnp2|207785|cysteine-serine-rich nuclear protein 2	AK146924|Csrnp2|207785|cysteine-serine-rich nuclear protein 2	AK050864|Csrnp2|207785|cysteine-serine-rich nuclear protein 2	AK166557|Csrnp2|207785|cysteine-serine-rich nuclear protein 2
mm9_v1_chr7_-_86531912_86531912	4.90198	SOX2.p2	AK140622|Rlbp1|19771|retinaldehyde binding protein 1	NM_001173483|Rlbp1|19771|retinaldehyde binding protein 1	NM_020599|Rlbp1|19771|retinaldehyde binding protein 1
mm9_v1_chr15_-_8660729_8660806	4.89948	SOX2.p2	BC058711|Slc1a3|20512|solute carrier family 1 (glial high affinity glutamate transporter), member 3	NM_148938|Slc1a3|20512|solute carrier family 1 (glial high affinity glutamate transporter), member 3
mm9_v1_chr18_-_6516073_6516084	4.87981	SOX2.p2	AK148194|Epc1|13831|enhancer of polycomb homolog 1 (Drosophila)	AF079765|Epc1|13831|enhancer of polycomb homolog 1 (Drosophila)	NM_007935|Epc1|13831|enhancer of polycomb homolog 1 (Drosophila)
mm9_v1_chr2_+_179777418_179777493	4.87642	SOX2.p2	AK173004|Ss18l1|269397|synovial sarcoma translocation gene on chromosome 18-like 1	AK054560|Ss18l1|269397|synovial sarcoma translocation gene on chromosome 18-like 1	AK038669|Ss18l1|269397|synovial sarcoma translocation gene on chromosome 18-like 1
mm9_v1_chr15_+_99532698_99532771	4.87149	SOX2.p2	NM_031842|Smarcd1|83797|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1	BC059921|Smarcd1|83797|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1	M25773|Smarcd1|83797|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1	U66620|Smarcd1|83797|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1	BC079839|Smarcd1|83797|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1
mm9_v1_chr15_-_84388245_84388282	4.86811	SOX2.p2	BC094559|Ldoc1l|223732|leucine zipper, down-regulated in cancer 1-like	NM_177630|Ldoc1l|223732|leucine zipper, down-regulated in cancer 1-like
mm9_v1_chr6_+_133242233_133242233	4.86371	SOX2.p2	AK017421|5530400C23Rik|232426|RIKEN cDNA 5530400C23 gene	NM_027784|5530400C23Rik|232426|RIKEN cDNA 5530400C23 gene
mm9_v1_chr18_+_37105758_37105860	4.85037	SOX2.p2	AK129120|Pcdha3|192163|protocadherin alpha 3	BC141348|Pcdha3|192163|protocadherin alpha 3	AY013761|Pcdha3|192163|protocadherin alpha 3	NM_138662|Pcdha3|192163|protocadherin alpha 3
mm9_v1_chr18_+_37921454_37921532	4.83365	SOX2.p2	BC139099|Pcdhgb8|93705|protocadherin gamma subfamily B, 8	BC139100|Pcdhgb8|93705|protocadherin gamma subfamily B, 8	NM_033580|Pcdhgb8|93705|protocadherin gamma subfamily B, 8	AY013810|Pcdhgb8|93705|protocadherin gamma subfamily B, 8
mm9_v1_chrX_-_92853721_92853847	4.83346	SOX2.p2	AK129302|Zc4h2|245522|zinc finger, C4H2 domain containing	AK162005|Zc4h2|245522|zinc finger, C4H2 domain containing	AK086554|Zc4h2|245522|zinc finger, C4H2 domain containing	BC050850|Zc4h2|245522|zinc finger, C4H2 domain containing	BC119285|Zc4h2|245522|zinc finger, C4H2 domain containing	BC119311|Zc4h2|245522|zinc finger, C4H2 domain containing	BC079862|Zc4h2|245522|zinc finger, C4H2 domain containing	NM_001003916|Zc4h2|245522|zinc finger, C4H2 domain containing	AK155445|Zc4h2|245522|zinc finger, C4H2 domain containing
mm9_v1_chr7_+_146271910_146271981	4.82673	SOX2.p2	BC046333|Dpysl4|26757|dihydropyrimidinase-like 4	AK090197|Dpysl4|26757|dihydropyrimidinase-like 4	BC090674|Dpysl4|26757|dihydropyrimidinase-like 4	AB006715|Dpysl4|26757|dihydropyrimidinase-like 4	BC138573|Dpysl4|26757|dihydropyrimidinase-like 4	BC138574|Dpysl4|26757|dihydropyrimidinase-like 4
mm9_v1_chr6_+_104443037_104443047	4.79941	SOX2.p2	BC076594|Cntn6|53870|contactin 6	NM_017383|Cntn6|53870|contactin 6
mm9_v1_chr11_+_119862650_119862652	4.78886	SOX2.p2	AK083201|Baiap2|108100|brain-specific angiogenesis inhibitor 1-associated protein 2
mm9_v1_chr2_+_158492468_158492468	4.78359	SOX2.p2	NM_153089|Ppp1r16b|228852|protein phosphatase 1, regulatory (inhibitor) subunit 16B
mm9_v1_chr16_+_41533317_41533456	4.78119	SOX2.p2	AK140043|Lsamp|268890|limbic system-associated membrane protein	NM_175548|Lsamp|268890|limbic system-associated membrane protein	AK044845|Lsamp|268890|limbic system-associated membrane protein	AK140663|Lsamp|268890|limbic system-associated membrane protein
mm9_v1_chr12_+_110800212_110800261	4.75396	SOX2.p2	AK018142|Meg3|17263|maternally expressed 3
mm9_v1_chr6_-_38077491_38077509	4.7432	SOX2.p2	BC059853|D630045J12Rik|330286|RIKEN cDNA D630045J12 gene	BC042666|D630045J12Rik|330286|RIKEN cDNA D630045J12 gene
mm9_v1_chr16_-_5013596_5013670	4.73345	SOX2.p2	AK046477|Rogdi|66049|rogdi homolog (Drosophila)	AK170144|Rogdi|66049|rogdi homolog (Drosophila)	AY036117|Rogdi|66049|rogdi homolog (Drosophila)	BC006914|Rogdi|66049|rogdi homolog (Drosophila)	AK002523|Rogdi|66049|rogdi homolog (Drosophila)	NM_133185|Rogdi|66049|rogdi homolog (Drosophila)
mm9_v1_chr2_+_55289530_55289587	4.71144	SOX2.p2	AK046778|Kcnj3|16519|potassium inwardly-rectifying channel, subfamily J, member 3	D45022|Kcnj3|16519|potassium inwardly-rectifying channel, subfamily J, member 3	NM_008426|Kcnj3|16519|potassium inwardly-rectifying channel, subfamily J, member 3	BC103671|Kcnj3|16519|potassium inwardly-rectifying channel, subfamily J, member 3	BC103673|Kcnj3|16519|potassium inwardly-rectifying channel, subfamily J, member 3	BC103674|Kcnj3|16519|potassium inwardly-rectifying channel, subfamily J, member 3	BC103672|Kcnj3|16519|potassium inwardly-rectifying channel, subfamily J, member 3
mm9_v1_chr1_+_40082070_40082114	4.70029	SOX2.p2	AK159799|Map4k4|26921|mitogen-activated protein kinase kinase kinase kinase 4
mm9_v1_chr11_+_58762401_58762421	4.69827	SOX2.p2	AK018765|Hist3h2ba|78303|histone cluster 3, H2ba	NM_030082|Hist3h2ba|78303|histone cluster 3, H2ba	BC051921|Hist3h2ba|78303|histone cluster 3, H2ba
mm9_v1_chr17_+_34052312_34052432	4.69542	SOX2.p2	
mm9_v1_chr17_-_6943173_6943193	4.68799	SOX2.p2	AK207973|Ezr|22350|ezrin	AK207113|Ezr|22350|ezrin
mm9_v1_chr11_+_29642667_29642710	4.68297	SOX2.p2	
mm9_v1_chr2_+_181498036_181498036	4.67477	SOX2.p2	BC063252|Myt1|17932|myelin transcription factor 1	NM_001171615|Myt1|17932|myelin transcription factor 1
mm9_v1_chr6_+_71657791_71657963	4.67261	SOX2.p2	AK035238|Reep1|52250|receptor accessory protein 1	AK045056|Reep1|52250|receptor accessory protein 1	NM_178608|Reep1|52250|receptor accessory protein 1	AK053158|Reep1|52250|receptor accessory protein 1	AK136916|Reep1|52250|receptor accessory protein 1	BC046826|Reep1|52250|receptor accessory protein 1	AY562229|Reep1|52250|receptor accessory protein 1
mm9_v1_chr6_+_115189004_115189072	4.67204	SOX2.p2	AK029181|Syn2|20965|synapsin II
mm9_v1_chr6_-_139989932_139989951	4.67104	SOX2.p2	BC106767|Plcz1|114875|phospholipase C, zeta 1	BC106768|Plcz1|114875|phospholipase C, zeta 1	AF435950|Plcz1|114875|phospholipase C, zeta 1	NM_054066|Plcz1|114875|phospholipase C, zeta 1	AK005949|Plcz1|114875|phospholipase C, zeta 1	AK006672|Plcz1|114875|phospholipase C, zeta 1
mm9_v1_chr15_-_84387921_84388066	4.65942	SOX2.p2	BC058638|Ldoc1l|223732|leucine zipper, down-regulated in cancer 1-like
mm9_v1_chr1_-_191167582_191167722	4.62956	SOX2.p2	NM_010607|Kcnk2|16526|potassium channel, subfamily K, member 2	U73488|Kcnk2|16526|potassium channel, subfamily K, member 2	AK080342|Kcnk2|16526|potassium channel, subfamily K, member 2
mm9_v1_chr10_+_90292453_90292587	4.62063	SOX2.p2	AK038609|Anks1b|77531|ankyrin repeat and sterile alpha motif domain containing 1B
mm9_v1_chr19_+_22767090_22767108	4.59198	SOX2.p2	AK086143|Trpm3|226025|transient receptor potential cation channel, subfamily M, member 3	AK085182|Trpm3|226025|transient receptor potential cation channel, subfamily M, member 3	NM_001035244|Trpm3|226025|transient receptor potential cation channel, subfamily M, member 3	NM_001035245|Trpm3|226025|transient receptor potential cation channel, subfamily M, member 3	NM_001035246|Trpm3|226025|transient receptor potential cation channel, subfamily M, member 3
mm9_v1_chr11_-_98190774_98191090	4.55118	SOX2.p2	D83507|Neurod2|18013|neurogenic differentiation 2	BC058965|Neurod2|18013|neurogenic differentiation 2	NM_010895|Neurod2|18013|neurogenic differentiation 2	U58471|Neurod2|18013|neurogenic differentiation 2	AK158767|Neurod2|18013|neurogenic differentiation 2
mm9_v1_chr18_+_37595274_37595294	4.55084	SOX2.p2	NM_053137|Pcdhb12|93883|protocadherin beta 12
mm9_v1_chr2_+_26171073_26171116	4.52574	SOX2.p2	AK082985|Gpsm1|67839|G-protein signalling modulator 1 (AGS3-like, C. elegans)	AK084631|Gpsm1|67839|G-protein signalling modulator 1 (AGS3-like, C. elegans)
mm9_v1_chr2_-_52414072_52414117	4.5105	SOX2.p2	AK043850|Cacnb4|12298|calcium channel, voltage-dependent, beta 4 subunit	AK079616|Cacnb4|12298|calcium channel, voltage-dependent, beta 4 subunit	AK038633|Cacnb4|12298|calcium channel, voltage-dependent, beta 4 subunit	NM_146123|Cacnb4|12298|calcium channel, voltage-dependent, beta 4 subunit
mm9_v1_chrX_-_161764912_161765057	4.50794	SOX2.p2	BC056342|Glra2|237213|glycine receptor, alpha 2 subunit	BC068987|Glra2|237213|glycine receptor, alpha 2 subunit	NM_183427|Glra2|237213|glycine receptor, alpha 2 subunit	AK135134|Glra2|237213|glycine receptor, alpha 2 subunit
mm9_v1_chr18_+_37839910_37840111	4.49216	SOX2.p2	BC054741|Pcdhgb1|93699|protocadherin gamma subfamily B, 1	BC098367|Pcdhgb1|93699|protocadherin gamma subfamily B, 1	AY013804|Pcdhgb1|93699|protocadherin gamma subfamily B, 1	NM_033574|Pcdhgb1|93699|protocadherin gamma subfamily B, 1
mm9_v1_chr2_-_91773029_91773128	4.49054	SOX2.p2	
mm9_v1_chr14_-_20796411_20796481	4.49003	SOX2.p2	AK158697|Gng2|14702|guanine nucleotide binding protein (G protein), gamma 2	NM_001038637|Gng2|14702|guanine nucleotide binding protein (G protein), gamma 2	NM_010315|Gng2|14702|guanine nucleotide binding protein (G protein), gamma 2
mm9_v1_chr13_-_55589463_55589528	4.45329	SOX2.p2	BC006714|Dbn1|56320|drebrin 1
mm9_v1_chr12_+_3365102_3365131	4.42465	SOX2.p2	AK220283|Kif3c|16570|kinesin family member 3C	NM_008445|Kif3c|16570|kinesin family member 3C
mm9_v1_chr7_-_107476113_107476159	4.41946	SOX2.p2	AK218423|Ppme1|72590|protein phosphatase methylesterase 1
mm9_v1_chr9_-_91255831_91255857	4.40561	SOX2.p2	AK141431|Zic1|22771|zinc finger protein of the cerebellum 1
mm9_v1_chr17_-_85461840_85461859	4.40328	SOX2.p2	AK019367|Prepl|213760|prolyl endopeptidase-like
mm9_v1_chr5_+_34326081_34326346	4.38973	SOX2.p2	BC147444|Gm1673|381633|predicted gene 1673	BC147468|Gm1673|381633|predicted gene 1673	BC048625|Gm1673|381633|predicted gene 1673	AK141724|Gm1673|381633|predicted gene 1673	NM_001033458|Gm1673|381633|predicted gene 1673	BC100514|Gm1673|381633|predicted gene 1673	BC055794|Gm1673|381633|predicted gene 1673	AK131594|Gm1673|381633|predicted gene 1673
mm9_v1_chr6_-_52190771_52190869	4.38547	SOX2.p2	L08758|Hoxa10|15395|homeobox A10	NM_001122950|Hoxa10|15395|homeobox A10
mm9_v1_chr15_-_8660462_8660476	4.3781	SOX2.p2	AK031831|Slc1a3|20512|solute carrier family 1 (glial high affinity glutamate transporter), member 3	AK040798|Slc1a3|20512|solute carrier family 1 (glial high affinity glutamate transporter), member 3	AK049090|Slc1a3|20512|solute carrier family 1 (glial high affinity glutamate transporter), member 3	AK082736|Slc1a3|20512|solute carrier family 1 (glial high affinity glutamate transporter), member 3	U75377|Slc1a3|20512|solute carrier family 1 (glial high affinity glutamate transporter), member 3
mm9_v1_chr7_+_107789414_107789679	4.37294	SOX2.p2	AK191812|Rab6|19346|RAB6, member RAS oncogene family
mm9_v1_chr11_-_74403603_74403659	4.36754	SOX2.p2	NM_001015046|Rap1gap2|380711|RAP1 GTPase activating protein 2
mm9_v1_chr2_-_44717141_44717141	4.36113	SOX2.p2	AK054272|Gtdc1|227835|glycosyltransferase-like domain containing 1	NM_172662|Gtdc1|227835|glycosyltransferase-like domain containing 1
mm9_v1_chr3_-_91887051_91887065	4.33823	SOX2.p2	BC058223|Lor|16939|loricrin	BC026781|Lor|16939|loricrin	M34398|Lor|16939|loricrin	NM_008508|Lor|16939|loricrin
mm9_v1_chr18_-_35374663_35374683	4.32751	SOX2.p2	AK122278|Lrrtm2|107065|leucine rich repeat transmembrane neuronal 2	AK036155|Lrrtm2|107065|leucine rich repeat transmembrane neuronal 2	AK044705|Lrrtm2|107065|leucine rich repeat transmembrane neuronal 2	AK046774|Lrrtm2|107065|leucine rich repeat transmembrane neuronal 2	NM_178005|Lrrtm2|107065|leucine rich repeat transmembrane neuronal 2
mm9_v1_chr8_+_96334879_96334940	4.32615	SOX2.p2	BC051989|Gnao1|14681|guanine nucleotide binding protein, alpha O
mm9_v1_chr17_-_90487479_90487653	4.3237	SOX2.p2	AK032032|Nrxn1|18189|neurexin I
mm9_v1_chrX_-_7783571_7783654	4.31782	SOX2.p2	BC027292|Porcn|53627|porcupine homolog (Drosophila)	BC032284|Porcn|53627|porcupine homolog (Drosophila)	AK010405|Porcn|53627|porcupine homolog (Drosophila)	AB036746|Porcn|53627|porcupine homolog (Drosophila)	AB036747|Porcn|53627|porcupine homolog (Drosophila)	AB036748|Porcn|53627|porcupine homolog (Drosophila)	AB036749|Porcn|53627|porcupine homolog (Drosophila)	NM_016913|Porcn|53627|porcupine homolog (Drosophila)	NM_023638|Porcn|53627|porcupine homolog (Drosophila)	NM_145907|Porcn|53627|porcupine homolog (Drosophila)	NM_145908|Porcn|53627|porcupine homolog (Drosophila)
mm9_v1_chr2_+_90858663_90858815	4.31562	SOX2.p2	AK080832|Celf1|13046|CUGBP, Elav-like family member 1	AK160135|Celf1|13046|CUGBP, Elav-like family member 1
mm9_v1_chr11_-_3763899_3763908	4.30681	SOX2.p2	AK049816|Osbp2|74309|oxysterol binding protein 2	NM_152818|Osbp2|74309|oxysterol binding protein 2
mm9_v1_chr8_+_56040211_56040342	4.28369	SOX2.p2	BC043130|Gpm6a|234267|glycoprotein m6a	AK147245|Gpm6a|234267|glycoprotein m6a	AK147280|Gpm6a|234267|glycoprotein m6a
mm9_v1_chr17_+_17539908_17539941	4.25996	SOX2.p2	AF351204|Lix1|66643|limb expression 1 homolog (chicken)
mm9_v1_chr2_+_26171051_26171062	4.22296	SOX2.p2	AK048691|Gpsm1|67839|G-protein signalling modulator 1 (AGS3-like, C. elegans)	NM_153410|Gpsm1|67839|G-protein signalling modulator 1 (AGS3-like, C. elegans)
mm9_v1_chr10_+_106708886_106708980	4.20391	SOX2.p2	NM_001033223|Lin7a|108030|lin-7 homolog A (C. elegans)	NM_001039354|Lin7a|108030|lin-7 homolog A (C. elegans)	BC105965|Lin7a|108030|lin-7 homolog A (C. elegans)	AK160671|Lin7a|108030|lin-7 homolog A (C. elegans)	BC029721|Lin7a|108030|lin-7 homolog A (C. elegans)
mm9_v1_chr4_-_43591258_43591425	4.18682	SOX2.p2	BC056935|Gba2|230101|glucosidase beta 2	BC031397|Gba2|230101|glucosidase beta 2	AK089192|Gba2|230101|glucosidase beta 2
mm9_v1_chr10_+_98486068_98486102	4.17112	SOX2.p2	AK136761|Atp2b1|67972|ATPase, Ca++ transporting, plasma membrane 1
mm9_v1_chr17_+_52742087_52742144	4.16656	SOX2.p2	NM_001031811|Kcnh8|211468|potassium voltage-gated channel, subfamily H (eag-related), member 8	AK048629|Kcnh8|211468|potassium voltage-gated channel, subfamily H (eag-related), member 8
mm9_v1_chr7_-_30290470_30290595	4.16115	SOX2.p2	AK171182|Sipa1l3|74206|signal-induced proliferation-associated 1 like 3	AK154121|Sipa1l3|74206|signal-induced proliferation-associated 1 like 3	NM_001081028|Sipa1l3|74206|signal-induced proliferation-associated 1 like 3
mm9_v1_chr18_-_16967754_16967859	4.15632	SOX2.p2	AK146981|Cdh2|12558|cadherin 2
mm9_v1_chr13_+_42804911_42805054	4.14929	SOX2.p2	BC048407|Phactr1|218194|phosphatase and actin regulator 1	BC061691|Phactr1|218194|phosphatase and actin regulator 1	NM_001005740|Phactr1|218194|phosphatase and actin regulator 1	AK048208|Phactr1|218194|phosphatase and actin regulator 1
mm9_v1_chr15_-_8660442_8660451	4.14845	SOX2.p2	AK084968|Slc1a3|20512|solute carrier family 1 (glial high affinity glutamate transporter), member 3
mm9_v1_chr1_+_60965868_60966014	4.14838	SOX2.p2	BC042741|Ctla4|12477|cytotoxic T-lymphocyte-associated protein 4	NM_009843|Ctla4|12477|cytotoxic T-lymphocyte-associated protein 4	AK138891|Ctla4|12477|cytotoxic T-lymphocyte-associated protein 4	X05719|Ctla4|12477|cytotoxic T-lymphocyte-associated protein 4	BC052683|Ctla4|12477|cytotoxic T-lymphocyte-associated protein 4	AB097214|Ctla4|12477|cytotoxic T-lymphocyte-associated protein 4
mm9_v1_chr16_+_17146981_17147071	4.12821	SOX2.p2	AK032396|Ydjc|69101|YdjC homolog (bacterial)	AK140044|Ydjc|69101|YdjC homolog (bacterial)	BC030425|Ydjc|69101|YdjC homolog (bacterial)	AK007503|Ydjc|69101|YdjC homolog (bacterial)	BC115584|Ydjc|69101|YdjC homolog (bacterial)	BC115585|Ydjc|69101|YdjC homolog (bacterial)	NM_026940|Ydjc|69101|YdjC homolog (bacterial)
mm9_v1_chr11_-_99105293_99105435	4.12651	SOX2.p2	BC079890|Krt222|268481|keratin 222	AK031954|Krt222|268481|keratin 222	NM_172946|Krt222|268481|keratin 222	AK044068|Krt222|268481|keratin 222	AK138778|Krt222|268481|keratin 222
mm9_v1_chr3_+_121129588_121129727	4.12141	SOX2.p2	BC085268|Cnn3|71994|calponin 3, acidic	AK180041|Cnn3|71994|calponin 3, acidic	AK184231|Cnn3|71994|calponin 3, acidic	AK179383|Cnn3|71994|calponin 3, acidic	AK216318|Cnn3|71994|calponin 3, acidic
mm9_v1_chr11_-_62206116_62206160	4.12003	SOX2.p2	AK137695|Ncor1|20185|nuclear receptor co-repressor 1
mm9_v1_chr15_+_99869071_99869185	4.11847	SOX2.p2	NM_001159361|Dip2b|239667|DIP2 disco-interacting protein 2 homolog B (Drosophila)	AK147562|Dip2b|239667|DIP2 disco-interacting protein 2 homolog B (Drosophila)
mm9_v1_chr13_+_43218207_43218244	4.11814	SOX2.p2	NM_001005748|Phactr1|218194|phosphatase and actin regulator 1	AK166463|Phactr1|218194|phosphatase and actin regulator 1	BC025873|Phactr1|218194|phosphatase and actin regulator 1
mm9_v1_chr3_+_13946371_13946410	4.11185	SOX2.p2	NM_001163329|Ralyl|76897|RALY RNA binding protein-like	NM_001163330|Ralyl|76897|RALY RNA binding protein-like	AK038465|Ralyl|76897|RALY RNA binding protein-like	BC052358|Ralyl|76897|RALY RNA binding protein-like
mm9_v1_chrX_+_13209894_13209986	4.10284	SOX2.p2	DQ103766|Gpr34|23890|G protein-coupled receptor 34	DQ103767|Gpr34|23890|G protein-coupled receptor 34	NM_011823|Gpr34|23890|G protein-coupled receptor 34	AK033675|Gpr34|23890|G protein-coupled receptor 34	AK039528|Gpr34|23890|G protein-coupled receptor 34	AK039041|Gpr34|23890|G protein-coupled receptor 34	AK140507|Gpr34|23890|G protein-coupled receptor 34
mm9_v1_chr5_+_29524545_29524545	4.06222	SOX2.p2	AF190664|Rnf32|56874|ring finger protein 32	NM_021470|Rnf32|56874|ring finger protein 32
mm9_v1_chr17_-_37712365_37712392	4.05711	SOX2.p2	NM_146289|Olfr113|258286|olfactory receptor 113	BC132178|Olfr113|258286|olfactory receptor 113	BC132180|Olfr113|258286|olfactory receptor 113
mm9_v1_chr8_+_87162885_87162891	4.05447	SOX2.p2	AK132071|Cacna1a|12286|calcium channel, voltage-dependent, P/Q type, alpha 1A subunit
mm9_v1_chrX_+_109714134_109714134	4.05383	SOX2.p2	AK038956|Zfp711|245595|zinc finger protein 711	NM_177747|Zfp711|245595|zinc finger protein 711
mm9_v1_chr6_-_13785233_13785235	4.04676	SOX2.p2	AK013598|Gpr85|64450|G protein-coupled receptor 85
mm9_v1_chr9_-_75458918_75458929	4.04057	SOX2.p2	AK018223|Tmod2|50876|tropomodulin 2
mm9_v1_chr7_+_58877199_58877199	4.04019	SOX2.p2	NM_080853|Slc17a6|140919|solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6
mm9_v1_chr18_-_78320126_78320164	4.03814	SOX2.p2	NM_001171010|Slc14a1|108052|solute carrier family 14 (urea transporter), member 1	NM_028122|Slc14a1|108052|solute carrier family 14 (urea transporter), member 1
mm9_v1_chr8_+_56040193_56040201	4.03079	SOX2.p2	AK081877|Gpm6a|234267|glycoprotein m6a
mm9_v1_chr15_-_8660479_8660490	4.0295	SOX2.p2	AK045949|Slc1a3|20512|solute carrier family 1 (glial high affinity glutamate transporter), member 3	AK080879|Slc1a3|20512|solute carrier family 1 (glial high affinity glutamate transporter), member 3
mm9_v1_chr1_-_166368439_166368560	4.02176	SOX2.p2	EF437334|Atp1b1|11931|ATPase, Na+/K+ transporting, beta 1 polypeptide
mm9_v1_chr1_-_194677940_194677940	4.0145	SOX2.p2	NM_001177794|Sertad4|214791|SERTA domain containing 4
mm9_v1_chr12_-_119474010_119474093	4.00781	SOX2.p2	AK017738|Sp4|20688|trans-acting transcription factor 4
mm9_v1_chr3_+_7503409_7503519	3.98515	SOX2.p2	NM_173181|Fam164a|67306|family with sequence similarity 164, member A	BC087731|Fam164a|67306|family with sequence similarity 164, member A	AK083941|Fam164a|67306|family with sequence similarity 164, member A	AK170609|Fam164a|67306|family with sequence similarity 164, member A	AK085187|Fam164a|67306|family with sequence similarity 164, member A	AK014202|Fam164a|67306|family with sequence similarity 164, member A	BC044809|Fam164a|67306|family with sequence similarity 164, member A
mm9_v1_chr18_+_23468585_23468619	3.9776	SOX2.p2	AK147279|Dtna|13527|dystrobrevin alpha
mm9_v1_chr4_-_109959366_109959438	3.96092	SOX2.p2	BC048159|Elavl4|15572|ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	NM_001163399|Elavl4|15572|ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	NM_010488|Elavl4|15572|ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)
mm9_v1_chrX_+_97963061_97963090	3.9564	SOX2.p2	AK122474|Dlg3|53310|discs, large homolog 3 (Drosophila)	NM_001177778|Dlg3|53310|discs, large homolog 3 (Drosophila)	BC094368|Dlg3|53310|discs, large homolog 3 (Drosophila)	NM_016747|Dlg3|53310|discs, large homolog 3 (Drosophila)	D87117|Dlg3|53310|discs, large homolog 3 (Drosophila)
mm9_v1_chr1_-_136131981_136132033	3.95138	SOX2.p2	NM_001008533|Adora1|11539|adenosine A1 receptor	AK038774|Adora1|11539|adenosine A1 receptor	NM_001039510|Adora1|11539|adenosine A1 receptor	AK134532|Adora1|11539|adenosine A1 receptor
mm9_v1_chr18_+_37170365_37170627	3.94861	SOX2.p2	AK141960|Pcdha11|12942|protocadherin alpha 11	AK139436|Pcdha11|12942|protocadherin alpha 11	AK043705|Pcdha11|12942|protocadherin alpha 11	BC141349|Pcdha11|12942|protocadherin alpha 11	AY013758|Pcdha11|12942|protocadherin alpha 11	NM_009960|Pcdha11|12942|protocadherin alpha 11	AB008182|Pcdha11|12942|protocadherin alpha 11
mm9_v1_chr11_-_22185840_22185840	3.94651	SOX2.p2	AF424697|Ehbp1|216565|EH domain binding protein 1	NM_153078|Ehbp1|216565|EH domain binding protein 1
mm9_v1_chr1_+_12708582_12708625	3.94389	SOX2.p2	AK037389|Sulf1|240725|sulfatase 1	AY101178|Sulf1|240725|sulfatase 1	BC034547|Sulf1|240725|sulfatase 1	BC049276|Sulf1|240725|sulfatase 1	NM_172294|Sulf1|240725|sulfatase 1
mm9_v1_chr5_-_123183537_123183571	3.9378	SOX2.p2	AK213252|Camkk2|207565|calcium/calmodulin-dependent protein kinase kinase 2, beta
mm9_v1_chr18_+_35750406_35750586	3.93613	SOX2.p2	AK139050|Matr3|17184|matrin 3	AK084822|Matr3|17184|matrin 3	AK148059|Matr3|17184|matrin 3
mm9_v1_chr6_-_56312170_56312512	3.90569	SOX2.p2	AK082497|Pde1c|18575|phosphodiesterase 1C	BC032277|Pde1c|18575|phosphodiesterase 1C	AK139923|Pde1c|18575|phosphodiesterase 1C	AK017183|Pde1c|18575|phosphodiesterase 1C	AK082180|Pde1c|18575|phosphodiesterase 1C	AK030423|Pde1c|18575|phosphodiesterase 1C	NM_001025568|Pde1c|18575|phosphodiesterase 1C	NM_001159952|Pde1c|18575|phosphodiesterase 1C	NM_001159953|Pde1c|18575|phosphodiesterase 1C	L76946|Pde1c|18575|phosphodiesterase 1C	NM_011054|Pde1c|18575|phosphodiesterase 1C
mm9_v1_chr16_+_5885447_5885760	3.90392	SOX2.p2	AB041596|Rbfox1|268859|RNA binding protein, fox-1 homolog (C. elegans) 1	AK158194|Rbfox1|268859|RNA binding protein, fox-1 homolog (C. elegans) 1
mm9_v1_chr1_+_60466462_60466491	3.86659	SOX2.p2	NM_001198570|Abi2|329165|abl-interactor 2	NM_001198571|Abi2|329165|abl-interactor 2	NM_198127|Abi2|329165|abl-interactor 2
mm9_v1_chr2_+_102498839_102498845	3.86276	SOX2.p2	AK134609|Slc1a2|20511|solute carrier family 1 (glial high affinity glutamate transporter), member 2	NM_001077514|Slc1a2|20511|solute carrier family 1 (glial high affinity glutamate transporter), member 2	AK140095|Slc1a2|20511|solute carrier family 1 (glial high affinity glutamate transporter), member 2
mm9_v1_chr18_+_37560490_37560542	3.85355	SOX2.p2	AK032626|Pcdhb9|93880|protocadherin beta 9	NM_053134|Pcdhb9|93880|protocadherin beta 9	BC055319|Pcdhb9|93880|protocadherin beta 9	BC062640|Pcdhb9|93880|protocadherin beta 9
mm9_v1_chr3_+_121160714_121160815	3.84967	SOX2.p2	AK181356|Cnn3|71994|calponin 3, acidic
mm9_v1_chr17_+_80615253_80615253	3.84589	SOX2.p2	BC118946|Ttc39d|67737|tetratricopeptide repeat domain 39D	BC118947|Ttc39d|67737|tetratricopeptide repeat domain 39D	NM_026351|Ttc39d|67737|tetratricopeptide repeat domain 39D
mm9_v1_chr2_+_65683823_65683911	3.84139	SOX2.p2	NM_153409|Csrnp3|77771|cysteine-serine-rich nuclear protein 3	NM_178634|Csrnp3|77771|cysteine-serine-rich nuclear protein 3	EF210820|Csrnp3|77771|cysteine-serine-rich nuclear protein 3	AK039150|Csrnp3|77771|cysteine-serine-rich nuclear protein 3	AK082649|Csrnp3|77771|cysteine-serine-rich nuclear protein 3	AK020730|Csrnp3|77771|cysteine-serine-rich nuclear protein 3	AK080761|Csrnp3|77771|cysteine-serine-rich nuclear protein 3	BC055701|Csrnp3|77771|cysteine-serine-rich nuclear protein 3
mm9_v1_chr3_-_83967952_83967954	3.84102	SOX2.p2	AK054540|Trim2|80890|tripartite motif-containing 2
mm9_v1_chr12_-_14158843_14158897	3.84002	SOX2.p2	BC005488|Fam84a|105005|family with sequence similarity 84, member A	NM_029007|Fam84a|105005|family with sequence similarity 84, member A	AK014625|Fam84a|105005|family with sequence similarity 84, member A
mm9_v1_chr9_-_110019806_110019945	3.83983	SOX2.p2	BC062885|Dhx30|72831|DEAH (Asp-Glu-Ala-His) box polypeptide 30	AK153969|Dhx30|72831|DEAH (Asp-Glu-Ala-His) box polypeptide 30	AK184646|Dhx30|72831|DEAH (Asp-Glu-Ala-His) box polypeptide 30	AK159601|Dhx30|72831|DEAH (Asp-Glu-Ala-His) box polypeptide 30	AK146326|Dhx30|72831|DEAH (Asp-Glu-Ala-His) box polypeptide 30
mm9_v1_chr13_+_118009379_118009441	3.83983	SOX2.p2	NM_010330|Emb|13723|embigin	AK138271|Emb|13723|embigin	AK079570|Emb|13723|embigin
mm9_v1_chr16_-_10796897_10796916	3.83463	SOX2.p2	K02926|Prm1|19118|protamine 1	M27500|Prm1|19118|protamine 1	AK006377|Prm1|19118|protamine 1	AK007068|Prm1|19118|protamine 1	BC049599|Prm1|19118|protamine 1	BC059733|Prm1|19118|protamine 1	NM_013637|Prm1|19118|protamine 1	X14003|Prm1|19118|protamine 1	AK018980|Prm1|19118|protamine 1
mm9_v1_chr15_+_79489607_79489701	3.8127	SOX2.p2	AF331040|Cby1|73739|chibby homolog 1 (Drosophila)	NM_028634|Cby1|73739|chibby homolog 1 (Drosophila)	AK003719|Cby1|73739|chibby homolog 1 (Drosophila)
mm9_v1_chr2_-_91772424_91772438	3.80708	SOX2.p2	AY864926|Mdk|17242|midkine	DQ323886|Mdk|17242|midkine	DQ323887|Mdk|17242|midkine	M34328|Mdk|17242|midkine	NM_010784|Mdk|17242|midkine
mm9_v1_chr13_-_55589377_55589460	3.79835	SOX2.p2	AK132060|Dbn1|56320|drebrin 1	AK162697|Dbn1|56320|drebrin 1	AB064321|Dbn1|56320|drebrin 1	AF187147|Dbn1|56320|drebrin 1	AF187148|Dbn1|56320|drebrin 1	NM_001177371|Dbn1|56320|drebrin 1	NM_001177372|Dbn1|56320|drebrin 1	NM_019813|Dbn1|56320|drebrin 1
mm9_v1_chr14_-_50403002_50403057	3.78974	SOX2.p2	AK014402|3632451O06Rik|67419|RIKEN cDNA 3632451O06 gene	BC023359|3632451O06Rik|67419|RIKEN cDNA 3632451O06 gene	AK028178|3632451O06Rik|67419|RIKEN cDNA 3632451O06 gene	AK032093|3632451O06Rik|67419|RIKEN cDNA 3632451O06 gene	NM_026142|3632451O06Rik|67419|RIKEN cDNA 3632451O06 gene	AK028180|3632451O06Rik|67419|RIKEN cDNA 3632451O06 gene	AK049427|3632451O06Rik|67419|RIKEN cDNA 3632451O06 gene	AK014563|3632451O06Rik|67419|RIKEN cDNA 3632451O06 gene
mm9_v1_chr1_-_46910333_46910455	3.77458	SOX2.p2	BC062918|Slc39a10|227059|solute carrier family 39 (zinc transporter), member 10	NM_172653|Slc39a10|227059|solute carrier family 39 (zinc transporter), member 10	BC052880|Slc39a10|227059|solute carrier family 39 (zinc transporter), member 10
mm9_v1_chr10_+_102830353_102830476	3.76811	SOX2.p2	AK082286|Slc6a15|103098|solute carrier family 6 (neurotransmitter transporter), member 15	BC076593|Slc6a15|103098|solute carrier family 6 (neurotransmitter transporter), member 15	AK036136|Slc6a15|103098|solute carrier family 6 (neurotransmitter transporter), member 15	AY149281|Slc6a15|103098|solute carrier family 6 (neurotransmitter transporter), member 15	AY149280|Slc6a15|103098|solute carrier family 6 (neurotransmitter transporter), member 15	NM_175328|Slc6a15|103098|solute carrier family 6 (neurotransmitter transporter), member 15
mm9_v1_chr3_+_101814059_101814199	3.7422	SOX2.p2	S40532|Nhlh2|18072|nescient helix loop helix 2	AK031747|Nhlh2|18072|nescient helix loop helix 2	NM_178777|Nhlh2|18072|nescient helix loop helix 2	AK053837|Nhlh2|18072|nescient helix loop helix 2	AK053046|Nhlh2|18072|nescient helix loop helix 2	AK082728|Nhlh2|18072|nescient helix loop helix 2	AK084160|Nhlh2|18072|nescient helix loop helix 2	AK084308|Nhlh2|18072|nescient helix loop helix 2	BC058413|Nhlh2|18072|nescient helix loop helix 2
mm9_v1_chr5_-_147396407_147396450	3.73494	SOX2.p2	D21061|Gpr12|14738|G-protein coupled receptor 12
mm9_v1_chr4_-_86873866_86873867	3.72798	SOX2.p2	NM_001110240|Slc24a2|76376|solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	BC115867|Slc24a2|76376|solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	BC116637|Slc24a2|76376|solute carrier family 24 (sodium/potassium/calcium exchanger), member 2
mm9_v1_chrX_+_133242520_133242603	3.72602	SOX2.p2	BC083157|Tceal1|237052|transcription elongation factor A (SII)-like 1	BC011290|Tceal1|237052|transcription elongation factor A (SII)-like 1	NM_146236|Tceal1|237052|transcription elongation factor A (SII)-like 1
mm9_v1_chr9_-_108363911_108363911	3.7078	SOX2.p2	AK019849|Klhdc8b|78267|kelch domain containing 8B	NM_030075|Klhdc8b|78267|kelch domain containing 8B
mm9_v1_chrX_+_6644644_6644708	3.70703	SOX2.p2	NM_009651|Akap4|11643|A kinase (PRKA) anchor protein 4	U10341|Akap4|11643|A kinase (PRKA) anchor protein 4	BC130271|Akap4|11643|A kinase (PRKA) anchor protein 4
mm9_v1_chr16_+_33500899_33501016	3.6998	SOX2.p2	AK037342|Zfp148|22661|zinc finger protein 148
mm9_v1_chr8_+_61390551_61390637	3.69976	SOX2.p2	BC030500|BC030500|234290|cDNA sequence BC030500	NM_173411|BC030500|234290|cDNA sequence BC030500
mm9_v1_chr19_+_7344253_7344253	3.69956	SOX2.p2	NM_054048|Rcor2|104383|REST corepressor 2	X83587|Rcor2|104383|REST corepressor 2
mm9_v1_chr9_+_107948285_107948372	3.69473	SOX2.p2	AK208685|Ip6k1|27399|inositol hexaphosphate kinase 1	AK211834|Ip6k1|27399|inositol hexaphosphate kinase 1	AK191619|Ip6k1|27399|inositol hexaphosphate kinase 1	AK215657|Ip6k1|27399|inositol hexaphosphate kinase 1
mm9_v1_chr10_-_61246611_61246701	3.68505	SOX2.p2	AF336305|H2afy2|404634|H2A histone family, member Y2	NM_207000|H2afy2|404634|H2A histone family, member Y2	BC045140|H2afy2|404634|H2A histone family, member Y2	AK165020|H2afy2|404634|H2A histone family, member Y2	AK018355|H2afy2|404634|H2A histone family, member Y2	BC046794|H2afy2|404634|H2A histone family, member Y2	AK078464|H2afy2|404634|H2A histone family, member Y2	AK032636|H2afy2|404634|H2A histone family, member Y2	AK020744|H2afy2|404634|H2A histone family, member Y2
mm9_v1_chr5_-_122497833_122497833	3.68244	SOX2.p2	BC065113|Cux2|13048|cut-like homeobox 2	NM_007804|Cux2|13048|cut-like homeobox 2
mm9_v1_chr8_-_41720091_41720170	3.679	SOX2.p2	AK028160|Mtmr7|54384|myotubularin related protein 7	AK081973|Mtmr7|54384|myotubularin related protein 7	BC032254|Mtmr7|54384|myotubularin related protein 7	AK148768|Mtmr7|54384|myotubularin related protein 7	NM_001040699|Mtmr7|54384|myotubularin related protein 7
mm9_v1_chr10_+_28388165_28388438	3.67533	SOX2.p2	AK041386|Themis|210757|thymocyte selection associated	AK088136|Themis|210757|thymocyte selection associated	AK089077|Themis|210757|thymocyte selection associated	NM_178666|Themis|210757|thymocyte selection associated	AK040594|Themis|210757|thymocyte selection associated	AK041622|Themis|210757|thymocyte selection associated	AK138701|Themis|210757|thymocyte selection associated	AK041562|Themis|210757|thymocyte selection associated	BC125486|Themis|210757|thymocyte selection associated	BC125488|Themis|210757|thymocyte selection associated	AB509340|Themis|210757|thymocyte selection associated	AK169558|Themis|210757|thymocyte selection associated
mm9_v1_chr18_+_37849488_37849707	3.67472	SOX2.p2	BC054557|Pcdhgb2|93700|protocadherin gamma subfamily B, 2	NM_033575|Pcdhgb2|93700|protocadherin gamma subfamily B, 2	AY013805|Pcdhgb2|93700|protocadherin gamma subfamily B, 2
mm9_v1_chr16_-_22811458_22811482	3.64614	SOX2.p2	BC056452|Crygs|12970|crystallin, gamma S	AF032995|Crygs|12970|crystallin, gamma S	AK143060|Crygs|12970|crystallin, gamma S	NM_009967|Crygs|12970|crystallin, gamma S
mm9_v1_chr5_+_48374328_48374415	3.64423	SOX2.p2	AK053182|Slit2|20563|slit homolog 2 (Drosophila)	AK053913|Slit2|20563|slit homolog 2 (Drosophila)	AK144573|Slit2|20563|slit homolog 2 (Drosophila)	NM_178804|Slit2|20563|slit homolog 2 (Drosophila)	AK084012|Slit2|20563|slit homolog 2 (Drosophila)	AK084293|Slit2|20563|slit homolog 2 (Drosophila)
mm9_v1_chr6_+_4853319_4853431	3.64403	SOX2.p2	AB091828|Ppp1r9a|243725|protein phosphatase 1, regulatory (inhibitor) subunit 9A	NM_181595|Ppp1r9a|243725|protein phosphatase 1, regulatory (inhibitor) subunit 9A	AK158559|Ppp1r9a|243725|protein phosphatase 1, regulatory (inhibitor) subunit 9A	BC053748|Ppp1r9a|243725|protein phosphatase 1, regulatory (inhibitor) subunit 9A
mm9_v1_chr11_-_102758340_102758449	3.63875	SOX2.p2	AF332061|Gfap|14580|glial fibrillary acidic protein	AF332062|Gfap|14580|glial fibrillary acidic protein	K01347|Gfap|14580|glial fibrillary acidic protein	M25937|Gfap|14580|glial fibrillary acidic protein	BC100737|Gfap|14580|glial fibrillary acidic protein	BC103571|Gfap|14580|glial fibrillary acidic protein	BC100728|Gfap|14580|glial fibrillary acidic protein	BC101968|Gfap|14580|glial fibrillary acidic protein	AK079577|Gfap|14580|glial fibrillary acidic protein	AK140151|Gfap|14580|glial fibrillary acidic protein
mm9_v1_chr5_-_8622882_8622951	3.63446	SOX2.p2	BC058808|Rundc3b|242819|RUN domain containing 3B	NM_198620|Rundc3b|242819|RUN domain containing 3B
mm9_v1_chr18_+_37501355_37501397	3.63065	SOX2.p2	AK034205|Pcdhb7|93878|protocadherin beta 7	NM_053132|Pcdhb7|93878|protocadherin beta 7	AK046463|Pcdhb7|93878|protocadherin beta 7	AK029340|Pcdhb7|93878|protocadherin beta 7	BC094897|Pcdhb7|93878|protocadherin beta 7	AK043979|Pcdhb7|93878|protocadherin beta 7
mm9_v1_chr2_-_73613381_73613446	3.62559	SOX2.p2	NM_001113246|Chn1|108699|chimerin (chimaerin) 1	NM_001166603|Chn1|108699|chimerin (chimaerin) 1
mm9_v1_chr3_+_94282752_94282752	3.62365	SOX2.p2	AY165052|Celf3|78784|VCUGBP, Elav-like family member 3	NM_172434|Celf3|78784|VCUGBP, Elav-like family member 3
mm9_v1_chr15_-_79489373_79489385	3.60854	SOX2.p2	AK046478|4933432B09Rik|75729|RIKEN cDNA 4933432B09 gene	AK039547|4933432B09Rik|75729|RIKEN cDNA 4933432B09 gene	AK039683|4933432B09Rik|75729|RIKEN cDNA 4933432B09 gene	NM_029407|4933432B09Rik|75729|RIKEN cDNA 4933432B09 gene
mm9_v1_chr2_+_81893814_81893814	3.60706	SOX2.p2	AK049881|Zfp804a|241514|zinc finger protein 804A	NM_175513|Zfp804a|241514|zinc finger protein 804A
mm9_v1_chr8_-_49760037_49760043	3.59839	SOX2.p2	BC145284|Odz3|23965|odd Oz/ten-m homolog 3 (Drosophila)	AB025412|Odz3|23965|odd Oz/ten-m homolog 3 (Drosophila)	NM_001145937|Odz3|23965|odd Oz/ten-m homolog 3 (Drosophila)	NM_011857|Odz3|23965|odd Oz/ten-m homolog 3 (Drosophila)
mm9_v1_chr15_-_77950450_77950459	3.59314	SOX2.p2	AK045362|Cacng2|12300|calcium channel, voltage-dependent, gamma subunit 2
mm9_v1_chr4_+_126800830_126800906	3.58797	SOX2.p2	BC060297|Zmym6|100177|zinc finger, MYM-type 6
mm9_v1_chr6_+_54251485_54251608	3.58633	SOX2.p2	
mm9_v1_chr16_-_17125198_17125232	3.57886	SOX2.p2	BC039993|2610318N02Rik|70458|RIKEN cDNA 2610318N02 gene	NM_183287|2610318N02Rik|70458|RIKEN cDNA 2610318N02 gene	AK012048|2610318N02Rik|70458|RIKEN cDNA 2610318N02 gene	AK146836|2610318N02Rik|70458|RIKEN cDNA 2610318N02 gene
mm9_v1_chr4_-_134409199_134409236	3.57258	SOX2.p2	BC042733|Tmem57|66146|transmembrane protein 57	BC044802|Tmem57|66146|transmembrane protein 57	BC037192|Tmem57|66146|transmembrane protein 57	BC019186|Tmem57|66146|transmembrane protein 57	AK020354|Tmem57|66146|transmembrane protein 57
mm9_v1_chr4_-_70195870_70195917	3.55357	SOX2.p2	BC088994|Megf9|230316|multiple EGF-like-domains 9	BC138128|Megf9|230316|multiple EGF-like-domains 9	BC138129|Megf9|230316|multiple EGF-like-domains 9
mm9_v1_chr7_+_97574821_97574821	3.55193	SOX2.p2	NM_027298|Ccdc89|70054|coiled-coil domain containing 89
mm9_v1_chr16_+_91225794_91225820	3.55186	SOX2.p2	BC051967|Olig2|50913|oligodendrocyte transcription factor 2	NM_016967|Olig2|50913|oligodendrocyte transcription factor 2	AB038697|Olig2|50913|oligodendrocyte transcription factor 2	AK080615|Olig2|50913|oligodendrocyte transcription factor 2
mm9_v1_chr4_+_34841027_34841057	3.53732	SOX2.p2	NM_009889|Cga|12640|glycoprotein hormones, alpha subunit	BC087926|Cga|12640|glycoprotein hormones, alpha subunit	J00643|Cga|12640|glycoprotein hormones, alpha subunit
mm9_v1_chr11_+_94828911_94828981	3.53725	SOX2.p2	BC061119|Hils1|54388|histone H1-like protein in spermatids 1	BC050966|Hils1|54388|histone H1-like protein in spermatids 1	AK005718|Hils1|54388|histone H1-like protein in spermatids 1	AB022320|Hils1|54388|histone H1-like protein in spermatids 1	AY286319|Hils1|54388|histone H1-like protein in spermatids 1	NM_018792|Hils1|54388|histone H1-like protein in spermatids 1	AB045724|Hils1|54388|histone H1-like protein in spermatids 1
mm9_v1_chr5_+_100468998_100469257	3.5339	SOX2.p2	AK167575|Enoph1|67870|enolase-phosphatase 1	NM_001163035|Enoph1|67870|enolase-phosphatase 1	NM_026421|Enoph1|67870|enolase-phosphatase 1	AK079062|Enoph1|67870|enolase-phosphatase 1	AK009954|Enoph1|67870|enolase-phosphatase 1	AK082747|Enoph1|67870|enolase-phosphatase 1	AK152021|Enoph1|67870|enolase-phosphatase 1	AK159356|Enoph1|67870|enolase-phosphatase 1	AK168696|Enoph1|67870|enolase-phosphatase 1	AK080714|Enoph1|67870|enolase-phosphatase 1	BC021429|Enoph1|67870|enolase-phosphatase 1	AK177338|Enoph1|67870|enolase-phosphatase 1	AK193770|Enoph1|67870|enolase-phosphatase 1
mm9_v1_chr5_-_33590505_33590587	3.5228	SOX2.p2	
mm9_v1_chr7_-_148615247_148615354	3.51822	SOX2.p2	AF243130|Cend1|57754|cell cycle exit and neuronal differentiation 1	AK005092|Cend1|57754|cell cycle exit and neuronal differentiation 1	BC023032|Cend1|57754|cell cycle exit and neuronal differentiation 1	AK079045|Cend1|57754|cell cycle exit and neuronal differentiation 1	NM_021316|Cend1|57754|cell cycle exit and neuronal differentiation 1
mm9_v1_chr18_-_34784206_34784257	3.50796	SOX2.p2	BC021482|Brd8|78656|bromodomain containing 8	AK132365|Brd8|78656|bromodomain containing 8	AK014475|Brd8|78656|bromodomain containing 8	BC023837|Brd8|78656|bromodomain containing 8	AK019151|Brd8|78656|bromodomain containing 8	AK032320|Brd8|78656|bromodomain containing 8	AK161689|Brd8|78656|bromodomain containing 8	AK042446|Brd8|78656|bromodomain containing 8	AK172658|Brd8|78656|bromodomain containing 8
mm9_v1_chr4_-_136604609_136604715	3.50319	SOX2.p2	BC059177|Zbtb40|230848|zinc finger and BTB domain containing 40	NM_198248|Zbtb40|230848|zinc finger and BTB domain containing 40	AK036584|Zbtb40|230848|zinc finger and BTB domain containing 40
mm9_v1_chr9_-_43951401_43951528	3.49673	SOX2.p2	
mm9_v1_chr19_+_8907691_8907773	3.48463	SOX2.p2	AK004010|Hnrnpul2|68693|heterogeneous nuclear ribonucleoprotein U-like 2
mm9_v1_chr4_-_117881591_117881662	3.47355	SOX2.p2	AK135889|Ptprf|19268|protein tyrosine phosphatase, receptor type, F
mm9_v1_chr18_-_46372017_46372260	3.4709	SOX2.p2	AY251389|Trim36|28105|tripartite motif-containing 36	AB103063|Trim36|28105|tripartite motif-containing 36	BC058106|Trim36|28105|tripartite motif-containing 36	NM_178872|Trim36|28105|tripartite motif-containing 36
mm9_v1_chr10_+_126504125_126504226	3.46974	SOX2.p2	
mm9_v1_chr18_+_44264117_44264290	3.46641	SOX2.p2	DQ437332|Spink12|78242|serine peptidase inhibitor, Kazal type 11	AK136616|Spink12|78242|serine peptidase inhibitor, Kazal type 11	NM_030061|Spink12|78242|serine peptidase inhibitor, Kazal type 11	AK020352|Spink12|78242|serine peptidase inhibitor, Kazal type 11	BC145914|Spink12|78242|serine peptidase inhibitor, Kazal type 11	BC145916|Spink12|78242|serine peptidase inhibitor, Kazal type 11
mm9_v1_chr8_-_70342105_70342226	3.45019	SOX2.p2	BC131913|Psd3|234353|pleckstrin and Sec7 domain containing 3	BC145641|Psd3|234353|pleckstrin and Sec7 domain containing 3	AK031477|Psd3|234353|pleckstrin and Sec7 domain containing 3	AK147606|Psd3|234353|pleckstrin and Sec7 domain containing 3	NM_027626|Psd3|234353|pleckstrin and Sec7 domain containing 3
mm9_v1_chr18_+_37673305_37673473	3.44912	SOX2.p2	AK134846|Pcdhb21|93892|protocadherin beta 21	NM_053146|Pcdhb21|93892|protocadherin beta 21	BC138121|Pcdhb21|93892|protocadherin beta 21	BC138122|Pcdhb21|93892|protocadherin beta 21	AF326314|Pcdhb21|93892|protocadherin beta 21	AY013783|Pcdhb21|93892|protocadherin beta 21
mm9_v1_chr14_+_68701838_68701963	3.4437	SOX2.p2	AK149219|Nefl|18039|neurofilament, light polypeptide	BC016436|Nefl|18039|neurofilament, light polypeptide	BC029203|Nefl|18039|neurofilament, light polypeptide	NM_010910|Nefl|18039|neurofilament, light polypeptide	DQ201635|Nefl|18039|neurofilament, light polypeptide
mm9_v1_chr4_-_149575220_149575330	3.43915	SOX2.p2	BC018582|Car6|12353|carbonic anhydrase 6	BC036270|Car6|12353|carbonic anhydrase 6	BC049973|Car6|12353|carbonic anhydrase 6	BC039657|Car6|12353|carbonic anhydrase 6	BC055437|Car6|12353|carbonic anhydrase 6	AK161216|Car6|12353|carbonic anhydrase 6	AK132599|Car6|12353|carbonic anhydrase 6	NM_009802|Car6|12353|carbonic anhydrase 6	AF079835|Car6|12353|carbonic anhydrase 6	BC006726|Car6|12353|carbonic anhydrase 6
mm9_v1_chr3_+_95985065_95985205	3.42524	SOX2.p2	AK080525|Sv2a|64051|synaptic vesicle glycoprotein 2 a	AK144166|Sv2a|64051|synaptic vesicle glycoprotein 2 a	BC046587|Sv2a|64051|synaptic vesicle glycoprotein 2 a	NM_022030|Sv2a|64051|synaptic vesicle glycoprotein 2 a	AK080502|Sv2a|64051|synaptic vesicle glycoprotein 2 a	AK028318|Sv2a|64051|synaptic vesicle glycoprotein 2 a
mm9_v1_chr17_+_29178865_29178883	3.4245	SOX2.p2	
mm9_v1_chr5_+_31754808_31754902	3.39992	SOX2.p2	NM_172993|Zfp512|269639|zinc finger protein 512	AK173267|Zfp512|269639|zinc finger protein 512	AK146353|Zfp512|269639|zinc finger protein 512	AK084205|Zfp512|269639|zinc finger protein 512	AK149921|Zfp512|269639|zinc finger protein 512	AK154918|Zfp512|269639|zinc finger protein 512	BC089160|Zfp512|269639|zinc finger protein 512	BC066136|Zfp512|269639|zinc finger protein 512
mm9_v1_chr6_+_139990045_139990101	3.39939	SOX2.p2	NM_007605|Capza3|12344|capping protein (actin filament) muscle Z-line, alpha 3	AK016391|Capza3|12344|capping protein (actin filament) muscle Z-line, alpha 3	BC049620|Capza3|12344|capping protein (actin filament) muscle Z-line, alpha 3	D87471|Capza3|12344|capping protein (actin filament) muscle Z-line, alpha 3
mm9_v1_chr11_-_94335350_94335511	3.39623	SOX2.p2	BC057399|Cacna1g|12291|calcium channel, voltage-dependent, T type, alpha 1G subunit	NM_001112813|Cacna1g|12291|calcium channel, voltage-dependent, T type, alpha 1G subunit	NM_001177888|Cacna1g|12291|calcium channel, voltage-dependent, T type, alpha 1G subunit	NM_001177890|Cacna1g|12291|calcium channel, voltage-dependent, T type, alpha 1G subunit	NM_009783|Cacna1g|12291|calcium channel, voltage-dependent, T type, alpha 1G subunit
mm9_v1_chr2_+_92025639_92025639	3.39545	SOX2.p2	AK037174|Phf21a|192285|PHD finger protein 21A	NM_001109691|Phf21a|192285|PHD finger protein 21A
mm9_v1_chr19_+_42126717_42126740	3.3953	SOX2.p2	NM_025752|4933411K16Rik|66765|RIKEN cDNA 4933411K16 gene	AK016775|4933411K16Rik|66765|RIKEN cDNA 4933411K16 gene	AK006374|4933411K16Rik|66765|RIKEN cDNA 4933411K16 gene	BC049703|4933411K16Rik|66765|RIKEN cDNA 4933411K16 gene
mm9_v1_chr16_-_34514112_34514198	3.39223	SOX2.p2	BC157950|Kalrn|545156|kalirin, RhoGEF kinase	BC172101|Kalrn|545156|kalirin, RhoGEF kinase	NM_001164268|Kalrn|545156|kalirin, RhoGEF kinase	NM_177357|Kalrn|545156|kalirin, RhoGEF kinase	AK147314|Kalrn|545156|kalirin, RhoGEF kinase	AK147518|Kalrn|545156|kalirin, RhoGEF kinase
mm9_v1_chr15_-_103164744_103164757	3.38867	SOX2.p2	BC017644|Zfp385a|29813|zinc finger protein 385A
mm9_v1_chr4_+_154932761_154932805	3.37315	SOX2.p2	AK194739|Gnb1|14688|guanine nucleotide binding protein (G protein), beta 1	AK203879|Gnb1|14688|guanine nucleotide binding protein (G protein), beta 1	AK205062|Gnb1|14688|guanine nucleotide binding protein (G protein), beta 1
mm9_v1_chr15_+_18750083_18750083	3.37275	SOX2.p2	AK138606|Cdh10|320873|cadherin 10	NM_009865|Cdh10|320873|cadherin 10
mm9_v1_chr15_-_95359136_95359208	3.37186	SOX2.p2	NM_016743|Nell2|54003|NEL-like 2 (chicken)
mm9_v1_chr18_-_16966954_16967033	3.37054	SOX2.p2	AK087418|Cdh2|12558|cadherin 2	BC022107|Cdh2|12558|cadherin 2	AK032826|Cdh2|12558|cadherin 2
mm9_v1_chr4_+_17780739_17780875	3.36265	SOX2.p2	AK053598|Mmp16|17389|matrix metallopeptidase 16	AK048543|Mmp16|17389|matrix metallopeptidase 16	AK046170|Mmp16|17389|matrix metallopeptidase 16	AB021228|Mmp16|17389|matrix metallopeptidase 16	AF282844|Mmp16|17389|matrix metallopeptidase 16
mm9_v1_chr11_-_86887549_86887638	3.34999	SOX2.p2	BC016541|Gdpd1|66569|glycerophosphodiester phosphodiesterase domain containing 1	AK011487|Gdpd1|66569|glycerophosphodiester phosphodiesterase domain containing 1	AK013864|Gdpd1|66569|glycerophosphodiester phosphodiesterase domain containing 1	AK016023|Gdpd1|66569|glycerophosphodiester phosphodiesterase domain containing 1	AK167812|Gdpd1|66569|glycerophosphodiester phosphodiesterase domain containing 1	NM_025638|Gdpd1|66569|glycerophosphodiester phosphodiesterase domain containing 1
mm9_v1_chr2_+_17976897_17976897	3.34622	SOX2.p2	BC070475|Mllt10|17354|myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10	NM_010804|Mllt10|17354|myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10
mm9_v1_chr6_+_57652448_57652452	3.34562	SOX2.p2	NM_133737|Lancl2|71835|LanC (bacterial lantibiotic synthetase component C)-like 2
mm9_v1_chr17_+_70871393_70871416	3.34454	SOX2.p2	AK036307|Dlgap1|224997|discs, large (Drosophila) homolog-associated protein 1
mm9_v1_chr3_-_87831317_87831504	3.33836	SOX2.p2	BC138584|Hapln2|73940|hyaluronan and proteoglycan link protein 2	BC138585|Hapln2|73940|hyaluronan and proteoglycan link protein 2	AB049055|Hapln2|73940|hyaluronan and proteoglycan link protein 2	AK081264|Hapln2|73940|hyaluronan and proteoglycan link protein 2	NM_022031|Hapln2|73940|hyaluronan and proteoglycan link protein 2	BC023911|Hapln2|73940|hyaluronan and proteoglycan link protein 2
mm9_v1_chr16_-_48772068_48772250	3.33465	SOX2.p2	BC104350|Trat1|77647|T cell receptor associated transmembrane adaptor 1	BC104351|Trat1|77647|T cell receptor associated transmembrane adaptor 1	NM_198297|Trat1|77647|T cell receptor associated transmembrane adaptor 1	AJ297969|Trat1|77647|T cell receptor associated transmembrane adaptor 1	AK138735|Trat1|77647|T cell receptor associated transmembrane adaptor 1	AK030807|Trat1|77647|T cell receptor associated transmembrane adaptor 1
mm9_v1_chr18_+_37975071_37975186	3.3345	SOX2.p2	AK139465|Pcdhgc4|93707|protocadherin gamma subfamily C, 4	AY013812|Pcdhgc4|93707|protocadherin gamma subfamily C, 4
mm9_v1_chr13_-_58228079_58228222	3.32871	SOX2.p2	AK004260|Hnrnpa0|77134|heterogeneous nuclear ribonucleoprotein A0
mm9_v1_chr8_-_122086343_122086607	3.32139	SOX2.p2	BC037193|Hsdl1|72552|hydroxysteroid dehydrogenase like 1	BC038480|Hsdl1|72552|hydroxysteroid dehydrogenase like 1	BC058121|Hsdl1|72552|hydroxysteroid dehydrogenase like 1
mm9_v1_chr5_-_100468240_100468240	3.30212	SOX2.p2	NM_016690|Hnrpdl|50926|heterogeneous nuclear ribonucleoprotein D-like
mm9_v1_chr5_-_103640272_103640352	3.2927	SOX2.p2	AK036275|Mapk10|26414|mitogen-activated protein kinase 10	BC046625|Mapk10|26414|mitogen-activated protein kinase 10	AK163206|Mapk10|26414|mitogen-activated protein kinase 10	AK076990|Mapk10|26414|mitogen-activated protein kinase 10	BC026697|Mapk10|26414|mitogen-activated protein kinase 10	AK082242|Mapk10|26414|mitogen-activated protein kinase 10	NM_001081567|Mapk10|26414|mitogen-activated protein kinase 10	NM_009158|Mapk10|26414|mitogen-activated protein kinase 10
mm9_v1_chr13_-_99754519_99754519	3.29185	SOX2.p2	AK006311|1700024P04Rik|69382|RIKEN cDNA 1700024P04 gene	NM_027064|1700024P04Rik|69382|RIKEN cDNA 1700024P04 gene
mm9_v1_chr16_-_42340613_42340763	3.28892	SOX2.p2	AK031908|Gap43|14432|growth associated protein 43	BC080758|Gap43|14432|growth associated protein 43	BC028288|Gap43|14432|growth associated protein 43	NM_008083|Gap43|14432|growth associated protein 43
mm9_v1_chr11_-_88579392_88579430	3.28381	SOX2.p2	AK051269|Msi2|76626|Musashi homolog 2 (Drosophila)	AK031365|Msi2|76626|Musashi homolog 2 (Drosophila)	AK153928|Msi2|76626|Musashi homolog 2 (Drosophila)	AK169846|Msi2|76626|Musashi homolog 2 (Drosophila)
mm9_v1_chr4_+_55093796_55093934	3.28367	SOX2.p2	AK035041|Zfp462|242466|zinc finger protein 462
mm9_v1_chr4_-_129235583_129235617	3.27995	SOX2.p2	M12056|Lck|16818|lymphocyte protein tyrosine kinase	AK134013|Lck|16818|lymphocyte protein tyrosine kinase	AK088001|Lck|16818|lymphocyte protein tyrosine kinase	NM_001162432|Lck|16818|lymphocyte protein tyrosine kinase	NM_010693|Lck|16818|lymphocyte protein tyrosine kinase
mm9_v1_chr17_-_35971913_35971974	3.2698	SOX2.p2	AK188748|Tubb5|22154|tubulin, beta 5	AK196888|Tubb5|22154|tubulin, beta 5
mm9_v1_chr6_-_42660031_42660117	3.26168	SOX2.p2	AK083917|Fam115a|77574|family with sequence similarity 115, member A	AK132148|Fam115a|77574|family with sequence similarity 115, member A	AK173013|Fam115a|77574|family with sequence similarity 115, member A	AK020704|Fam115a|77574|family with sequence similarity 115, member A	AK014379|Fam115a|77574|family with sequence similarity 115, member A
mm9_v1_chr4_-_109959185_109959241	3.25986	SOX2.p2	D31953|Elavl4|15572|ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	AK014133|Elavl4|15572|ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	DQ437511|Elavl4|15572|ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)
mm9_v1_chr15_-_96472392_96472392	3.25844	SOX2.p2	AK034130|Slc38a1|105727|solute carrier family 38, member 1	NM_134086|Slc38a1|105727|solute carrier family 38, member 1
mm9_v1_chr1_+_66368571_66368671	3.25048	SOX2.p2	AK046341|Mtap2|17756|microtubule-associated protein 2	AK086484|Mtap2|17756|microtubule-associated protein 2	M21041|Mtap2|17756|microtubule-associated protein 2	AK141458|Mtap2|17756|microtubule-associated protein 2
mm9_v1_chr1_-_160286359_160286472	3.24838	SOX2.p2	BC067038|Fam5b|240843|family with sequence similarity 5, member B	BC076572|Fam5b|240843|family with sequence similarity 5, member B	NM_207583|Fam5b|240843|family with sequence similarity 5, member B	AK032297|Fam5b|240843|family with sequence similarity 5, member B	AK047824|Fam5b|240843|family with sequence similarity 5, member B	AK122549|Fam5b|240843|family with sequence similarity 5, member B
mm9_v1_chrX_+_102318792_102318798	3.24746	SOX2.p2	AK209904|Magee1|107528|melanoma antigen, family E, 1
mm9_v1_chr12_+_53800369_53800393	3.24608	SOX2.p2	AK147248|Akap6|238161|A kinase (PRKA) anchor protein 6	AK147371|Akap6|238161|A kinase (PRKA) anchor protein 6	NM_198111|Akap6|238161|A kinase (PRKA) anchor protein 6
mm9_v1_chr9_+_44448105_44448130	3.24259	SOX2.p2	AK003265|Ddx6|13209|DEAD (Asp-Glu-Ala-Asp) box polypeptide 6
mm9_v1_chr10_+_68996455_68996596	3.23669	SOX2.p2	NM_146005|Ank3|11735|ankyrin 3, epithelial	NM_170688|Ank3|11735|ankyrin 3, epithelial	NM_170689|Ank3|11735|ankyrin 3, epithelial	NM_170690|Ank3|11735|ankyrin 3, epithelial	NM_170728|Ank3|11735|ankyrin 3, epithelial	NM_170729|Ank3|11735|ankyrin 3, epithelial	NM_170730|Ank3|11735|ankyrin 3, epithelial	AK162547|Ank3|11735|ankyrin 3, epithelial	AK042330|Ank3|11735|ankyrin 3, epithelial	BC021657|Ank3|11735|ankyrin 3, epithelial
mm9_v1_chr5_+_73398142_73398230	3.23609	SOX2.p2	AK087479|Slc10a4|231290|solute carrier family 10 (sodium/bile acid cotransporter family), member 4	AK149202|Slc10a4|231290|solute carrier family 10 (sodium/bile acid cotransporter family), member 4	NM_173403|Slc10a4|231290|solute carrier family 10 (sodium/bile acid cotransporter family), member 4	BC132529|Slc10a4|231290|solute carrier family 10 (sodium/bile acid cotransporter family), member 4	BC138048|Slc10a4|231290|solute carrier family 10 (sodium/bile acid cotransporter family), member 4
mm9_v1_chr2_-_122194653_122194653	3.23237	SOX2.p2	NM_001013829|Shf|435684|Src homology 2 domain containing F
mm9_v1_chr8_-_61390372_61390423	3.22661	SOX2.p2	BC111102|Galntl6|270049|UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 6	AK080614|Galntl6|270049|UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 6	NM_175032|Galntl6|270049|UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 6
mm9_v1_chr18_-_3299475_3299553	3.20974	SOX2.p2	AK076797|Crem|12916|cAMP responsive element modulator	NM_001110853|Crem|12916|cAMP responsive element modulator	AK016156|Crem|12916|cAMP responsive element modulator	AK015641|Crem|12916|cAMP responsive element modulator
mm9_v1_chr17_+_30763879_30763935	3.20729	SOX2.p2	AK161258|Dnahc8|13417|dynein, axonemal, heavy chain 8	AF356520|Dnahc8|13417|dynein, axonemal, heavy chain 8	AF356521|Dnahc8|13417|dynein, axonemal, heavy chain 8	NM_013811|Dnahc8|13417|dynein, axonemal, heavy chain 8	AF356522|Dnahc8|13417|dynein, axonemal, heavy chain 8	AF356523|Dnahc8|13417|dynein, axonemal, heavy chain 8	AF363577|Dnahc8|13417|dynein, axonemal, heavy chain 8
mm9_v1_chr9_+_18282802_18282838	3.19938	SOX2.p2	AK018931|Mbd3l1|73503|methyl-CpG binding domain protein 3-like 1	BC049738|Mbd3l1|73503|methyl-CpG binding domain protein 3-like 1	BC061034|Mbd3l1|73503|methyl-CpG binding domain protein 3-like 1	AK006927|Mbd3l1|73503|methyl-CpG binding domain protein 3-like 1	NM_028557|Mbd3l1|73503|methyl-CpG binding domain protein 3-like 1
mm9_v1_chr17_+_44090341_44090399	3.19743	SOX2.p2	BC047153|Rcan2|53901|regulator of calcineurin 2	AF237887|Rcan2|53901|regulator of calcineurin 2	AF237791|Rcan2|53901|regulator of calcineurin 2
mm9_v1_chr19_+_44368165_44368165	3.19687	SOX2.p2	AK147406|Scd2|20250|stearoyl-Coenzyme A desaturase 2	NM_009128|Scd2|20250|stearoyl-Coenzyme A desaturase 2
mm9_v1_chr2_-_125549883_125549883	3.19601	SOX2.p2	AK036946|Shc4|271849|SHC (Src homology 2 domain containing) family, member 4	NM_199022|Shc4|271849|SHC (Src homology 2 domain containing) family, member 4
mm9_v1_chr5_+_7304126_7304163	3.18304	SOX2.p2	BC049718|4921511H03Rik|70920|RIKEN cDNA 4921511H03 gene	AK133311|4921511H03Rik|70920|RIKEN cDNA 4921511H03 gene	AK014870|4921511H03Rik|70920|RIKEN cDNA 4921511H03 gene	AK076678|4921511H03Rik|70920|RIKEN cDNA 4921511H03 gene	NM_027603|4921511H03Rik|70920|RIKEN cDNA 4921511H03 gene
mm9_v1_chr17_+_28667805_28667828	3.17669	SOX2.p2	AK015756|4930511I11Rik|67645|RIKEN cDNA 4930511I11 gene	NM_026290|4930511I11Rik|67645|RIKEN cDNA 4930511I11 gene	BC049559|4930511I11Rik|67645|RIKEN cDNA 4930511I11 gene	AK005672|4930511I11Rik|67645|RIKEN cDNA 4930511I11 gene	EU477370|4930511I11Rik|67645|RIKEN cDNA 4930511I11 gene
mm9_v1_chr18_-_34784463_34784463	3.16111	SOX2.p2	NM_030147|Brd8|78656|bromodomain containing 8
mm9_v1_chr8_+_34681015_34681015	3.15805	SOX2.p2	AF285589|Tex15|104271|testis expressed gene 15	NM_031374|Tex15|104271|testis expressed gene 15
mm9_v1_chr6_-_148893155_148893361	3.15782	SOX2.p2	AK046519|Fam60a|56306|family with sequence similarity 60, member A
mm9_v1_chr19_-_41151561_41151602	3.15526	SOX2.p2	BC060980|Opalin|226115|oligodendrocytic myelin paranodal and inner loop protein	AK140031|Opalin|226115|oligodendrocytic myelin paranodal and inner loop protein	NM_153520|Opalin|226115|oligodendrocytic myelin paranodal and inner loop protein
mm9_v1_chr13_+_42776161_42776182	3.15366	SOX2.p2	AK047654|Phactr1|218194|phosphatase and actin regulator 1	AY993932|Phactr1|218194|phosphatase and actin regulator 1
mm9_v1_chr11_-_86509102_86509123	3.153	SOX2.p2	AK018633|Cltc|67300|clathrin, heavy polypeptide (Hc)
mm9_v1_chr2_+_52716901_52716906	3.14687	SOX2.p2	NM_172409|Fmnl2|71409|formin-like 2
mm9_v1_chr5_-_72978788_72978788	3.13983	SOX2.p2	AK084047|Gm5868|545758|predicted gene 5868	NM_001024147|Gm5868|545758|predicted gene 5868
mm9_v1_chr14_+_28435613_28435695	3.12088	SOX2.p2	AK147213|Erc2|238988|ELKS/RAB6-interacting/CAST family member 2	BC056760|Erc2|238988|ELKS/RAB6-interacting/CAST family member 2	NM_177814|Erc2|238988|ELKS/RAB6-interacting/CAST family member 2	AK032385|Erc2|238988|ELKS/RAB6-interacting/CAST family member 2
mm9_v1_chrX_-_92928599_92928603	3.10882	SOX2.p2	AK005817|1700010D01Rik|76386|RIKEN cDNA 1700010D01 gene	NM_029590|1700010D01Rik|76386|RIKEN cDNA 1700010D01 gene	BC059715|1700010D01Rik|76386|RIKEN cDNA 1700010D01 gene
mm9_v1_chr18_+_37885359_37885546	3.09143	SOX2.p2	BC054787|Pcdhga8|93716|protocadherin gamma subfamily A, 8	NM_033591|Pcdhga8|93716|protocadherin gamma subfamily A, 8	BC054555|Pcdhga8|93716|protocadherin gamma subfamily A, 8	AK220461|Pcdhga8|93716|protocadherin gamma subfamily A, 8	AY013802|Pcdhga8|93716|protocadherin gamma subfamily A, 8
mm9_v1_chr18_+_20823908_20823925	3.08878	SOX2.p2	AK018701|Ttr|22139|transthyretin	AK014454|Ttr|22139|transthyretin	AK075588|Ttr|22139|transthyretin	BC086926|Ttr|22139|transthyretin	D89076|Ttr|22139|transthyretin	X03351|Ttr|22139|transthyretin	AK050155|Ttr|22139|transthyretin	BC032069|Ttr|22139|transthyretin
mm9_v1_chr8_+_108404773_108404850	3.08132	SOX2.p2	AK152963|Edc4|234699|enhancer of mRNA decapping 4	AK146527|Edc4|234699|enhancer of mRNA decapping 4	BC053081|Edc4|234699|enhancer of mRNA decapping 4	NM_181594|Edc4|234699|enhancer of mRNA decapping 4
mm9_v1_chr8_+_11728104_11728202	3.07847	SOX2.p2	NM_001113517|Arhgef7|54126|Rho guanine nucleotide exchange factor (GEF7)	AK129064|Arhgef7|54126|Rho guanine nucleotide exchange factor (GEF7)	AK139156|Arhgef7|54126|Rho guanine nucleotide exchange factor (GEF7)
mm9_v1_chr2_-_77541328_77541435	3.07445	SOX2.p2	BC048543|Zfp385b|241494|zinc finger protein 385B	NM_001113399|Zfp385b|241494|zinc finger protein 385B	AK047859|Zfp385b|241494|zinc finger protein 385B
mm9_v1_chr1_-_136131963_136131973	3.07074	SOX2.p2	AK043954|Adora1|11539|adenosine A1 receptor
mm9_v1_chr2_+_164313584_164313634	3.04782	SOX2.p2	NM_001048229|Dbndd2|52840|dysbindin (dystrobrevin binding protein 1) domain containing 2
mm9_v1_chr6_-_134837738_134837876	3.03302	SOX2.p2	U46923|Gpr19|14760|G protein-coupled receptor 19	BC050187|Gpr19|14760|G protein-coupled receptor 19	NM_001167697|Gpr19|14760|G protein-coupled receptor 19	NM_001167699|Gpr19|14760|G protein-coupled receptor 19	NM_008157|Gpr19|14760|G protein-coupled receptor 19
mm9_v1_chr7_-_91520991_91521040	3.02543	SOX2.p2	AK032628|Arnt2|11864|aryl hydrocarbon receptor nuclear translocator 2
mm9_v1_chr18_-_16967100_16967238	3.02516	SOX2.p2	AB008811|Cdh2|12558|cadherin 2	M31131|Cdh2|12558|cadherin 2
mm9_v1_chr12_-_113749363_113749407	3.01551	SOX2.p2	AK047810|Tmem179|104885|transmembrane protein 179	NM_178915|Tmem179|104885|transmembrane protein 179	BC046482|Tmem179|104885|transmembrane protein 179	AK090230|Tmem179|104885|transmembrane protein 179
mm9_v1_chrX_-_54646073_54646213	3.01312	SOX2.p2	AK207357|Rbmx|19655|RNA binding motif protein, X chromosome	AJ237846|Rbmx|19655|RNA binding motif protein, X chromosome	AJ237847|Rbmx|19655|RNA binding motif protein, X chromosome	AK165006|Rbmx|19655|RNA binding motif protein, X chromosome	BC003710|Rbmx|19655|RNA binding motif protein, X chromosome	AK083899|Rbmx|19655|RNA binding motif protein, X chromosome	AK135164|Rbmx|19655|RNA binding motif protein, X chromosome	NM_001166623|Rbmx|19655|RNA binding motif protein, X chromosome	NM_011252|Rbmx|19655|RNA binding motif protein, X chromosome
mm9_v1_chr6_+_83087016_83087103	3.01065	SOX2.p2	NM_009106|Rtkn|20166|rhotekin	NM_133641|Rtkn|20166|rhotekin	U54638|Rtkn|20166|rhotekin	BC013820|Rtkn|20166|rhotekin
mm9_v1_chr8_+_56122680_56122847	3.007	SOX2.p2	BC023461|Gpm6a|234267|glycoprotein m6a
mm9_v1_chr7_+_53693190_53693196	3.00209	SOX2.p2	AK079373|Kcnc1|16502|potassium voltage gated channel, Shaw-related subfamily, member 1
mm9_v1_chr8_-_9771020_9771022	3.00056	SOX2.p2	BC117535|Fam155a|270028|family with sequence similarity 155, member A	AK032202|Fam155a|270028|family with sequence similarity 155, member A	NM_173446|Fam155a|270028|family with sequence similarity 155, member A
mm9_v1_chr4_-_70195952_70195978	2.9949	SOX2.p2	AK122378|Megf9|230316|multiple EGF-like-domains 9	AK035987|Megf9|230316|multiple EGF-like-domains 9	AK039319|Megf9|230316|multiple EGF-like-domains 9	AK162891|Megf9|230316|multiple EGF-like-domains 9	NM_172694|Megf9|230316|multiple EGF-like-domains 9	AK170687|Megf9|230316|multiple EGF-like-domains 9
mm9_v1_chr5_+_88746336_88746345	2.9839	SOX2.p2	NM_008644|Prol1|17830|proline rich, lacrimal 1	U37531|Prol1|17830|proline rich, lacrimal 1	BC042902|Prol1|17830|proline rich, lacrimal 1	BC021158|Prol1|17830|proline rich, lacrimal 1	AF247816|Prol1|17830|proline rich, lacrimal 1	BC021401|Prol1|17830|proline rich, lacrimal 1
mm9_v1_chrX_+_149932693_149932774	2.98378	SOX2.p2	AK076159|Ubqln2|54609|ubiquilin 2	AF177346|Ubqln2|54609|ubiquilin 2	BC053022|Ubqln2|54609|ubiquilin 2	NM_018798|Ubqln2|54609|ubiquilin 2
mm9_v1_chr3_-_58999025_58999026	2.98185	SOX2.p2	AK080394|Gpr87|84111|G protein-coupled receptor 87
mm9_v1_chr9_+_45178521_45178551	2.97872	SOX2.p2	BC042579|Fxyd6|59095|FXYD domain-containing ion transport regulator 6	AK042808|Fxyd6|59095|FXYD domain-containing ion transport regulator 6	AK018354|Fxyd6|59095|FXYD domain-containing ion transport regulator 6	AB032010|Fxyd6|59095|FXYD domain-containing ion transport regulator 6
mm9_v1_chr9_-_102256709_102256791	2.97728	SOX2.p2	AK036148|Ephb1|270190|Eph receptor B1
mm9_v1_chr9_-_102256962_102257026	2.97102	SOX2.p2	BC057301|Ephb1|270190|Eph receptor B1	AK135018|Ephb1|270190|Eph receptor B1	AK033966|Ephb1|270190|Eph receptor B1	AK036211|Ephb1|270190|Eph receptor B1	AK082061|Ephb1|270190|Eph receptor B1	AK039530|Ephb1|270190|Eph receptor B1	NM_001168296|Ephb1|270190|Eph receptor B1	NM_173447|Ephb1|270190|Eph receptor B1
mm9_v1_chr10_+_3366075_3366075	2.96965	SOX2.p2	AK157384|Ipcef1|320495|interaction protein for cytohesin exchange factors 1	NM_001170800|Ipcef1|320495|interaction protein for cytohesin exchange factors 1	NM_001170801|Ipcef1|320495|interaction protein for cytohesin exchange factors 1	NM_001170802|Ipcef1|320495|interaction protein for cytohesin exchange factors 1
mm9_v1_chr19_-_4333914_4333961	2.96674	SOX2.p2	
mm9_v1_chr8_-_8667108_8667134	2.96666	SOX2.p2	AK034581|Arglu1|234023|arginine and glutamate rich 1
mm9_v1_chr17_-_35975148_35975258	2.96193	SOX2.p2	BC003825|Tubb5|22154|tubulin, beta 5	AK076196|Tubb5|22154|tubulin, beta 5	AK148978|Tubb5|22154|tubulin, beta 5	AK167808|Tubb5|22154|tubulin, beta 5	AK168271|Tubb5|22154|tubulin, beta 5	AK169123|Tubb5|22154|tubulin, beta 5	AK011263|Tubb5|22154|tubulin, beta 5	AK165249|Tubb5|22154|tubulin, beta 5	AK169210|Tubb5|22154|tubulin, beta 5	AK010960|Tubb5|22154|tubulin, beta 5	AK011765|Tubb5|22154|tubulin, beta 5	AK012350|Tubb5|22154|tubulin, beta 5	AK017806|Tubb5|22154|tubulin, beta 5	AK051164|Tubb5|22154|tubulin, beta 5	AK051393|Tubb5|22154|tubulin, beta 5	AK083327|Tubb5|22154|tubulin, beta 5	AK146567|Tubb5|22154|tubulin, beta 5	AK151215|Tubb5|22154|tubulin, beta 5	AK151670|Tubb5|22154|tubulin, beta 5	AK160225|Tubb5|22154|tubulin, beta 5	AK161575|Tubb5|22154|tubulin, beta 5	AK167691|Tubb5|22154|tubulin, beta 5	AK167779|Tubb5|22154|tubulin, beta 5	AK167926|Tubb5|22154|tubulin, beta 5	AK169295|Tubb5|22154|tubulin, beta 5	AK169606|Tubb5|22154|tubulin, beta 5	NM_011655|Tubb5|22154|tubulin, beta 5
mm9_v1_chr2_+_69588414_69588564	2.95614	SOX2.p2	AK079931|Ppig|228005|peptidyl-prolyl isomerase G (cyclophilin G)	AK045812|Ppig|228005|peptidyl-prolyl isomerase G (cyclophilin G)
mm9_v1_chr9_-_103382586_103382657	2.94988	SOX2.p2	AK134810|Bfsp2|107993|beaded filament structural protein 2, phakinin	BC068172|Bfsp2|107993|beaded filament structural protein 2, phakinin	NM_001002896|Bfsp2|107993|beaded filament structural protein 2, phakinin
mm9_v1_chr16_-_98073389_98073456	2.94834	SOX2.p2	BC072597|Prdm15|114604|PR domain containing 15	AK144820|Prdm15|114604|PR domain containing 15
mm9_v1_chrX_-_57400778_57400876	2.94554	SOX2.p2	BC125435|Mcf2|109904|mcf.2 transforming sequence	AB052945|Mcf2|109904|mcf.2 transforming sequence	AB101616|Mcf2|109904|mcf.2 transforming sequence	NM_133197|Mcf2|109904|mcf.2 transforming sequence	AK032122|Mcf2|109904|mcf.2 transforming sequence
mm9_v1_chr16_+_57152994_57153228	2.94034	SOX2.p2	BC025450|Tomm70a|28185|translocase of outer mitochondrial membrane 70 homolog A (yeast)	AK011763|Tomm70a|28185|translocase of outer mitochondrial membrane 70 homolog A (yeast)
mm9_v1_chr17_+_29178771_29178812	2.94006	SOX2.p2	
mm9_v1_chr12_+_109843975_109843976	2.9343	SOX2.p2	AK134563|Evl|14026|Ena-vasodilator stimulated phosphoprotein	NM_001163395|Evl|14026|Ena-vasodilator stimulated phosphoprotein
mm9_v1_chr15_+_91991704_91991862	2.93209	SOX2.p2	NM_001159647|Cntn1|12805|contactin 1	BC066864|Cntn1|12805|contactin 1
mm9_v1_chr6_-_132160538_132160538	2.93198	SOX2.p2	BC011176|Prb1|381833|proline-rich protein BstNI subfamily 1	NM_198669|Prb1|381833|proline-rich protein BstNI subfamily 1
mm9_v1_chr7_+_149135990_149136036	2.92797	SOX2.p2	AY533672|Brsk2|75770|BR serine/threonine kinase 2	AY533673|Brsk2|75770|BR serine/threonine kinase 2	AY533674|Brsk2|75770|BR serine/threonine kinase 2	NM_001009929|Brsk2|75770|BR serine/threonine kinase 2	NM_001009930|Brsk2|75770|BR serine/threonine kinase 2
mm9_v1_chr6_+_114081227_114081234	2.91899	SOX2.p2	AK140423|Slc6a11|243616|solute carrier family 6 (neurotransmitter transporter, GABA), member 11	AK053078|Slc6a11|243616|solute carrier family 6 (neurotransmitter transporter, GABA), member 11	NM_172890|Slc6a11|243616|solute carrier family 6 (neurotransmitter transporter, GABA), member 11
mm9_v1_chr9_+_45178485_45178507	2.91812	SOX2.p2	BC051127|Fxyd6|59095|FXYD domain-containing ion transport regulator 6	AK003888|Fxyd6|59095|FXYD domain-containing ion transport regulator 6
mm9_v1_chr11_+_98629709_98629729	2.918	SOX2.p2	
mm9_v1_chr7_+_28438881_28439052	2.91177	SOX2.p2	AK013779|Ttc9b|73032|tetratricopeptide repeat domain 9B	BC089566|Ttc9b|73032|tetratricopeptide repeat domain 9B	NM_028417|Ttc9b|73032|tetratricopeptide repeat domain 9B	BC048750|Ttc9b|73032|tetratricopeptide repeat domain 9B
mm9_v1_chr10_+_87553816_87553819	2.90977	SOX2.p2	AK138363|Pmch|110312|pro-melanin-concentrating hormone	BC048534|Pmch|110312|pro-melanin-concentrating hormone	NM_029971|Pmch|110312|pro-melanin-concentrating hormone	AK020723|Pmch|110312|pro-melanin-concentrating hormone
mm9_v1_chr7_+_103359146_103359146	2.90476	SOX2.p2	AK147329|Odz4|23966|odd Oz/ten-m homolog 4 (Drosophila)	NM_011858|Odz4|23966|odd Oz/ten-m homolog 4 (Drosophila)
mm9_v1_chr5_+_108494692_108494781	2.90451	SOX2.p2	AK031409|Mtf2|17765|metal response element binding transcription factor 2	BC024889|Mtf2|17765|metal response element binding transcription factor 2	AK032798|Mtf2|17765|metal response element binding transcription factor 2	AK032819|Mtf2|17765|metal response element binding transcription factor 2	AK137539|Mtf2|17765|metal response element binding transcription factor 2	BC050826|Mtf2|17765|metal response element binding transcription factor 2	AK030752|Mtf2|17765|metal response element binding transcription factor 2	AB050541|Mtf2|17765|metal response element binding transcription factor 2	BC092237|Mtf2|17765|metal response element binding transcription factor 2	NM_013827|Mtf2|17765|metal response element binding transcription factor 2	BC100340|Mtf2|17765|metal response element binding transcription factor 2	BC029076|Mtf2|17765|metal response element binding transcription factor 2
mm9_v1_chr15_+_98957150_98957201	2.89045	SOX2.p2	AK159335|Spats2|72572|spermatogenesis associated, serine-rich 2
mm9_v1_chr4_-_118293009_118293009	2.88906	SOX2.p2	NM_026789|Wdr65|68625|WD repeat domain 65
mm9_v1_chr6_-_56312803_56312803	2.88412	SOX2.p2	AK050499|Pde1c|18575|phosphodiesterase 1C	NM_001159960|Pde1c|18575|phosphodiesterase 1C
mm9_v1_chr17_+_44090139_44090183	2.88169	SOX2.p2	BC049096|Rcan2|53901|regulator of calcineurin 2	NM_030598|Rcan2|53901|regulator of calcineurin 2
mm9_v1_chr2_-_38569891_38570061	2.87661	SOX2.p2	AF511594|Nr5a1|26423|nuclear receptor subfamily 5, group A, member 1	BC110476|Nr5a1|26423|nuclear receptor subfamily 5, group A, member 1	BC110477|Nr5a1|26423|nuclear receptor subfamily 5, group A, member 1	AK144376|Nr5a1|26423|nuclear receptor subfamily 5, group A, member 1	AK156911|Nr5a1|26423|nuclear receptor subfamily 5, group A, member 1	AK134378|Nr5a1|26423|nuclear receptor subfamily 5, group A, member 1	NM_139051|Nr5a1|26423|nuclear receptor subfamily 5, group A, member 1
mm9_v1_chrX_+_131252542_131252558	2.87136	SOX2.p2	AK019405|Armcx1|78248|armadillo repeat containing, X-linked 1	BC021410|Armcx1|78248|armadillo repeat containing, X-linked 1
mm9_v1_chr2_+_14525932_14526000	2.87097	SOX2.p2	AK034054|Cacnb2|12296|calcium channel, voltage-dependent, beta 2 subunit	NM_023116|Cacnb2|12296|calcium channel, voltage-dependent, beta 2 subunit	FM872408|Cacnb2|12296|calcium channel, voltage-dependent, beta 2 subunit	BC109156|Cacnb2|12296|calcium channel, voltage-dependent, beta 2 subunit	BC109157|Cacnb2|12296|calcium channel, voltage-dependent, beta 2 subunit
mm9_v1_chr7_+_13466525_13466568	2.86997	SOX2.p2	AK132244|Zfp128|243833|zinc finger protein 128	AK035906|Zfp128|243833|zinc finger protein 128	NM_153802|Zfp128|243833|zinc finger protein 128	AK032046|Zfp128|243833|zinc finger protein 128	BC088998|Zfp128|243833|zinc finger protein 128	BC094248|Zfp128|243833|zinc finger protein 128	AF480861|Zfp128|243833|zinc finger protein 128
mm9_v1_chr3_+_136566015_136566156	2.86724	SOX2.p2	AK076570|Ppp3ca|19055|protein phosphatase 3, catalytic subunit, alpha isoform
mm9_v1_chr3_+_94964364_94964444	2.83643	SOX2.p2	AK165085|Sema6c|20360|sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	BC083186|Sema6c|20360|sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	BC059007|Sema6c|20360|sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	BC051979|Sema6c|20360|sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	AK031131|Sema6c|20360|sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C
mm9_v1_chr8_-_23763885_23763908	2.83371	SOX2.p2	AF513911|Polb|18970|polymerase (DNA directed), beta	BC060998|Polb|18970|polymerase (DNA directed), beta	AK077127|Polb|18970|polymerase (DNA directed), beta	AK151436|Polb|18970|polymerase (DNA directed), beta	AK146745|Polb|18970|polymerase (DNA directed), beta	BC006681|Polb|18970|polymerase (DNA directed), beta	NM_011130|Polb|18970|polymerase (DNA directed), beta
mm9_v1_chr16_+_17070249_17070422	2.83039	SOX2.p2	AK011452|Ypel1|106369|yippee-like 1 (Drosophila)	AK076063|Ypel1|106369|yippee-like 1 (Drosophila)	AK133401|Ypel1|106369|yippee-like 1 (Drosophila)	AF190624|Ypel1|106369|yippee-like 1 (Drosophila)	BC049737|Ypel1|106369|yippee-like 1 (Drosophila)	AK139453|Ypel1|106369|yippee-like 1 (Drosophila)	AK006137|Ypel1|106369|yippee-like 1 (Drosophila)	AK006858|Ypel1|106369|yippee-like 1 (Drosophila)	AK005955|Ypel1|106369|yippee-like 1 (Drosophila)	AK006049|Ypel1|106369|yippee-like 1 (Drosophila)	AK019819|Ypel1|106369|yippee-like 1 (Drosophila)	AK014931|Ypel1|106369|yippee-like 1 (Drosophila)	NM_023249|Ypel1|106369|yippee-like 1 (Drosophila)	AK018910|Ypel1|106369|yippee-like 1 (Drosophila)	AK006505|Ypel1|106369|yippee-like 1 (Drosophila)
mm9_v1_chr3_+_32607424_32607471	2.82778	SOX2.p2	NM_019673|Actl6a|56456|actin-like 6A	AK013221|Actl6a|56456|actin-like 6A
mm9_v1_chr4_+_129190824_129190856	2.82055	SOX2.p2	NM_010807|Marcksl1|17357|MARCKS-like 1
mm9_v1_chr5_-_100467887_100467935	2.81778	SOX2.p2	BC021374|Hnrpdl|50926|heterogeneous nuclear ribonucleoprotein D-like	AK172629|Hnrpdl|50926|heterogeneous nuclear ribonucleoprotein D-like	AK011581|Hnrpdl|50926|heterogeneous nuclear ribonucleoprotein D-like	AK011767|Hnrpdl|50926|heterogeneous nuclear ribonucleoprotein D-like
mm9_v1_chr17_+_44090222_44090252	2.81365	SOX2.p2	AK160865|Rcan2|53901|regulator of calcineurin 2
mm9_v1_chr3_+_94758936_94758955	2.81261	SOX2.p2	NM_017395|Rfx5|53970|regulatory factor X, 5 (influences HLA class II expression)	AB221679|Rfx5|53970|regulatory factor X, 5 (influences HLA class II expression)	AF209854|Rfx5|53970|regulatory factor X, 5 (influences HLA class II expression)	BC118948|Rfx5|53970|regulatory factor X, 5 (influences HLA class II expression)	BC118949|Rfx5|53970|regulatory factor X, 5 (influences HLA class II expression)
mm9_v1_chr6_-_18464792_18464824	2.80093	SOX2.p2	AK028980|Cttnbp2|30785|cortactin binding protein 2	AK019384|Cttnbp2|30785|cortactin binding protein 2	BC141407|Cttnbp2|30785|cortactin binding protein 2	NM_080285|Cttnbp2|30785|cortactin binding protein 2
mm9_v1_chr3_+_88373199_88373199	2.79691	SOX2.p2	AK207994|Ubqln4|94232|ubiquilin 4
mm9_v1_chr13_-_76081343_76081394	2.79424	SOX2.p2	AK081381|Rhobtb3|73296|Rho-related BTB domain containing 3
mm9_v1_chr5_-_122906470_122906515	2.78917	SOX2.p2	AK081191|Atp2a2|11938|ATPase, Ca++ transporting, cardiac muscle, slow twitch 2
mm9_v1_chr18_+_37663917_37664076	2.78668	SOX2.p2	AK045399|Pcdhb20|93891|protocadherin beta 20	NM_053145|Pcdhb20|93891|protocadherin beta 20	AK046137|Pcdhb20|93891|protocadherin beta 20	AF326313|Pcdhb20|93891|protocadherin beta 20	AK045527|Pcdhb20|93891|protocadherin beta 20	BC031895|Pcdhb20|93891|protocadherin beta 20	AY013782|Pcdhb20|93891|protocadherin beta 20
mm9_v1_chr16_-_89818596_89818596	2.78622	SOX2.p2	AK136856|Tiam1|21844|T-cell lymphoma invasion and metastasis 1	NM_001145887|Tiam1|21844|T-cell lymphoma invasion and metastasis 1
mm9_v1_chr13_-_54850954_54851046	2.78344	SOX2.p2	BC057044|Gprin1|26913|G protein-regulated inducer of neurite outgrowth 1	AK138306|Gprin1|26913|G protein-regulated inducer of neurite outgrowth 1	NM_012014|Gprin1|26913|G protein-regulated inducer of neurite outgrowth 1	AK144210|Gprin1|26913|G protein-regulated inducer of neurite outgrowth 1
mm9_v1_chr4_-_43496556_43496593	2.77512	SOX2.p2	AJ236881|Sit1|54390|suppression inducing transmembrane adaptor 1	AK079882|Sit1|54390|suppression inducing transmembrane adaptor 1	NM_019436|Sit1|54390|suppression inducing transmembrane adaptor 1	BC064055|Sit1|54390|suppression inducing transmembrane adaptor 1
mm9_v1_chr18_+_37460452_37460636	2.77323	SOX2.p2	AK030570|Pcdhb3|93874|protocadherin beta 3	NM_053128|Pcdhb3|93874|protocadherin beta 3	BC079557|Pcdhb3|93874|protocadherin beta 3	AF326296|Pcdhb3|93874|protocadherin beta 3	AY013785|Pcdhb3|93874|protocadherin beta 3
mm9_v1_chr18_-_15562126_15562266	2.76734	SOX2.p2	AK044074|Aqp4|11829|aquaporin 4	BC024526|Aqp4|11829|aquaporin 4	NM_009700|Aqp4|11829|aquaporin 4	AF469168|Aqp4|11829|aquaporin 4
mm9_v1_chr11_-_100131176_100131184	2.76589	SOX2.p2	BC112371|Krt42|68239|keratin 42	AY459292|Krt42|68239|keratin 42	BC148204|Krt42|68239|keratin 42	NM_212483|Krt42|68239|keratin 42
mm9_v1_chr18_+_37890662_37890807	2.76377	SOX2.p2	BC057403|Pcdhgb5|93702|protocadherin gamma subfamily B, 5	AK156301|Pcdhgb5|93702|protocadherin gamma subfamily B, 5	AY013807|Pcdhgb5|93702|protocadherin gamma subfamily B, 5	NM_033577|Pcdhgb5|93702|protocadherin gamma subfamily B, 5
mm9_v1_chr6_+_86578167_86578196	2.76161	SOX2.p2	DQ841260|Asprv1|67855|aspartic peptidase, retroviral-like 1	NM_026414|Asprv1|67855|aspartic peptidase, retroviral-like 1	BC057938|Asprv1|67855|aspartic peptidase, retroviral-like 1
mm9_v1_chr4_+_13711928_13711928	2.75713	SOX2.p2	D32007|Runx1t1|12395|runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	NM_009822|Runx1t1|12395|runt-related transcription factor 1; translocated to, 1 (cyclin D-related)
mm9_v1_chr12_-_106003060_106003147	2.75446	SOX2.p2	BC027232|Clmn|94040|calmin
mm9_v1_chr12_-_32398730_32398790	2.75301	SOX2.p2	AK140577|Gpr22|73010|G protein-coupled receptor 22	AK034194|Gpr22|73010|G protein-coupled receptor 22	AK013755|Gpr22|73010|G protein-coupled receptor 22	AK048077|Gpr22|73010|G protein-coupled receptor 22	AK141569|Gpr22|73010|G protein-coupled receptor 22	BC089509|Gpr22|73010|G protein-coupled receptor 22	NM_175191|Gpr22|73010|G protein-coupled receptor 22
mm9_v1_chr18_+_37911236_37911432	2.75032	SOX2.p2	BC066823|Pcdhgb7|93704|protocadherin gamma subfamily B, 7	AY013809|Pcdhgb7|93704|protocadherin gamma subfamily B, 7	NM_033579|Pcdhgb7|93704|protocadherin gamma subfamily B, 7
mm9_v1_chr19_-_10944196_10944284	2.74343	SOX2.p2	BC006896|Tmem132a|98170|transmembrane protein 132A	AK173207|Tmem132a|98170|transmembrane protein 132A	AK036651|Tmem132a|98170|transmembrane protein 132A	AK032956|Tmem132a|98170|transmembrane protein 132A	AK048556|Tmem132a|98170|transmembrane protein 132A	AK164646|Tmem132a|98170|transmembrane protein 132A	NM_133804|Tmem132a|98170|transmembrane protein 132A
mm9_v1_chr1_-_65109982_65110015	2.73418	SOX2.p2	K02583|Crygd|12967|crystallin, gamma D	BC057013|Crygd|12967|crystallin, gamma D	AK136286|Crygd|12967|crystallin, gamma D	BC132116|Crygd|12967|crystallin, gamma D	BC132118|Crygd|12967|crystallin, gamma D	NM_007776|Crygd|12967|crystallin, gamma D
mm9_v1_chr7_+_138712015_138712162	2.73401	SOX2.p2	AK039977|Bub3|12237|budding uninhibited by benzimidazoles 3 homolog (S. cerevisiae)	AK079742|Bub3|12237|budding uninhibited by benzimidazoles 3 homolog (S. cerevisiae)
mm9_v1_chr3_+_94282235_94282264	2.72905	SOX2.p2	AK044506|Celf3|78784|VCUGBP, Elav-like family member 3	AK087536|Celf3|78784|VCUGBP, Elav-like family member 3
mm9_v1_chr1_-_64167574_64167617	2.72368	SOX2.p2	AB221646|Klf7|93691|Kruppel-like factor 7 (ubiquitous)
mm9_v1_chr15_-_95358306_95358472	2.72135	SOX2.p2	BC051968|Nell2|54003|NEL-like 2 (chicken)
mm9_v1_chr11_+_80290571_80290592	2.71586	SOX2.p2	AK043203|Cdk5r1|12569|cyclin-dependent kinase 5, regulatory subunit 1 (p35)	AK084003|Cdk5r1|12569|cyclin-dependent kinase 5, regulatory subunit 1 (p35)
mm9_v1_chr1_-_37776633_37776680	2.69753	SOX2.p2	AK039052|2010300C02Rik|72097|RIKEN cDNA 2010300C02 gene	BC072639|2010300C02Rik|72097|RIKEN cDNA 2010300C02 gene	NM_028096|2010300C02Rik|72097|RIKEN cDNA 2010300C02 gene
mm9_v1_chr3_-_122241909_122241984	2.69602	SOX2.p2	AK019185|Fnbp1l|214459|formin binding protein 1-like
mm9_v1_chr12_+_71008808_71008844	2.68885	SOX2.p2	AK140185|Atl1|73991|atlastin GTPase 1	AK046919|Atl1|73991|atlastin GTPase 1	BC050784|Atl1|73991|atlastin GTPase 1
mm9_v1_chr5_-_38550627_38550759	2.68729	SOX2.p2	AF035683|Nsg1|18196|neuron specific gene family member 1	AK144503|Nsg1|18196|neuron specific gene family member 1	BC008272|Nsg1|18196|neuron specific gene family member 1	AK078054|Nsg1|18196|neuron specific gene family member 1	AK148941|Nsg1|18196|neuron specific gene family member 1	AX775765|Nsg1|18196|neuron specific gene family member 1	NM_010942|Nsg1|18196|neuron specific gene family member 1
mm9_v1_chr12_-_99816091_99816149	2.68593	SOX2.p2	BC132487|Kcnk10|72258|potassium channel, subfamily K, member 10	BC137869|Kcnk10|72258|potassium channel, subfamily K, member 10	AK082153|Kcnk10|72258|potassium channel, subfamily K, member 10	NM_029911|Kcnk10|72258|potassium channel, subfamily K, member 10
mm9_v1_chrX_+_131252456_131252527	2.68092	SOX2.p2	NM_001166377|Armcx1|78248|armadillo repeat containing, X-linked 1	NM_001166378|Armcx1|78248|armadillo repeat containing, X-linked 1	NM_001166379|Armcx1|78248|armadillo repeat containing, X-linked 1	NM_001166380|Armcx1|78248|armadillo repeat containing, X-linked 1	NM_030066|Armcx1|78248|armadillo repeat containing, X-linked 1	BC026488|Armcx1|78248|armadillo repeat containing, X-linked 1	AK147002|Armcx1|78248|armadillo repeat containing, X-linked 1	BC068228|Armcx1|78248|armadillo repeat containing, X-linked 1
mm9_v1_chr17_-_80689434_80689517	2.66734	SOX2.p2	BC079618|Dhx57|106794|DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	BC066091|Dhx57|106794|DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	BC065169|Dhx57|106794|DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	AK042947|Dhx57|106794|DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57
mm9_v1_chr14_+_66963139_66963219	2.66715	SOX2.p2	BC014707|Stmn4|56471|stathmin-like 4	BC046752|Stmn4|56471|stathmin-like 4	NM_019675|Stmn4|56471|stathmin-like 4
mm9_v1_chr18_+_37633193_37633199	2.66567	SOX2.p2	BC066178|Pcdhb15|93886|protocadherin beta 15	AK038663|Pcdhb15|93886|protocadherin beta 15	NM_053140|Pcdhb15|93886|protocadherin beta 15
mm9_v1_chr8_+_32239179_32239274	2.65564	SOX2.p2	AK004356|Rnf122|68867|ring finger protein 122
mm9_v1_chr9_-_73781373_73781373	2.65221	SOX2.p2	NM_001081153|Unc13c|208898|unc-13 homolog C (C. elegans)
mm9_v1_chr7_+_130337876_130337891	2.64855	SOX2.p2	AK014218|Tnrc6a|233833|trinucleotide repeat containing 6a
mm9_v1_chr9_-_112090150_112090479	2.64542	SOX2.p2	BC128376|Arpp21|74100|cyclic AMP-regulated phosphoprotein, 21	AF324451|Arpp21|74100|cyclic AMP-regulated phosphoprotein, 21	NM_033264|Arpp21|74100|cyclic AMP-regulated phosphoprotein, 21	AK159004|Arpp21|74100|cyclic AMP-regulated phosphoprotein, 21	AK002950|Arpp21|74100|cyclic AMP-regulated phosphoprotein, 21	BC027107|Arpp21|74100|cyclic AMP-regulated phosphoprotein, 21	AK160860|Arpp21|74100|cyclic AMP-regulated phosphoprotein, 21	NM_001177615|Arpp21|74100|cyclic AMP-regulated phosphoprotein, 21	NM_001177620|Arpp21|74100|cyclic AMP-regulated phosphoprotein, 21	NM_028755|Arpp21|74100|cyclic AMP-regulated phosphoprotein, 21
mm9_v1_chr4_-_134409044_134409108	2.64504	SOX2.p2	AY364165|Tmem57|66146|transmembrane protein 57	BC054355|Tmem57|66146|transmembrane protein 57	BC010714|Tmem57|66146|transmembrane protein 57
mm9_v1_chr5_+_130731488_130731494	2.6423	SOX2.p2	AK045279|Tyw1|100929|tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	NM_178897|Tyw1|100929|tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)
mm9_v1_chr17_-_27717411_27717581	2.63771	SOX2.p2	AK195385|Nudt3|56409|nudix (nucleotide diphosphate linked moiety X)-type motif 3	AK205576|Nudt3|56409|nudix (nucleotide diphosphate linked moiety X)-type motif 3	AK003601|Nudt3|56409|nudix (nucleotide diphosphate linked moiety X)-type motif 3	AK211644|Nudt3|56409|nudix (nucleotide diphosphate linked moiety X)-type motif 3
mm9_v1_chr4_-_120642197_120642226	2.63665	SOX2.p2	AB029329|Smap2|69780|stromal membrane-associated GTPase-activating protein 2
mm9_v1_chr9_+_117161650_117161701	2.63319	SOX2.p2	
mm9_v1_chr11_-_33743416_33743626	2.62539	SOX2.p2	AY647242|Kcnip1|70357|Kv channel-interacting protein 1	AY171234|Kcnip1|70357|Kv channel-interacting protein 1	BC034241|Kcnip1|70357|Kv channel-interacting protein 1	DQ148493|Kcnip1|70357|Kv channel-interacting protein 1	AK013657|Kcnip1|70357|Kv channel-interacting protein 1	AK014313|Kcnip1|70357|Kv channel-interacting protein 1	AK046398|Kcnip1|70357|Kv channel-interacting protein 1	AK045948|Kcnip1|70357|Kv channel-interacting protein 1	NM_001190885|Kcnip1|70357|Kv channel-interacting protein 1	NM_027398|Kcnip1|70357|Kv channel-interacting protein 1
mm9_v1_chr4_-_34754469_34754554	2.62532	SOX2.p2	AB221605|Zfp292|30046|zinc finger protein 292
mm9_v1_chr11_-_99855307_99855307	2.62279	SOX2.p2	AK020698|Krtap17-1|77914|keratin associated protein 17-1	NM_001099774|Krtap17-1|77914|keratin associated protein 17-1
mm9_v1_chr7_-_111161213_111161263	2.62065	SOX2.p2	NM_147084|Olfr639|259088|olfactory receptor 639	BC145837|Olfr639|259088|olfactory receptor 639
mm9_v1_chr15_+_12808445_12808493	2.61947	SOX2.p2	BC040801|Drosha|14000|drosha, ribonuclease type III
mm9_v1_chr2_-_165710128_165710217	2.61797	SOX2.p2	AK038961|Zmynd8|228880|zinc finger, MYND-type containing 8	AK155864|Zmynd8|228880|zinc finger, MYND-type containing 8	BC048186|Zmynd8|228880|zinc finger, MYND-type containing 8	NM_027230|Zmynd8|228880|zinc finger, MYND-type containing 8
mm9_v1_chr1_-_134539434_134539434	2.6142	SOX2.p2	NM_001160316|Nfasc|269116|neurofascin
mm9_v1_chr2_-_56976530_56976555	2.61346	SOX2.p2	AK087495|Nr4a2|18227|nuclear receptor subfamily 4, group A, member 2
mm9_v1_chr11_+_56825307_56825536	2.61068	SOX2.p2	AK049958|Gria1|14799|glutamate receptor, ionotropic, AMPA1 (alpha 1)	BC056397|Gria1|14799|glutamate receptor, ionotropic, AMPA1 (alpha 1)	AB102773|Gria1|14799|glutamate receptor, ionotropic, AMPA1 (alpha 1)	AB102774|Gria1|14799|glutamate receptor, ionotropic, AMPA1 (alpha 1)	BC060702|Gria1|14799|glutamate receptor, ionotropic, AMPA1 (alpha 1)
mm9_v1_chrX_+_90920450_90920749	2.6061	SOX2.p2	NM_211138|Pcyt1b|236899|phosphate cytidylyltransferase 1, choline, beta isoform	BC048917|Pcyt1b|236899|phosphate cytidylyltransferase 1, choline, beta isoform	AY189949|Pcyt1b|236899|phosphate cytidylyltransferase 1, choline, beta isoform	AK032027|Pcyt1b|236899|phosphate cytidylyltransferase 1, choline, beta isoform
mm9_v1_chr12_-_82480450_82480472	2.60424	SOX2.p2	BC141094|Gm4787|214321|predicted gene 4787	NM_001038995|Gm4787|214321|predicted gene 4787
mm9_v1_chr2_+_146047656_146047846	2.59909	SOX2.p2	BC051240|Insm1|53626|insulinoma-associated 1	NM_016889|Insm1|53626|insulinoma-associated 1	AF044669|Insm1|53626|insulinoma-associated 1	BC082809|Insm1|53626|insulinoma-associated 1
mm9_v1_chr6_+_79969636_79969636	2.59868	SOX2.p2	NM_178731|Lrrtm4|243499|leucine rich repeat transmembrane neuronal 4
mm9_v1_chr16_-_79091336_79091341	2.5973	SOX2.p2	NM_008941|Tmprss15|19146|transmembrane protease, serine 15	U73378|Tmprss15|19146|transmembrane protease, serine 15	BC117917|Tmprss15|19146|transmembrane protease, serine 15	BC117918|Tmprss15|19146|transmembrane protease, serine 15	AK033582|Tmprss15|19146|transmembrane protease, serine 15	NM_178855|Tmprss15|19146|transmembrane protease, serine 15
mm9_v1_chr16_-_31314534_31314685	2.59609	SOX2.p2	X82648|Apod|11815|apolipoprotein D	AK158118|Apod|11815|apolipoprotein D	AK157925|Apod|11815|apolipoprotein D	AK135046|Apod|11815|apolipoprotein D	AK157917|Apod|11815|apolipoprotein D	AK160729|Apod|11815|apolipoprotein D	AK162392|Apod|11815|apolipoprotein D	NM_007470|Apod|11815|apolipoprotein D	AK158405|Apod|11815|apolipoprotein D
mm9_v1_chr4_+_13670582_13670631	2.59571	SOX2.p2	AK032132|Runx1t1|12395|runt-related transcription factor 1; translocated to, 1 (cyclin D-related)
mm9_v1_chr5_-_92483744_92484066	2.59425	SOX2.p2	AK169571|G3bp2|23881|GTPase activating protein (SH3 domain) binding protein 2	AK220349|G3bp2|23881|GTPase activating protein (SH3 domain) binding protein 2
mm9_v1_chr3_-_57496415_57496458	2.59005	SOX2.p2	AK134766|Gm410|242037|predicted gene 410	AK138483|Gm410|242037|predicted gene 410	NM_001033349|Gm410|242037|predicted gene 410
mm9_v1_chr9_+_24429544_24429647	2.58694	SOX2.p2	BC147783|Cypt4|235067|cysteine-rich perinuclear theca 4	AF463501|Cypt4|235067|cysteine-rich perinuclear theca 4	NM_173412|Cypt4|235067|cysteine-rich perinuclear theca 4	AK005791|Cypt4|235067|cysteine-rich perinuclear theca 4	BC048530|Cypt4|235067|cysteine-rich perinuclear theca 4	BC060952|Cypt4|235067|cysteine-rich perinuclear theca 4	AM040453|Cypt4|235067|cysteine-rich perinuclear theca 4	AM040458|Cypt9|664724|cysteine-rich perinuclear theca 9	AM040459|Cypt10|664726|cysteine-rich perinuclear theca 10	NM_001039942|Cypt9|664724|cysteine-rich perinuclear theca 9	NM_001039944|Cypt10|664726|cysteine-rich perinuclear theca 10
mm9_v1_chr16_+_17045125_17045167	2.57957	SOX2.p2	AK163692|Mapk1|26413|mitogen-activated protein kinase 1
mm9_v1_chr11_+_117623703_117623821	2.57738	SOX2.p2	AK137381|Tnrc6c|217351|trinucleotide repeat containing 6C
mm9_v1_chr4_+_128820458_128820467	2.57602	SOX2.p2	AK137327|Fndc5|384061|fibronectin type III domain containing 5
mm9_v1_chr3_+_13471643_13471656	2.57382	SOX2.p2	NM_001163328|Ralyl|76897|RALY RNA binding protein-like	NM_178631|Ralyl|76897|RALY RNA binding protein-like
mm9_v1_chr3_+_19431246_19431246	2.57214	SOX2.p2	NM_001163537|Dnajc5b|66326|DnaJ (Hsp40) homolog, subfamily C, member 5 beta
mm9_v1_chr7_-_13595141_13595224	2.56885	SOX2.p2	BC094359|Zbtb45|232879|zinc finger and BTB domain containing 45	NM_001024699|Zbtb45|232879|zinc finger and BTB domain containing 45	AK155880|Zbtb45|232879|zinc finger and BTB domain containing 45	AK166382|Zbtb45|232879|zinc finger and BTB domain containing 45	AK154877|Zbtb45|232879|zinc finger and BTB domain containing 45
mm9_v1_chr4_+_102242664_102242699	2.56505	SOX2.p2	NM_001177980|Pde4b|18578|phosphodiesterase 4B, cAMP specific	BC023751|Pde4b|18578|phosphodiesterase 4B, cAMP specific
mm9_v1_chr8_-_89090481_89090488	2.56199	SOX2.p2	BC138380|Abcc12|244562|ATP-binding cassette, sub-family C (CFTR/MRP), member 12	BC138381|Abcc12|244562|ATP-binding cassette, sub-family C (CFTR/MRP), member 12	BC171952|Abcc12|244562|ATP-binding cassette, sub-family C (CFTR/MRP), member 12	AF502146|Abcc12|244562|ATP-binding cassette, sub-family C (CFTR/MRP), member 12	AF514414|Abcc12|244562|ATP-binding cassette, sub-family C (CFTR/MRP), member 12	AF514415|Abcc12|244562|ATP-binding cassette, sub-family C (CFTR/MRP), member 12	NM_172912|Abcc12|244562|ATP-binding cassette, sub-family C (CFTR/MRP), member 12
mm9_v1_chr13_+_59234737_59234835	2.56157	SOX2.p2	AK021108|Ntrk2|18212|neurotrophic tyrosine kinase, receptor, type 2
mm9_v1_chr9_+_21172314_21172446	2.55559	SOX2.p2	AK150276|Ilf3|16201|interleukin enhancer binding factor 3	AK128936|Ilf3|16201|interleukin enhancer binding factor 3	AK048096|Ilf3|16201|interleukin enhancer binding factor 3	AK077560|Ilf3|16201|interleukin enhancer binding factor 3	BC047272|Ilf3|16201|interleukin enhancer binding factor 3	AF497751|Ilf3|16201|interleukin enhancer binding factor 3	AF497752|Ilf3|16201|interleukin enhancer binding factor 3	DQ104405|Ilf3|16201|interleukin enhancer binding factor 3	DQ104406|Ilf3|16201|interleukin enhancer binding factor 3	NM_001042707|Ilf3|16201|interleukin enhancer binding factor 3	NM_001042708|Ilf3|16201|interleukin enhancer binding factor 3	NM_001042709|Ilf3|16201|interleukin enhancer binding factor 3	NM_010561|Ilf3|16201|interleukin enhancer binding factor 3
mm9_v1_chr10_+_57206184_57206291	2.55091	SOX2.p2	AK053976|Hsf2|15500|heat shock factor 2	NM_008297|Hsf2|15500|heat shock factor 2	BC018414|Hsf2|15500|heat shock factor 2	AK052270|Hsf2|15500|heat shock factor 2
mm9_v1_chr17_+_3482314_3482460	2.54623	SOX2.p2	AK158489|Tiam2|24001|T-cell lymphoma invasion and metastasis 2
mm9_v1_chr14_-_34260323_34260352	2.54138	SOX2.p2	AK139498|Mapk8|26419|mitogen-activated protein kinase 8	AK032486|Mapk8|26419|mitogen-activated protein kinase 8	AK043102|Mapk8|26419|mitogen-activated protein kinase 8	AK085745|Mapk8|26419|mitogen-activated protein kinase 8	AK030767|Mapk8|26419|mitogen-activated protein kinase 8	NM_016700|Mapk8|26419|mitogen-activated protein kinase 8
mm9_v1_chr2_+_155890933_155891049	2.53248	SOX2.p2	AK220494|Spag4|245865|sperm associated antigen 4	NM_139151|Spag4|245865|sperm associated antigen 4	AK043812|Spag4|245865|sperm associated antigen 4	AK028080|Spag4|245865|sperm associated antigen 4	BC107321|Spag4|245865|sperm associated antigen 4
mm9_v1_chr3_-_92242684_92242702	2.52833	SOX2.p2	X91825|Sprr1b|20754|small proline-rich protein 1B	BC119288|Sprr1b|20754|small proline-rich protein 1B	BC119290|Sprr1b|20754|small proline-rich protein 1B	AK003398|Sprr1b|20754|small proline-rich protein 1B	AK009752|Sprr1b|20754|small proline-rich protein 1B	NM_009265|Sprr1b|20754|small proline-rich protein 1B
mm9_v1_chr15_-_95358989_95359075	2.52717	SOX2.p2	AK039790|Nell2|54003|NEL-like 2 (chicken)
mm9_v1_chr4_+_48598013_48598089	2.52278	SOX2.p2	BC057598|Tmeff1|230157|transmembrane protein with EGF-like and two follistatin-like domains 1	NM_021436|Tmeff1|230157|transmembrane protein with EGF-like and two follistatin-like domains 1
mm9_v1_chr4_-_134409149_134409155	2.51253	SOX2.p2	AK038972|Tmem57|66146|transmembrane protein 57	BC054769|Tmem57|66146|transmembrane protein 57
mm9_v1_chr17_+_33130067_33130141	2.50566	SOX2.p2	AK050612|Zfp952|240067|zinc finger protein 952	BC057593|Zfp952|240067|zinc finger protein 952	NM_001045559|Zfp952|240067|zinc finger protein 952	BC051011|Zfp952|240067|zinc finger protein 952
mm9_v1_chr15_-_37389073_37389150	2.50374	SOX2.p2	BC026979|Ncald|52589|neurocalcin delta	AK167313|Ncald|52589|neurocalcin delta	AK034031|Ncald|52589|neurocalcin delta	NM_001170867|Ncald|52589|neurocalcin delta	NM_001170868|Ncald|52589|neurocalcin delta
mm9_v1_chr17_-_56615861_56615871	2.50193	SOX2.p2	BC083188|Ptprs|19280|protein tyrosine phosphatase, receptor type, S	AK163915|Ptprs|19280|protein tyrosine phosphatase, receptor type, S
mm9_v1_chr3_+_53292633_53292714	2.50052	SOX2.p2	BC138667|Stoml3|229277|stomatin (Epb7.2)-like 3	BC138668|Stoml3|229277|stomatin (Epb7.2)-like 3	BC058224|Stoml3|229277|stomatin (Epb7.2)-like 3	BC080859|Stoml3|229277|stomatin (Epb7.2)-like 3	AB085692|Stoml3|229277|stomatin (Epb7.2)-like 3	BC140135|Stoml3|229277|stomatin (Epb7.2)-like 3	BC140175|Stoml3|229277|stomatin (Epb7.2)-like 3	BC143035|Stoml3|229277|stomatin (Epb7.2)-like 3	BC143150|Stoml3|229277|stomatin (Epb7.2)-like 3	NM_153156|Stoml3|229277|stomatin (Epb7.2)-like 3
mm9_v1_chr3_+_103811134_103811169	2.49944	SOX2.p2	
mm9_v1_chr16_-_91044623_91044646	2.49397	SOX2.p2	NM_026110|Gcfc1|67367|GC-rich sequence DNA-binding factor 1
mm9_v1_chr4_-_148001104_148001104	2.49377	SOX2.p2	NM_001003898|Tardbp|230908|TAR DNA binding protein	NM_001003899|Tardbp|230908|TAR DNA binding protein	NM_001008545|Tardbp|230908|TAR DNA binding protein	NM_001008546|Tardbp|230908|TAR DNA binding protein	NM_145556|Tardbp|230908|TAR DNA binding protein
mm9_v1_chr1_-_25886551_25886551	2.48653	SOX2.p2	BC099951|Bai3|210933|brain-specific angiogenesis inhibitor 3	NM_175642|Bai3|210933|brain-specific angiogenesis inhibitor 3
mm9_v1_chr7_+_52769075_52769124	2.4855	SOX2.p2	NM_001045555|Tulp2|56734|tubby-like protein 2	NM_008807|Tulp2|56734|tubby-like protein 2	AK077200|Tulp2|56734|tubby-like protein 2	AF105712|Tulp2|56734|tubby-like protein 2
mm9_v1_chr11_-_97637190_97637231	2.48447	SOX2.p2	AK005619|1700001P01Rik|72215|RIKEN cDNA 1700001P01 gene	BC048607|1700001P01Rik|72215|RIKEN cDNA 1700001P01 gene	NM_028156|1700001P01Rik|72215|RIKEN cDNA 1700001P01 gene
mm9_v1_chr8_-_73987384_73987575	2.48335	SOX2.p2	AK178916|Abhd8|64296|abhydrolase domain containing 8	AK212822|Abhd8|64296|abhydrolase domain containing 8	BC026540|Abhd8|64296|abhydrolase domain containing 8	AK037669|Abhd8|64296|abhydrolase domain containing 8	AK003090|Abhd8|64296|abhydrolase domain containing 8	AB030191|Abhd8|64296|abhydrolase domain containing 8	AK080618|Abhd8|64296|abhydrolase domain containing 8	AK155503|Abhd8|64296|abhydrolase domain containing 8	NM_022419|Abhd8|64296|abhydrolase domain containing 8
mm9_v1_chr4_-_118081793_118081882	2.4833	SOX2.p2	GU433214|Szt2|230676|seizure threshold 2	FJ998170|Szt2|230676|seizure threshold 2	NM_198170|Szt2|230676|seizure threshold 2
mm9_v1_chr15_+_30102306_30102347	2.48325	SOX2.p2	NM_008729|Ctnnd2|18163|catenin (cadherin associated protein), delta 2	U90331|Ctnnd2|18163|catenin (cadherin associated protein), delta 2
mm9_v1_chr19_+_8667671_8667730	2.47928	SOX2.p2	NM_001164635|Slc22a8|19879|solute carrier family 22 (organic anion transporter), member 8	AK157891|Slc22a8|19879|solute carrier family 22 (organic anion transporter), member 8	BC014762|Slc22a8|19879|solute carrier family 22 (organic anion transporter), member 8	AK044336|Slc22a8|19879|solute carrier family 22 (organic anion transporter), member 8	AF078869|Slc22a8|19879|solute carrier family 22 (organic anion transporter), member 8
mm9_v1_chr12_-_111932287_111932415	2.47357	SOX2.p2	BC090391|Gm12346|544800|heat shock protein 1, alpha pseudogene
mm9_v1_chr9_-_50535949_50536088	2.47317	SOX2.p2	AY549884|Dixdc1|330938|DIX domain containing 1	AK016205|Dixdc1|330938|DIX domain containing 1	BC048182|Dixdc1|330938|DIX domain containing 1	BC063085|Dixdc1|330938|DIX domain containing 1	AK164424|Dixdc1|330938|DIX domain containing 1	NM_178118|Dixdc1|330938|DIX domain containing 1
mm9_v1_chr1_-_16509276_16509454	2.46519	SOX2.p2	AK031102|Stau2|29819|staufen (RNA binding protein) homolog 2 (Drosophila)	AF459099|Stau2|29819|staufen (RNA binding protein) homolog 2 (Drosophila)	AF459100|Stau2|29819|staufen (RNA binding protein) homolog 2 (Drosophila)	AK171076|Stau2|29819|staufen (RNA binding protein) homolog 2 (Drosophila)	NM_001111272|Stau2|29819|staufen (RNA binding protein) homolog 2 (Drosophila)	NM_025303|Stau2|29819|staufen (RNA binding protein) homolog 2 (Drosophila)
mm9_v1_chr15_+_83610459_83610521	2.46138	SOX2.p2	AK165755|Mpped1|223726|metallophosphoesterase domain containing 1
mm9_v1_chr19_+_23833310_23833547	2.45632	SOX2.p2	NM_177034|Apba1|319924|amyloid beta (A4) precursor protein binding, family A, member 1	AK147583|Apba1|319924|amyloid beta (A4) precursor protein binding, family A, member 1	AK147623|Apba1|319924|amyloid beta (A4) precursor protein binding, family A, member 1	BC141181|Apba1|319924|amyloid beta (A4) precursor protein binding, family A, member 1
mm9_v1_chr6_-_92656148_92656177	2.44701	SOX2.p2	BC099897|Prickle2|243548|prickle homolog 2 (Drosophila)	NM_001081146|Prickle2|243548|prickle homolog 2 (Drosophila)
mm9_v1_chr16_+_17045284_17045304	2.44603	SOX2.p2	AK018549|Mapk1|26413|mitogen-activated protein kinase 1
mm9_v1_chr18_+_37880036_37880207	2.4445	SOX2.p2	AK083581|Pcdhgb4|93701|protocadherin gamma subfamily B, 4	BC138701|Pcdhgb4|93701|protocadherin gamma subfamily B, 4	AY013806|Pcdhgb4|93701|protocadherin gamma subfamily B, 4	NM_033576|Pcdhgb4|93701|protocadherin gamma subfamily B, 4
mm9_v1_chr17_+_89025866_89025960	2.43909	SOX2.p2	NM_029858|Ston1|77057|stonin 1	AK029959|Ston1|77057|stonin 1	AK029878|Ston1|77057|stonin 1	AK014958|Ston1|77057|stonin 1
mm9_v1_chr5_-_24236497_24236497	2.43497	SOX2.p2	BC059069|Wdr86|269633|WD repeat domain 86	NM_001081441|Wdr86|269633|WD repeat domain 86
mm9_v1_chr4_-_126114651_126114748	2.4331	SOX2.p2	AK141219|Eif2c1|236511|eukaryotic translation initiation factor 2C, 1
mm9_v1_chr7_+_121184667_121184743	2.42875	SOX2.p2	AK084717|Spon1|233744|spondin 1, (f-spondin) extracellular matrix protein
mm9_v1_chr15_-_95358674_95358735	2.42554	SOX2.p2	U59230|Nell2|54003|NEL-like 2 (chicken)
mm9_v1_chr14_-_20796255_20796277	2.42127	SOX2.p2	AK003588|Gng2|14702|guanine nucleotide binding protein (G protein), gamma 2	AK036138|Gng2|14702|guanine nucleotide binding protein (G protein), gamma 2
mm9_v1_chr14_+_121434765_121434823	2.41272	SOX2.p2	AK134958|Farp1|223254|FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived)	NM_134082|Farp1|223254|FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived)
mm9_v1_chr10_+_20059547_20059574	2.41055	SOX2.p2	AK169491|Bclaf1|72567|BCL2-associated transcription factor 1
mm9_v1_chr1_-_134603848_134603902	2.40236	SOX2.p2	AK129207|Nfasc|269116|neurofascin	NM_001160318|Nfasc|269116|neurofascin
mm9_v1_chr19_+_28909559_28909655	2.40063	SOX2.p2	AK018188|Slc1a1|20510|solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	AK045632|Slc1a1|20510|solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	AK051428|Slc1a1|20510|solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	AK083097|Slc1a1|20510|solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	BC065099|Slc1a1|20510|solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	BC064797|Slc1a1|20510|solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	D43797|Slc1a1|20510|solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	NM_009199|Slc1a1|20510|solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	U73521|Slc1a1|20510|solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1
mm9_v1_chrX_-_101396356_101396482	2.39052	SOX2.p2	AK220439|C77370|245555|expressed sequence C77370	DQ975302|C77370|245555|expressed sequence C77370	DQ975303|C77370|245555|expressed sequence C77370	NM_001077354|C77370|245555|expressed sequence C77370	AK038635|C77370|245555|expressed sequence C77370
mm9_v1_chr11_+_59476129_59476146	2.38395	SOX2.p2	U73200|Mprip|26936|myosin phosphatase Rho interacting protein
mm9_v1_chr7_-_67285104_67285104	2.38089	SOX2.p2	NM_001082962|Snrpn|20646|small nuclear ribonucleoprotein N
mm9_v1_chr11_+_59476181_59476356	2.38079	SOX2.p2	AK155630|Mprip|26936|myosin phosphatase Rho interacting protein	AK044512|Mprip|26936|myosin phosphatase Rho interacting protein	BC049803|Mprip|26936|myosin phosphatase Rho interacting protein
mm9_v1_chr9_+_59465036_59465209	2.38054	SOX2.p2	NM_029922|Parp6|67287|poly (ADP-ribose) polymerase family, member 6	BC052064|Parp6|67287|poly (ADP-ribose) polymerase family, member 6	AK076321|Parp6|67287|poly (ADP-ribose) polymerase family, member 6	AK007206|Parp6|67287|poly (ADP-ribose) polymerase family, member 6	AK035349|Parp6|67287|poly (ADP-ribose) polymerase family, member 6	AK021076|Parp6|67287|poly (ADP-ribose) polymerase family, member 6
mm9_v1_chr13_-_58456221_58456222	2.37598	SOX2.p2	BC116646|Kif27|75050|kinesin family member 27	NM_175214|Kif27|75050|kinesin family member 27
mm9_v1_chrX_-_103124651_103124717	2.37484	SOX2.p2	AK135019|Atrx|22589|alpha thalassemia/mental retardation syndrome X-linked homolog (human)	AF026032|Atrx|22589|alpha thalassemia/mental retardation syndrome X-linked homolog (human)	AK088095|Atrx|22589|alpha thalassemia/mental retardation syndrome X-linked homolog (human)	NM_009530|Atrx|22589|alpha thalassemia/mental retardation syndrome X-linked homolog (human)
mm9_v1_chr6_-_136783899_136783972	2.37477	SOX2.p2	AK047766|C030030A07Rik|654818|RIKEN cDNA C030030A07 gene	AK045581|C030030A07Rik|654818|RIKEN cDNA C030030A07 gene	NM_001039558|C030030A07Rik|654818|RIKEN cDNA C030030A07 gene	AK078719|C030030A07Rik|654818|RIKEN cDNA C030030A07 gene
mm9_v1_chr8_+_68142423_68142423	2.37409	SOX2.p2	BC066008|March1|72925|membrane-associated ring finger (C3HC4) 1	NM_175188|March1|72925|membrane-associated ring finger (C3HC4) 1
mm9_v1_chrX_-_131343759_131343759	2.36955	SOX2.p2	AK172960|Armcx2|67416|armadillo repeat containing, X-linked 2	NM_001166397|Armcx2|67416|armadillo repeat containing, X-linked 2	NM_001166398|Armcx2|67416|armadillo repeat containing, X-linked 2	NM_026139|Armcx2|67416|armadillo repeat containing, X-linked 2
mm9_v1_chr4_-_34830178_34830200	2.36733	SOX2.p2	AK017652|Zfp292|30046|zinc finger protein 292	AK018067|Zfp292|30046|zinc finger protein 292	NM_013889|Zfp292|30046|zinc finger protein 292	BC036997|Zfp292|30046|zinc finger protein 292
mm9_v1_chr8_-_89996089_89996284	2.36644	SOX2.p2	AK161846|Cbln1|12404|cerebellin 1 precursor protein	BC051956|Cbln1|12404|cerebellin 1 precursor protein	BC055730|Cbln1|12404|cerebellin 1 precursor protein	BC132120|Cbln1|12404|cerebellin 1 precursor protein	BC132122|Cbln1|12404|cerebellin 1 precursor protein
mm9_v1_chr12_-_4344470_4344503	2.36132	SOX2.p2	U64606|Ncoa1|17977|nuclear receptor coactivator 1	BC068177|Ncoa1|17977|nuclear receptor coactivator 1
mm9_v1_chr11_-_102758460_102758513	2.35691	SOX2.p2	BC139357|Gfap|14580|glial fibrillary acidic protein	BC139358|Gfap|14580|glial fibrillary acidic protein	NM_001131020|Gfap|14580|glial fibrillary acidic protein	NM_010277|Gfap|14580|glial fibrillary acidic protein
mm9_v1_chr3_+_154374096_154374176	2.3541	SOX2.p2	AK076632|4922501L14Rik|209601|RIKEN cDNA 4922501L14 gene	NM_175176|4922501L14Rik|209601|RIKEN cDNA 4922501L14 gene	BC138236|4922501L14Rik|209601|RIKEN cDNA 4922501L14 gene	BC145840|4922501L14Rik|209601|RIKEN cDNA 4922501L14 gene
mm9_v1_chr1_-_159038775_159038780	2.35355	SOX2.p2	BC099580|1700057K13Rik|73435|RIKEN cDNA 1700057K13 gene	NM_028540|1700057K13Rik|73435|RIKEN cDNA 1700057K13 gene	BC115790|1700057K13Rik|73435|RIKEN cDNA 1700057K13 gene	AK006825|1700057K13Rik|73435|RIKEN cDNA 1700057K13 gene
mm9_v1_chr14_+_119187092_119187139	2.34837	SOX2.p2	NM_001160096|Cldn10|58187|claudin 10	NM_001160097|Cldn10|58187|claudin 10	NM_001160098|Cldn10|58187|claudin 10	NM_023878|Cldn10|58187|claudin 10	AK020131|Cldn10|58187|claudin 10	BC021770|Cldn10|58187|claudin 10
mm9_v1_chr4_+_21774729_21774865	2.3354	SOX2.p2	NM_025669|Sfrs18|66625|serine/arginine-rich splicing factor 18	BC141031|Sfrs18|66625|serine/arginine-rich splicing factor 18
mm9_v1_chr8_+_85689973_85690078	2.33154	SOX2.p2	AK134614|Tbc1d9|71310|TBC1 domain family, member 9	AK173050|Tbc1d9|71310|TBC1 domain family, member 9
mm9_v1_chr1_-_170361525_170361683	2.33133	SOX2.p2	BC002244|Pbx1|18514|pre B-cell leukemia transcription factor 1	AB221563|Pbx1|18514|pre B-cell leukemia transcription factor 1	HM369110|Pbx1|18514|pre B-cell leukemia transcription factor 1	L27453|Pbx1|18514|pre B-cell leukemia transcription factor 1
mm9_v1_chr13_-_106084378_106084564	2.33126	SOX2.p2	AK157911|Rnf180|71816|ring finger protein 180	AK032259|Rnf180|71816|ring finger protein 180	AK151379|Rnf180|71816|ring finger protein 180	AK152404|Rnf180|71816|ring finger protein 180	BC046775|Rnf180|71816|ring finger protein 180	BC075700|Rnf180|71816|ring finger protein 180
mm9_v1_chr7_-_90883999_90884032	2.32884	SOX2.p2	AF175292|Il16|16170|interleukin 16	NM_010551|Il16|16170|interleukin 16	AK220455|Il16|16170|interleukin 16	BC058709|Il16|16170|interleukin 16
mm9_v1_chr2_+_68495940_68495940	2.32797	SOX2.p2	AK016523|4932414N04Rik|75721|RIKEN cDNA 4932414N04 gene	NM_183113|4932414N04Rik|75721|RIKEN cDNA 4932414N04 gene
mm9_v1_chr11_+_116780161_116780176	2.32145	SOX2.p2	BC063084|Mgat5b|268510|mannoside acetylglucosaminyltransferase 5, isoenzyme B	BC094604|Mgat5b|268510|mannoside acetylglucosaminyltransferase 5, isoenzyme B	NM_172948|Mgat5b|268510|mannoside acetylglucosaminyltransferase 5, isoenzyme B
mm9_v1_chr13_+_88961034_88961117	2.32105	SOX2.p2	AF031525|Edil3|13612|EGF-like repeats and discoidin I-like domains 3	AK046885|Edil3|13612|EGF-like repeats and discoidin I-like domains 3	NM_001037987|Edil3|13612|EGF-like repeats and discoidin I-like domains 3	NM_010103|Edil3|13612|EGF-like repeats and discoidin I-like domains 3	AK157810|Edil3|13612|EGF-like repeats and discoidin I-like domains 3	AK141907|Edil3|13612|EGF-like repeats and discoidin I-like domains 3	AK135220|Edil3|13612|EGF-like repeats and discoidin I-like domains 3	AK139093|Edil3|13612|EGF-like repeats and discoidin I-like domains 3	AK036117|Edil3|13612|EGF-like repeats and discoidin I-like domains 3
mm9_v1_chr6_-_6832067_6832086	2.315	SOX2.p2	AF072452|Dlx5|13395|distal-less homeobox 5	AF072453|Dlx5|13395|distal-less homeobox 5	NM_010056|Dlx5|13395|distal-less homeobox 5	NM_198854|Dlx5|13395|distal-less homeobox 5	AK158121|Dlx5|13395|distal-less homeobox 5	U67840|Dlx5|13395|distal-less homeobox 5
mm9_v1_chr11_-_58996703_58996716	2.30448	SOX2.p2	AK046609|Gjc2|118454|gap junction protein, gamma 2	AY394498|Gjc2|118454|gap junction protein, gamma 2	NM_080454|Gjc2|118454|gap junction protein, gamma 2
mm9_v1_chrX_+_71002395_71002441	2.30268	SOX2.p2	AK138168|Plxnb3|140571|plexin B3	AK138631|Plxnb3|140571|plexin B3	AK140240|Plxnb3|140571|plexin B3	NM_019587|Plxnb3|140571|plexin B3
mm9_v1_chr2_+_156246644_156246847	2.29904	SOX2.p2	AK147611|Epb4.1l1|13821|erythrocyte protein band 4.1-like 1	AK147272|Epb4.1l1|13821|erythrocyte protein band 4.1-like 1	AK165479|Epb4.1l1|13821|erythrocyte protein band 4.1-like 1	NM_001003815|Epb4.1l1|13821|erythrocyte protein band 4.1-like 1	NM_013510|Epb4.1l1|13821|erythrocyte protein band 4.1-like 1	AK044744|Epb4.1l1|13821|erythrocyte protein band 4.1-like 1	AK154704|Epb4.1l1|13821|erythrocyte protein band 4.1-like 1	AF061283|Epb4.1l1|13821|erythrocyte protein band 4.1-like 1	BC034751|Epb4.1l1|13821|erythrocyte protein band 4.1-like 1
mm9_v1_chr15_-_96471920_96471958	2.29832	SOX2.p2	AK047459|Slc38a1|105727|solute carrier family 38, member 1	AK165188|Slc38a1|105727|solute carrier family 38, member 1
mm9_v1_chr12_+_110782654_110782752	2.29114	SOX2.p2	BC024818|Meg3|17263|maternally expressed 3
mm9_v1_chr16_+_5884885_5884885	2.28777	SOX2.p2	BC053009|Rbfox1|268859|RNA binding protein, fox-1 homolog (C. elegans) 1	NM_021477|Rbfox1|268859|RNA binding protein, fox-1 homolog (C. elegans) 1
mm9_v1_chr8_-_83262881_83263070	2.28013	SOX2.p2	AF325921|Smarca5|93762|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	BC009130|Smarca5|93762|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	AF375046|Smarca5|93762|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5
mm9_v1_chr2_+_154262286_154262318	2.28	SOX2.p2	BC138410|Cbfa2t2|12396|core-binding factor, runt domain, alpha subunit 2, translocated to, 2 (human)	BC145266|Cbfa2t2|12396|core-binding factor, runt domain, alpha subunit 2, translocated to, 2 (human)	BC145679|Cbfa2t2|12396|core-binding factor, runt domain, alpha subunit 2, translocated to, 2 (human)	AK153602|Cbfa2t2|12396|core-binding factor, runt domain, alpha subunit 2, translocated to, 2 (human)
mm9_v1_chr4_+_138012860_138012969	2.27832	SOX2.p2	AK021100|Camk2n1|66259|calcium/calmodulin-dependent protein kinase II inhibitor 1
mm9_v1_chr9_-_49606959_49607009	2.27648	SOX2.p2	AK053403|Ncam1|17967|neural cell adhesion molecule 1	BC062942|Ncam1|17967|neural cell adhesion molecule 1	X15049|Ncam1|17967|neural cell adhesion molecule 1	Y00051|Ncam1|17967|neural cell adhesion molecule 1
mm9_v1_chr1_-_52784161_52784228	2.27645	SOX2.p2	AK035995|Mfsd6|98682|major facilitator superfamily domain containing 6	NM_133829|Mfsd6|98682|major facilitator superfamily domain containing 6	NM_178081|Mfsd6|98682|major facilitator superfamily domain containing 6	AK171946|Mfsd6|98682|major facilitator superfamily domain containing 6
mm9_v1_chr12_+_81619976_81620155	2.27316	SOX2.p2	NM_001081421|Galntl1|108760|UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 1	AB045325|Galntl1|108760|UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 1	AK138883|Galntl1|108760|UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 1	AB175683|Galntl1|108760|UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 1
mm9_v1_chr11_-_99982808_99982882	2.27149	SOX2.p2	NM_010662|Krt13|16663|keratin 13	BC060286|Krt13|16663|keratin 13	AK004635|Krt13|16663|keratin 13	AK010156|Krt13|16663|keratin 13	AK132640|Krt13|16663|keratin 13
mm9_v1_chr4_+_120204835_120204835	2.27139	SOX2.p2	AK077106|Slfnl1|194219|schlafen like 1	NM_177570|Slfnl1|194219|schlafen like 1
mm9_v1_chr9_-_60535274_60535340	2.26742	SOX2.p2	AK051325|Lrrc49|102747|leucine rich repeat containing 49	NM_001146047|Lrrc49|102747|leucine rich repeat containing 49
mm9_v1_chr1_+_138027943_138028013	2.26602	SOX2.p2	NM_001039472|Kif21b|16565|kinesin family member 21B
mm9_v1_chr11_-_78311204_78311255	2.26303	SOX2.p2	BC058534|Sarm1|237868|sterile alpha and HEAT/Armadillo motif containing 1	BC080850|Sarm1|237868|sterile alpha and HEAT/Armadillo motif containing 1	NM_001168521|Sarm1|237868|sterile alpha and HEAT/Armadillo motif containing 1	NM_172795|Sarm1|237868|sterile alpha and HEAT/Armadillo motif containing 1
mm9_v1_chr16_-_36334417_36334427	2.26157	SOX2.p2	AY169235|BC117090|100038854|cDNA sequence BC1179090	BC117064|BC117090|100038854|cDNA sequence BC1179090	BC117090|BC117090|100038854|cDNA sequence BC1179090	NM_001001332|BC117090|100038854|cDNA sequence BC1179090
mm9_v1_chr6_+_86578225_86578230	2.26026	SOX2.p2	AK160494|Asprv1|67855|aspartic peptidase, retroviral-like 1
mm9_v1_chr9_+_39955706_39955790	2.24895	SOX2.p2	AK006538|Tmem225|75667|transmembrane protein 225	NM_029379|Tmem225|75667|transmembrane protein 225	BC116869|Tmem225|75667|transmembrane protein 225	BC116871|Tmem225|75667|transmembrane protein 225
mm9_v1_chr7_+_34806501_34806586	2.2454	SOX2.p2	BC132436|Abpa|11354|androgen binding protein alpha	BC016132|Abpa|11354|androgen binding protein alpha	NM_009596|Abpa|11354|androgen binding protein alpha	GU269231|Abpa|11354|androgen binding protein alpha
mm9_v1_chr17_+_44090192_44090211	2.24501	SOX2.p2	AB061524|Rcan2|53901|regulator of calcineurin 2	AK049006|Rcan2|53901|regulator of calcineurin 2
mm9_v1_chr11_+_42234760_42234851	2.24338	SOX2.p2	U14419|Gabrb2|14401|gamma-aminobutyric acid (GABA) A receptor, subunit beta 2	AK034069|Gabrb2|14401|gamma-aminobutyric acid (GABA) A receptor, subunit beta 2	GU086167|Gabrb2|14401|gamma-aminobutyric acid (GABA) A receptor, subunit beta 2
mm9_v1_chr1_-_38878059_38878110	2.23545	SOX2.p2	NM_001029878|Lonrf2|381338|LON peptidase N-terminal domain and ring finger 2	BC139127|Lonrf2|381338|LON peptidase N-terminal domain and ring finger 2	BC139130|Lonrf2|381338|LON peptidase N-terminal domain and ring finger 2
mm9_v1_chr19_+_4711207_4711210	2.22996	SOX2.p2	AK147671|Spnb3|20743|spectrin beta 3
mm9_v1_chr14_+_14286471_14286627	2.22889	SOX2.p2	NM_001163032|Synpr|72003|synaptoporin	AK033999|Synpr|72003|synaptoporin	AK032442|Synpr|72003|synaptoporin	AK045705|Synpr|72003|synaptoporin	AK049661|Synpr|72003|synaptoporin
mm9_v1_chr3_-_66100663_66100758	2.22686	SOX2.p2	AK164725|Veph1|72789|ventricular zone expressed PH domain homolog 1 (zebrafish)	AB085187|Veph1|72789|ventricular zone expressed PH domain homolog 1 (zebrafish)	NM_145820|Veph1|72789|ventricular zone expressed PH domain homolog 1 (zebrafish)	BC075649|Veph1|72789|ventricular zone expressed PH domain homolog 1 (zebrafish)
mm9_v1_chr7_-_53069599_53069692	2.22183	SOX2.p2	BC004662|Cyth2|19158|cytohesin 2	AB013466|Cyth2|19158|cytohesin 2	AK168979|Cyth2|19158|cytohesin 2	AK143829|Cyth2|19158|cytohesin 2	AK172050|Cyth2|19158|cytohesin 2	AF079971|Cyth2|19158|cytohesin 2	AK045451|Cyth2|19158|cytohesin 2	BC088833|Cyth2|19158|cytohesin 2	AK078067|Cyth2|19158|cytohesin 2	NM_001112701|Cyth2|19158|cytohesin 2	NM_011181|Cyth2|19158|cytohesin 2
mm9_v1_chr6_-_122287014_122287032	2.20846	SOX2.p2	U63386|Phc1|13619|polyhomeotic-like 1 (Drosophila)	NM_001042623|Phc1|13619|polyhomeotic-like 1 (Drosophila)	NM_007905|Phc1|13619|polyhomeotic-like 1 (Drosophila)
mm9_v1_chr6_+_86578550_86578720	2.20493	SOX2.p2	BC119099|Asprv1|67855|aspartic peptidase, retroviral-like 1	BC119101|Asprv1|67855|aspartic peptidase, retroviral-like 1	AK004007|Asprv1|67855|aspartic peptidase, retroviral-like 1
mm9_v1_chrX_-_140367467_140367853	2.202	SOX2.p2	AY560329|Dcx|13193|doublecortin	AK048410|Dcx|13193|doublecortin	AF045547|Dcx|13193|doublecortin	AK164119|Dcx|13193|doublecortin	BC056391|Dcx|13193|doublecortin	AK049050|Dcx|13193|doublecortin	NM_001110222|Dcx|13193|doublecortin	BC057010|Dcx|13193|doublecortin	BC062974|Dcx|13193|doublecortin	AK014264|Dcx|13193|doublecortin	NM_001110223|Dcx|13193|doublecortin	NM_001110224|Dcx|13193|doublecortin	NM_010025|Dcx|13193|doublecortin	AB011678|Dcx|13193|doublecortin
mm9_v1_chr4_-_148500769_148500849	2.19831	SOX2.p2	AF013253|Cort|12854|cortistatin	AK013496|Cort|12854|cortistatin	NM_007745|Cort|12854|cortistatin
mm9_v1_chrX_+_20281028_20281089	2.194	SOX2.p2	NM_145628|Usp11|236733|ubiquitin specific peptidase 11	AK031767|Usp11|236733|ubiquitin specific peptidase 11	AK166523|Usp11|236733|ubiquitin specific peptidase 11	AK049053|Usp11|236733|ubiquitin specific peptidase 11
mm9_v1_chr3_-_127540408_127540409	2.19114	SOX2.p2	NM_145964|Ap1ar|211556|adaptor-related protein complex 1 associated regulatory protein
mm9_v1_chr3_+_152009436_152009469	2.19015	SOX2.p2	AK087467|Usp33|170822|ubiquitin specific peptidase 33	NM_001076676|Usp33|170822|ubiquitin specific peptidase 33	NM_133247|Usp33|170822|ubiquitin specific peptidase 33	AF383174|Usp33|170822|ubiquitin specific peptidase 33	AK082251|Usp33|170822|ubiquitin specific peptidase 33	AK082943|Usp33|170822|ubiquitin specific peptidase 33
mm9_v1_chr18_-_10706693_10706710	2.18872	SOX2.p2	AF429302|Abhd3|106861|abhydrolase domain containing 3	BC026770|Abhd3|106861|abhydrolase domain containing 3	NM_134130|Abhd3|106861|abhydrolase domain containing 3	AK134676|Abhd3|106861|abhydrolase domain containing 3	AK144238|Abhd3|106861|abhydrolase domain containing 3
mm9_v1_chr3_+_93246251_93246251	2.18503	SOX2.p2	NM_001163098|Tchh|99681|trichohyalin
mm9_v1_chr4_-_134409254_134409295	2.18425	SOX2.p2	AY846873|Tmem57|66146|transmembrane protein 57	AY846874|Tmem57|66146|transmembrane protein 57	NM_025382|Tmem57|66146|transmembrane protein 57
mm9_v1_chr4_+_108132023_108132030	2.18369	SOX2.p2	AK041821|Zcchc11|230594|zinc finger, CCHC domain containing 11	NM_175472|Zcchc11|230594|zinc finger, CCHC domain containing 11
mm9_v1_chr19_-_41922577_41922621	2.18321	SOX2.p2	BC034214|Frat2|212398|frequently rearranged in advanced T-cell lymphomas 2	BC085510|Frat2|212398|frequently rearranged in advanced T-cell lymphomas 2	AK081171|Frat2|212398|frequently rearranged in advanced T-cell lymphomas 2	NM_177603|Frat2|212398|frequently rearranged in advanced T-cell lymphomas 2
mm9_v1_chr1_+_179375951_179375951	2.18072	SOX2.p2	AF140224|Zfp238|30928|zinc finger protein 238	NM_013915|Zfp238|30928|zinc finger protein 238
mm9_v1_chr13_+_42775991_42775991	2.17782	SOX2.p2	NM_198419|Phactr1|218194|phosphatase and actin regulator 1
mm9_v1_chr18_+_23910833_23910892	2.16575	SOX2.p2	AK158570|Mapre2|212307|microtubule-associated protein, RP/EB family, member 2	NM_001162942|Mapre2|212307|microtubule-associated protein, RP/EB family, member 2	AK168834|Mapre2|212307|microtubule-associated protein, RP/EB family, member 2
mm9_v1_chr1_+_167415313_167415432	2.16448	SOX2.p2	AK029849|Adcy10|271639|adenylate cyclase 10	AK133181|Adcy10|271639|adenylate cyclase 10	NM_173029|Adcy10|271639|adenylate cyclase 10	AK015262|Adcy10|271639|adenylate cyclase 10	BC138448|Adcy10|271639|adenylate cyclase 10	BC145283|Adcy10|271639|adenylate cyclase 10
mm9_v1_chr8_-_70434808_70434844	2.16356	SOX2.p2	BC052365|Psd3|234353|pleckstrin and Sec7 domain containing 3	AK161498|Psd3|234353|pleckstrin and Sec7 domain containing 3	NM_030263|Psd3|234353|pleckstrin and Sec7 domain containing 3
mm9_v1_chr7_+_97575023_97575086	2.161	SOX2.p2	BC060150|Ccdc89|70054|coiled-coil domain containing 89
mm9_v1_chr11_-_58996318_58996331	2.15855	SOX2.p2	AK046421|Gjc2|118454|gap junction protein, gamma 2	NM_175452|Gjc2|118454|gap junction protein, gamma 2
mm9_v1_chr11_-_41814008_41814185	2.15833	SOX2.p2	M86572|Gabrg2|14406|gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2	BC031762|Gabrg2|14406|gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2	M62374|Gabrg2|14406|gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2	NM_008073|Gabrg2|14406|gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2	AK034338|Gabrg2|14406|gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2
mm9_v1_chr9_+_57982471_57982471	2.15703	SOX2.p2	NM_001162479|Stra6|20897|stimulated by retinoic acid gene 6
mm9_v1_chr6_-_135204232_135204353	2.15562	SOX2.p2	D87325|Gsg1|14840|germ cell-specific gene 1	NM_001080553|Gsg1|14840|germ cell-specific gene 1	NM_010352|Gsg1|14840|germ cell-specific gene 1
mm9_v1_chr5_-_86947601_86947624	2.15176	SOX2.p2	BC118660|9930032O22Rik|320454|RIKEN cDNA 9930032O22 gene	BC118611|9930032O22Rik|320454|RIKEN cDNA 9930032O22 gene	AK036981|9930032O22Rik|320454|RIKEN cDNA 9930032O22 gene	NM_177162|9930032O22Rik|320454|RIKEN cDNA 9930032O22 gene
mm9_v1_chr16_-_50591201_50591266	2.14661	SOX2.p2	AK005741|Ccdc54|69339|coiled-coil domain containing 54	BC049741|Ccdc54|69339|coiled-coil domain containing 54	NM_027046|Ccdc54|69339|coiled-coil domain containing 54
mm9_v1_chr2_-_56976413_56976478	2.14585	SOX2.p2	NM_001139509|Nr4a2|18227|nuclear receptor subfamily 4, group A, member 2
mm9_v1_chrX_+_68809103_68809115	2.14317	SOX2.p2	AK159119|Hmgb3|15354|high mobility group box 3	AK159322|Hmgb3|15354|high mobility group box 3
mm9_v1_chr8_-_8690519_8690552	2.14072	SOX2.p2	BC046971|Arglu1|234023|arginine and glutamate rich 1	NM_176849|Arglu1|234023|arginine and glutamate rich 1
mm9_v1_chr4_-_155159937_155159982	2.13769	SOX2.p2	BC147318|Tmem88b|320587|transmembrane protein 88B	BC147319|Tmem88b|320587|transmembrane protein 88B	AK035998|Tmem88b|320587|transmembrane protein 88B	AK158459|Tmem88b|320587|transmembrane protein 88B	NM_001033394|Tmem88b|320587|transmembrane protein 88B
mm9_v1_chrX_-_47141382_47141419	2.13765	SOX2.p2	BC119264|Igsf1|209268|immunoglobulin superfamily, member 1	BC119266|Igsf1|209268|immunoglobulin superfamily, member 1	BC144762|Igsf1|209268|immunoglobulin superfamily, member 1	AK076427|Igsf1|209268|immunoglobulin superfamily, member 1	AY227774|Igsf1|209268|immunoglobulin superfamily, member 1	AK030701|Igsf1|209268|immunoglobulin superfamily, member 1	NM_183336|Igsf1|209268|immunoglobulin superfamily, member 1
mm9_v1_chr5_-_110772051_110772230	2.13751	SOX2.p2	NM_001164833|P2rx2|231602|purinergic receptor P2X, ligand-gated ion channel, 2	NM_001164834|P2rx2|231602|purinergic receptor P2X, ligand-gated ion channel, 2	NM_153400|P2rx2|231602|purinergic receptor P2X, ligand-gated ion channel, 2	BC106963|P2rx2|231602|purinergic receptor P2X, ligand-gated ion channel, 2	BC106964|P2rx2|231602|purinergic receptor P2X, ligand-gated ion channel, 2	AY044240|P2rx2|231602|purinergic receptor P2X, ligand-gated ion channel, 2
mm9_v1_chr11_+_98667577_98667599	2.13536	SOX2.p2	AK031902|Msl1|74026|male-specific lethal 1 homolog (Drosophila)
mm9_v1_chr19_-_7877136_7877156	2.13339	SOX2.p2	BC014805|BC014805|236149|cDNA sequence BC014805	NM_146232|BC014805|236149|cDNA sequence BC014805
mm9_v1_chr11_+_78156930_78157077	2.12804	SOX2.p2	AF030169|Unc119|22248|unc-119 homolog (C. elegans)	AK131955|Unc119|22248|unc-119 homolog (C. elegans)	BC001990|Unc119|22248|unc-119 homolog (C. elegans)	NM_011676|Unc119|22248|unc-119 homolog (C. elegans)
mm9_v1_chr15_-_95358578_95358610	2.12686	SOX2.p2	AK048913|Nell2|54003|NEL-like 2 (chicken)
mm9_v1_chr1_-_170085342_170085390	2.12378	SOX2.p2	AK083616|Pbx1|18514|pre B-cell leukemia transcription factor 1
mm9_v1_chr5_+_121099226_121099366	2.12109	SOX2.p2	AK156050|Rasal1|19415|RAS protein activator like 1 (GAP1 like)	AF086714|Rasal1|19415|RAS protein activator like 1 (GAP1 like)
mm9_v1_chr8_-_67071497_67071512	2.12089	SOX2.p2	
mm9_v1_chrX_-_108651553_108651553	2.12012	SOX2.p2	NM_025949|Rps6ka6|67071|ribosomal protein S6 kinase polypeptide 6
mm9_v1_chr12_+_86337250_86337338	2.11887	SOX2.p2	AK044440|Ylpm1|56531|YLP motif containing 1	NM_178363|Ylpm1|56531|YLP motif containing 1	BC031541|Ylpm1|56531|YLP motif containing 1	AK087500|Ylpm1|56531|YLP motif containing 1	AB033168|Ylpm1|56531|YLP motif containing 1
mm9_v1_chr13_-_58228748_58228812	2.1177	SOX2.p2	BC023150|Hnrnpa0|77134|heterogeneous nuclear ribonucleoprotein A0
mm9_v1_chr13_-_8870231_8870293	2.11692	SOX2.p2	AK129254|Wdr37|207615|WD repeat domain 37	AK032582|Wdr37|207615|WD repeat domain 37	AK146209|Wdr37|207615|WD repeat domain 37	AK014128|Wdr37|207615|WD repeat domain 37	AK044740|Wdr37|207615|WD repeat domain 37	AK036203|Wdr37|207615|WD repeat domain 37	NM_001039389|Wdr37|207615|WD repeat domain 37	NM_172445|Wdr37|207615|WD repeat domain 37
mm9_v1_chr6_-_149050067_149050107	2.10811	SOX2.p2	AK135015|Dennd5b|320560|DENN/MADD domain containing 5B	AK038858|Dennd5b|320560|DENN/MADD domain containing 5B
mm9_v1_chr1_-_141273617_141273676	2.10806	SOX2.p2	AF406641|Crb1|170788|crumbs homolog 1 (Drosophila)	AY450552|Crb1|170788|crumbs homolog 1 (Drosophila)	NM_133239|Crb1|170788|crumbs homolog 1 (Drosophila)	AF492496|Crb1|170788|crumbs homolog 1 (Drosophila)
mm9_v1_chr6_+_64992584_64992660	2.10354	SOX2.p2	NM_007958|Smarcad1|13990|SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	X69942|Smarcad1|13990|SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1
mm9_v1_chr4_-_115453621_115453638	2.09873	SOX2.p2	BC119474|4930544O15Rik|75173|RIKEN cDNA 4930544O15 gene	BC152479|4930544O15Rik|75173|RIKEN cDNA 4930544O15 gene	AK016041|4930544O15Rik|75173|RIKEN cDNA 4930544O15 gene	NM_029196|4930544O15Rik|75173|RIKEN cDNA 4930544O15 gene
mm9_v1_chr5_-_110771973_110772012	2.09396	SOX2.p2	AB094663|P2rx2|231602|purinergic receptor P2X, ligand-gated ion channel, 2	AB094664|P2rx2|231602|purinergic receptor P2X, ligand-gated ion channel, 2	AK158334|P2rx2|231602|purinergic receptor P2X, ligand-gated ion channel, 2	AK141196|P2rx2|231602|purinergic receptor P2X, ligand-gated ion channel, 2
mm9_v1_chr3_-_38383688_38383798	2.09329	SOX2.p2	AK129484|Ankrd50|99696|ankyrin repeat domain 50	NM_001167883|Ankrd50|99696|ankyrin repeat domain 50
mm9_v1_chr14_-_118450875_118451546	2.09016	SOX2.p2	EU554632|Dct|13190|dopachrome tautomerase	AK214181|Dct|13190|dopachrome tautomerase	AK214448|Dct|13190|dopachrome tautomerase	AK217087|Dct|13190|dopachrome tautomerase	AK212164|Dct|13190|dopachrome tautomerase	AK219002|Dct|13190|dopachrome tautomerase	BC082330|Dct|13190|dopachrome tautomerase	AK209892|Dct|13190|dopachrome tautomerase	AK191654|Dct|13190|dopachrome tautomerase	BC067064|Dct|13190|dopachrome tautomerase	X63349|Dct|13190|dopachrome tautomerase	AK033040|Dct|13190|dopachrome tautomerase	NM_010024|Dct|13190|dopachrome tautomerase	AK202452|Dct|13190|dopachrome tautomerase
mm9_v1_chr3_+_130813214_130813388	2.08914	SOX2.p2	BC057543|Lef1|16842|lymphoid enhancer binding factor 1	AK131979|Lef1|16842|lymphoid enhancer binding factor 1	AK158769|Lef1|16842|lymphoid enhancer binding factor 1	NM_010703|Lef1|16842|lymphoid enhancer binding factor 1	X58636|Lef1|16842|lymphoid enhancer binding factor 1
mm9_v1_chr12_-_60305853_60305917	2.08271	SOX2.p2	BC006669|Fbxo33|70611|F-box protein 33
mm9_v1_chrX_-_131285919_131285957	2.07513	SOX2.p2	BC027264|Armcx6|278097|armadillo repeat containing, X-linked 6	AK148507|Armcx6|278097|armadillo repeat containing, X-linked 6	AK160766|Armcx6|278097|armadillo repeat containing, X-linked 6	NM_001007578|Armcx6|278097|armadillo repeat containing, X-linked 6
mm9_v1_chr4_+_83063621_83063661	2.07172	SOX2.p2	AK049933|Snapc3|77634|small nuclear RNA activating complex, polypeptide 3	AK016168|Snapc3|77634|small nuclear RNA activating complex, polypeptide 3	AK007563|Snapc3|77634|small nuclear RNA activating complex, polypeptide 3	AK010932|Snapc3|77634|small nuclear RNA activating complex, polypeptide 3	AK031870|Snapc3|77634|small nuclear RNA activating complex, polypeptide 3	AK031924|Snapc3|77634|small nuclear RNA activating complex, polypeptide 3	BC048713|Snapc3|77634|small nuclear RNA activating complex, polypeptide 3	NM_029949|Snapc3|77634|small nuclear RNA activating complex, polypeptide 3	AK019863|Snapc3|77634|small nuclear RNA activating complex, polypeptide 3
mm9_v1_chr19_+_44368557_44368575	2.07143	SOX2.p2	AK083922|Scd2|20250|stearoyl-Coenzyme A desaturase 2
mm9_v1_chr19_-_19185685_19185685	2.07067	SOX2.p2	NM_001043354|Rorb|225998|RAR-related orphan receptor beta
mm9_v1_chr16_-_98072833_98072833	2.07033	SOX2.p2	NM_144789|Prdm15|114604|PR domain containing 15
mm9_v1_chr17_+_26551909_26551909	2.06753	SOX2.p2	DQ839448|Neurl1b|240055|neuralized homolog 1b (Drosophila)	GQ414760|Neurl1b|240055|neuralized homolog 1b (Drosophila)	NM_001081656|Neurl1b|240055|neuralized homolog 1b (Drosophila)
mm9_v1_chrX_-_69901382_69901584	2.05591	SOX2.p2	BC119317|Gabra3|14396|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 3	BC120686|Gabra3|14396|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 3	M86568|Gabra3|14396|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 3	AK134760|Gabra3|14396|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 3	AK039144|Gabra3|14396|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 3	NM_008067|Gabra3|14396|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 3
mm9_v1_chr5_+_77269623_77269643	2.04968	SOX2.p2	AK030106|C530008M17Rik|320827|RIKEN cDNA C530008M17 gene	NM_001163793|C530008M17Rik|320827|RIKEN cDNA C530008M17 gene	AK015929|C530008M17Rik|320827|RIKEN cDNA C530008M17 gene
mm9_v1_chrY_-_1976583_1976583	2.0495	SOX2.p2	EU315689|Gm6026|547210|predicted gene 6026	NM_001113395|Gm16501|100042840|predicted gene 16501	NM_001177569|Gm6026|547210|predicted gene 6026
mm9_v1_chr3_+_92211912_92211941	2.04545	SOX2.p2	AY158993|Sprr2i|20763|small proline-rich protein 2I	NM_011475|Sprr2i|20763|small proline-rich protein 2I	BC120622|Sprr2i|20763|small proline-rich protein 2I
mm9_v1_chr1_-_33871218_33871259	2.04481	SOX2.p2	BC062154|Zfp451|98403|zinc finger protein 451
mm9_v1_chr15_-_96473193_96473343	2.0436	SOX2.p2	AK162612|Slc38a1|105727|solute carrier family 38, member 1	AK081724|Slc38a1|105727|solute carrier family 38, member 1	NM_001166458|Slc38a1|105727|solute carrier family 38, member 1
mm9_v1_chr5_+_35341726_35341726	2.04357	SOX2.p2	AK014569|Rgs12|71729|regulator of G-protein signaling 12	AK161129|Rgs12|71729|regulator of G-protein signaling 12	NM_001163512|Rgs12|71729|regulator of G-protein signaling 12
mm9_v1_chr6_-_128493413_128493444	2.0427	SOX2.p2	BC048546|BC048546|232400|cDNA sequence BC048546
mm9_v1_chr8_+_26960094_26960127	2.03909	SOX2.p2	NM_008432|Kcnu1|16532|potassium channel, subfamily U, member 1	AF039213|Kcnu1|16532|potassium channel, subfamily U, member 1
mm9_v1_chr6_+_40914752_40914770	2.0345	SOX2.p2	BC132243|1810009J06Rik|73626|RIKEN cDNA 1810009J06 gene	BC132245|1810009J06Rik|73626|RIKEN cDNA 1810009J06 gene	AK007406|1810009J06Rik|73626|RIKEN cDNA 1810009J06 gene	NM_023707|1810009J06Rik|73626|RIKEN cDNA 1810009J06 gene
mm9_v1_chr16_-_14159346_14159388	2.03267	SOX2.p2	AK158881|4921513D23Rik|223989|RIKEN cDNA 4921513D23 gene	NM_001081154|4921513D23Rik|223989|RIKEN cDNA 4921513D23 gene
mm9_v1_chr7_+_127883070_127883070	2.03089	SOX2.p2	AK132732|Vwa3a|233813|von Willebrand factor A domain containing 3A	NM_177697|Vwa3a|233813|von Willebrand factor A domain containing 3A
mm9_v1_chr18_+_37637421_37637642	2.02932	SOX2.p2	NM_053141|Pcdhb16|93887|protocadherin beta 16	AK030612|Pcdhb16|93887|protocadherin beta 16	AK036829|Pcdhb16|93887|protocadherin beta 16	BC115720|Pcdhb16|93887|protocadherin beta 16	BC116625|Pcdhb16|93887|protocadherin beta 16	AY013777|Pcdhb16|93887|protocadherin beta 16
mm9_v1_chr6_-_6831907_6832001	2.02627	SOX2.p2	AF033011|Dlx5|13395|distal-less homeobox 5	AF022075|Dlx5|13395|distal-less homeobox 5	AF022076|Dlx5|13395|distal-less homeobox 5	AF022077|Dlx5|13395|distal-less homeobox 5	AK134920|Dlx5|13395|distal-less homeobox 5	AK158772|Dlx5|13395|distal-less homeobox 5
mm9_v1_chr18_+_37979242_37979328	2.02105	SOX2.p2	BC138677|Pcdhgc5|93708|protocadherin gamma subfamily C, 5	AF464160|Pcdhgc5|93708|protocadherin gamma subfamily C, 5	AY013813|Pcdhgc5|93708|protocadherin gamma subfamily C, 5
mm9_v1_chr6_-_132264751_132264774	2.01838	SOX2.p2	BC055856|Prpmp5|381832|proline-rich protein MP5	BC061494|Prpmp5|381832|proline-rich protein MP5	BC080748|Prpmp5|381832|proline-rich protein MP5	BC092075|Prpmp5|381832|proline-rich protein MP5	BC110664|Prpmp5|381832|proline-rich protein MP5	NM_001024705|Prpmp5|381832|proline-rich protein MP5	AK132583|Prpmp5|381832|proline-rich protein MP5
mm9_v1_chr1_-_89283173_89283296	2.01758	SOX2.p2	
mm9_v1_chr2_+_121183509_121183535	2.01489	SOX2.p2	BC025976|Ckmt1|12716|creatine kinase, mitochondrial 1, ubiquitous
mm9_v1_chr18_+_37656644_37656807	2.0105	SOX2.p2	AK029163|Pcdhb19|93890|protocadherin beta 19	AK147520|Pcdhb19|93890|protocadherin beta 19	AK160654|Pcdhb19|93890|protocadherin beta 19	NM_053144|Pcdhb19|93890|protocadherin beta 19	AK046363|Pcdhb19|93890|protocadherin beta 19	BC141290|Pcdhb19|93890|protocadherin beta 19	BC141291|Pcdhb19|93890|protocadherin beta 19	AF326312|Pcdhb19|93890|protocadherin beta 19	AY013780|Pcdhb19|93890|protocadherin beta 19
mm9_v1_chr16_-_89508565_89508569	2.00839	SOX2.p2	AK017387|Krtap7-1|71363|keratin associated protein 7-1	NM_027771|Krtap7-1|71363|keratin associated protein 7-1
mm9_v1_chr1_-_168168870_168168874	2.00401	SOX2.p2	AK077103|Mael|98558|maelstrom homolog (Drosophila)	AK165801|Mael|98558|maelstrom homolog (Drosophila)	BC050800|Mael|98558|maelstrom homolog (Drosophila)	NM_175296|Mael|98558|maelstrom homolog (Drosophila)
mm9_v1_chr12_-_15822792_15822800	2.00389	SOX2.p2	AK080064|Trib2|217410|tribbles homolog 2 (Drosophila)	AK082329|Trib2|217410|tribbles homolog 2 (Drosophila)
mm9_v1_chrX_-_131343508_131343539	2.00261	SOX2.p2	BC052383|Armcx2|67416|armadillo repeat containing, X-linked 2	BC049088|Armcx2|67416|armadillo repeat containing, X-linked 2	AK144319|Armcx2|67416|armadillo repeat containing, X-linked 2	AK034621|Armcx2|67416|armadillo repeat containing, X-linked 2	AK053354|Armcx2|67416|armadillo repeat containing, X-linked 2	AK044926|Armcx2|67416|armadillo repeat containing, X-linked 2	AK014329|Armcx2|67416|armadillo repeat containing, X-linked 2	AK034185|Armcx2|67416|armadillo repeat containing, X-linked 2	AK043440|Armcx2|67416|armadillo repeat containing, X-linked 2	AK081299|Armcx2|67416|armadillo repeat containing, X-linked 2
mm9_v1_chr8_-_89996474_89996540	2.00028	SOX2.p2	AK158818|Cbln1|12404|cerebellin 1 precursor protein	NM_019626|Cbln1|12404|cerebellin 1 precursor protein	AK158885|Cbln1|12404|cerebellin 1 precursor protein
mm9_v1_chr18_-_15222079_15222098	1.99941	SOX2.p2	NM_001142731|Kctd1|106931|potassium channel tetramerisation domain containing 1
mm9_v1_chr7_+_132512374_132512374	1.99466	SOX2.p2	NM_001145759|4930571K23Rik|75861|RIKEN cDNA 4930571K23 gene
mm9_v1_chr12_+_110884340_110884400	1.99244	SOX2.p2	AF498294|Rian|75745|RNA imprinted and accumulated in nucleus	AB063319|Rian|75745|RNA imprinted and accumulated in nucleus	AK017440|Rian|75745|RNA imprinted and accumulated in nucleus
mm9_v1_chr11_-_101888199_101888275	1.98974	SOX2.p2	AF079366|Mpp3|13384|membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3)	BC062642|Mpp3|13384|membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3)	AK032270|Mpp3|13384|membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3)	AK047456|Mpp3|13384|membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3)	AK163205|Mpp3|13384|membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3)	NM_007863|Mpp3|13384|membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3)
mm9_v1_chr6_-_137519272_137519292	1.987	SOX2.p2	AK155022|Eps8|13860|epidermal growth factor receptor pathway substrate 8
mm9_v1_chr6_-_94233855_94233910	1.98526	SOX2.p2	AK046635|Magi1|14924|membrane associated guanylate kinase, WW and PDZ domain containing 1	BC095943|Magi1|14924|membrane associated guanylate kinase, WW and PDZ domain containing 1	NM_001029850|Magi1|14924|membrane associated guanylate kinase, WW and PDZ domain containing 1	NM_010367|Magi1|14924|membrane associated guanylate kinase, WW and PDZ domain containing 1	AK147358|Magi1|14924|membrane associated guanylate kinase, WW and PDZ domain containing 1
mm9_v1_chr10_-_79850388_79850445	1.98233	SOX2.p2	NM_198615|Mex3d|237400|mex3 homolog D (C. elegans)
mm9_v1_chr18_-_70212948_70213022	1.97815	SOX2.p2	BC032928|Rab27b|80718|RAB27b, member RAS oncogene family	AB067775|Rab27b|80718|RAB27b, member RAS oncogene family	AF328893|Rab27b|80718|RAB27b, member RAS oncogene family	BC018443|Rab27b|80718|RAB27b, member RAS oncogene family	NM_030554|Rab27b|80718|RAB27b, member RAS oncogene family
mm9_v1_chr7_+_26070287_26070322	1.97807	SOX2.p2	BC058665|Cic|71722|capicua homolog (Drosophila)
mm9_v1_chr4_+_155266340_155266446	1.97133	SOX2.p2	BC098196|Acap3|140500|ArfGAP with coiled-coil, ankyrin repeat and PH domains 3	BC025556|Acap3|140500|ArfGAP with coiled-coil, ankyrin repeat and PH domains 3
mm9_v1_chr5_+_143722032_143722059	1.96961	SOX2.p2	NM_007984|Fscn1|14086|fascin homolog 1, actin bundling protein (Strongylocentrotus purpuratus)	AK083935|Fscn1|14086|fascin homolog 1, actin bundling protein (Strongylocentrotus purpuratus)	AK167670|Fscn1|14086|fascin homolog 1, actin bundling protein (Strongylocentrotus purpuratus)	BC052408|Fscn1|14086|fascin homolog 1, actin bundling protein (Strongylocentrotus purpuratus)	BC029281|Fscn1|14086|fascin homolog 1, actin bundling protein (Strongylocentrotus purpuratus)	BC010338|Fscn1|14086|fascin homolog 1, actin bundling protein (Strongylocentrotus purpuratus)	BC037137|Fscn1|14086|fascin homolog 1, actin bundling protein (Strongylocentrotus purpuratus)	L33726|Fscn1|14086|fascin homolog 1, actin bundling protein (Strongylocentrotus purpuratus)
mm9_v1_chr12_-_113749313_113749357	1.96897	SOX2.p2	AK049973|Tmem179|104885|transmembrane protein 179	AK044254|Tmem179|104885|transmembrane protein 179
mm9_v1_chr7_+_16657269_16657290	1.96875	SOX2.p2	BC157962|Zfp541|666528|zinc finger protein 541	DQ864732|Zfp541|666528|zinc finger protein 541	NM_001099277|Zfp541|666528|zinc finger protein 541
mm9_v1_chr11_+_80290509_80290569	1.963	SOX2.p2	AK142868|Cdk5r1|12569|cyclin-dependent kinase 5, regulatory subunit 1 (p35)	AK086621|Cdk5r1|12569|cyclin-dependent kinase 5, regulatory subunit 1 (p35)	AK141549|Cdk5r1|12569|cyclin-dependent kinase 5, regulatory subunit 1 (p35)	AK169667|Cdk5r1|12569|cyclin-dependent kinase 5, regulatory subunit 1 (p35)	AK079557|Cdk5r1|12569|cyclin-dependent kinase 5, regulatory subunit 1 (p35)	BC050768|Cdk5r1|12569|cyclin-dependent kinase 5, regulatory subunit 1 (p35)	NM_009871|Cdk5r1|12569|cyclin-dependent kinase 5, regulatory subunit 1 (p35)	AK039999|Cdk5r1|12569|cyclin-dependent kinase 5, regulatory subunit 1 (p35)	BC058697|Cdk5r1|12569|cyclin-dependent kinase 5, regulatory subunit 1 (p35)	BC046823|Cdk5r1|12569|cyclin-dependent kinase 5, regulatory subunit 1 (p35)	AK048617|Cdk5r1|12569|cyclin-dependent kinase 5, regulatory subunit 1 (p35)
mm9_v1_chr4_-_150026205_150026286	1.95911	SOX2.p2	AK134677|Slc45a1|242773|solute carrier family 45, member 1	BC051188|Slc45a1|242773|solute carrier family 45, member 1	AK134683|Slc45a1|242773|solute carrier family 45, member 1	AK158002|Slc45a1|242773|solute carrier family 45, member 1	AK082651|Slc45a1|242773|solute carrier family 45, member 1	NM_173774|Slc45a1|242773|solute carrier family 45, member 1
mm9_v1_chr15_+_81626455_81626512	1.95686	SOX2.p2	AJ223207|Zc3h7b|20286|zinc finger CCCH type containing 7B
mm9_v1_chr15_+_83610434_83610456	1.9568	SOX2.p2	AK048421|Mpped1|223726|metallophosphoesterase domain containing 1	NM_172610|Mpped1|223726|metallophosphoesterase domain containing 1
mm9_v1_chr2_+_172298047_172298053	1.95425	SOX2.p2	AK006503|1700029J11Rik|76426|RIKEN cDNA 1700029J11 gene	BC137932|1700029J11Rik|76426|RIKEN cDNA 1700029J11 gene	BC137933|1700029J11Rik|76426|RIKEN cDNA 1700029J11 gene	NM_029608|1700029J11Rik|76426|RIKEN cDNA 1700029J11 gene
mm9_v1_chr2_+_130230994_130231035	1.95054	SOX2.p2	NM_029375|1700020A23Rik|75656|RIKEN cDNA 1700020A23 gene	BC049710|1700020A23Rik|75656|RIKEN cDNA 1700020A23 gene	NM_001163483|1700020A23Rik|75656|RIKEN cDNA 1700020A23 gene	BC137914|1700020A23Rik|75656|RIKEN cDNA 1700020A23 gene	BC137915|1700020A23Rik|75656|RIKEN cDNA 1700020A23 gene
mm9_v1_chrX_-_71070284_71070317	1.9467	SOX2.p2	AK046101|Pdzd4|245469|PDZ domain containing 4	NM_001029868|Pdzd4|245469|PDZ domain containing 4
mm9_v1_chr2_+_71367501_71367643	1.94496	SOX2.p2	NM_010053|Dlx1|13390|distal-less homeobox 1	U51001|Dlx1|13390|distal-less homeobox 1	BC079609|Dlx1|13390|distal-less homeobox 1
mm9_v1_chr9_+_106356125_106356294	1.94484	SOX2.p2	NM_021567|Pcbp4|59092|poly(rC) binding protein 4	AK004580|Pcbp4|59092|poly(rC) binding protein 4	AK005383|Pcbp4|59092|poly(rC) binding protein 4	AK077632|Pcbp4|59092|poly(rC) binding protein 4	AK082005|Pcbp4|59092|poly(rC) binding protein 4	BC010694|Pcbp4|59092|poly(rC) binding protein 4	AF176328|Pcbp4|59092|poly(rC) binding protein 4
mm9_v1_chr18_+_40418014_40418040	1.93995	SOX2.p2	NM_026135|Kctd16|383348|potassium channel tetramerisation domain containing 16	AK220381|Kctd16|383348|potassium channel tetramerisation domain containing 16
mm9_v1_chr18_+_56748001_56748079	1.93426	SOX2.p2	AK006893|1700065I17Rik|67343|RIKEN cDNA 1700065I17 gene	NM_026099|1700065I17Rik|67343|RIKEN cDNA 1700065I17 gene	AK018985|1700065I17Rik|67343|RIKEN cDNA 1700065I17 gene	BC099538|1700065I17Rik|67343|RIKEN cDNA 1700065I17 gene	FJ211594|1700065I17Rik|67343|RIKEN cDNA 1700065I17 gene	BC048449|1700065I17Rik|67343|RIKEN cDNA 1700065I17 gene	BC048448|1700065I17Rik|67343|RIKEN cDNA 1700065I17 gene
mm9_v1_chr5_-_138596915_138596971	1.93087	SOX2.p2	BC052453|Zfp113|56314|zinc finger protein 113	BC054525|Zfp113|56314|zinc finger protein 113	BC056991|Zfp113|56314|zinc finger protein 113	AF167320|Zfp113|56314|zinc finger protein 113	AK076349|Zfp113|56314|zinc finger protein 113	AK220556|Zfp113|56314|zinc finger protein 113	NM_019747|Zfp113|56314|zinc finger protein 113
mm9_v1_chr18_+_20823750_20823857	1.9297	SOX2.p2	NM_013697|Ttr|22139|transthyretin	BC024702|Ttr|22139|transthyretin
mm9_v1_chr17_-_85463965_85464074	1.92174	SOX2.p2	
mm9_v1_chr6_-_149049906_149050060	1.92138	SOX2.p2	BC132199|Dennd5b|320560|DENN/MADD domain containing 5B	BC132535|Dennd5b|320560|DENN/MADD domain containing 5B	BC145128|Dennd5b|320560|DENN/MADD domain containing 5B	AK052296|Dennd5b|320560|DENN/MADD domain containing 5B	AK050728|Dennd5b|320560|DENN/MADD domain containing 5B
mm9_v1_chr10_+_4795808_4795848	1.91906	SOX2.p2	AF535143|Syne1|64009|synaptic nuclear envelope 1	NM_153399|Syne1|64009|synaptic nuclear envelope 1
mm9_v1_chr14_+_58693951_58693999	1.91861	SOX2.p2	AK158584|Fgf9|14180|fibroblast growth factor 9
mm9_v1_chr15_-_97561769_97561835	1.9185	SOX2.p2	AK132616|Endou|19011|endonuclease, polyU-specific	NM_001168693|Endou|19011|endonuclease, polyU-specific
mm9_v1_chr6_+_47194393_47194453	1.91491	SOX2.p2	NM_025771|Cntnap2|66797|contactin associated protein-like 2	AK017341|Cntnap2|66797|contactin associated protein-like 2	AK013139|Cntnap2|66797|contactin associated protein-like 2	BC029826|Cntnap2|66797|contactin associated protein-like 2	BC103799|Cntnap2|66797|contactin associated protein-like 2
mm9_v1_chr13_+_21570775_21570839	1.91307	SOX2.p2	NM_001039115|Zkscan4|544922|zinc finger with KRAB and SCAN domains 4	BC141222|Zkscan4|544922|zinc finger with KRAB and SCAN domains 4
mm9_v1_chr11_-_76384852_76384920	1.9129	SOX2.p2	AK142364|Abr|109934|active BCR-related gene	NM_198895|Abr|109934|active BCR-related gene
mm9_v1_chr5_+_74931439_74931607	1.90732	SOX2.p2	AK168464|Fip1l1|66899|FIP1 like 1 (S. cerevisiae)	NM_001159573|Fip1l1|66899|FIP1 like 1 (S. cerevisiae)	NM_001159574|Fip1l1|66899|FIP1 like 1 (S. cerevisiae)	NM_024183|Fip1l1|66899|FIP1 like 1 (S. cerevisiae)	AK049672|Fip1l1|66899|FIP1 like 1 (S. cerevisiae)	AK008561|Fip1l1|66899|FIP1 like 1 (S. cerevisiae)	AK005061|Fip1l1|66899|FIP1 like 1 (S. cerevisiae)	AK164105|Fip1l1|66899|FIP1 like 1 (S. cerevisiae)	BC003263|Fip1l1|66899|FIP1 like 1 (S. cerevisiae)
mm9_v1_chr5_-_122907269_122907331	1.90579	SOX2.p2	AK195483|Atp2a2|11938|ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	AK198267|Atp2a2|11938|ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	AK202908|Atp2a2|11938|ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	AK209825|Atp2a2|11938|ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	BC022584|Atp2a2|11938|ATPase, Ca++ transporting, cardiac muscle, slow twitch 2
mm9_v1_chr12_+_111903331_111903389	1.89037	SOX2.p2	AK151489|Dync1h1|13424|dynein cytoplasmic 1 heavy chain 1
mm9_v1_chr11_-_104330747_104330787	1.88391	SOX2.p2	AK037800|1700081L11Rik|76719|RIKEN cDNA 1700081L11 gene
mm9_v1_chr12_+_79792521_79792674	1.88131	SOX2.p2	AK014851|Fam71d|70897|family with sequence similarity 71, member D	NM_027597|Fam71d|70897|family with sequence similarity 71, member D	NM_029069|Fam71d|70897|family with sequence similarity 71, member D	BC051149|Fam71d|70897|family with sequence similarity 71, member D	AK015802|Fam71d|70897|family with sequence similarity 71, member D
mm9_v1_chr8_+_96335202_96335227	1.87389	SOX2.p2	M36778|Gnao1|14681|guanine nucleotide binding protein, alpha O	M36777|Gnao1|14681|guanine nucleotide binding protein, alpha O
mm9_v1_chr15_-_98781060_98781163	1.87239	SOX2.p2	M28729|Tuba1a|22142|tubulin, alpha 1A	AK201449|Tuba1a|22142|tubulin, alpha 1A
mm9_v1_chr2_+_181531011_181531011	1.87192	SOX2.p2	AF004294|Myt1|17932|myelin transcription factor 1	NM_001171680|Myt1|17932|myelin transcription factor 1
mm9_v1_chr18_+_6603626_6603630	1.87047	SOX2.p2	BC049627|4921524L21Rik|70901|RIKEN cDNA 4921524L21 gene	AK014961|4921524L21Rik|70901|RIKEN cDNA 4921524L21 gene	NM_027598|4921524L21Rik|70901|RIKEN cDNA 4921524L21 gene
mm9_v1_chrX_+_68809163_68809181	1.86757	SOX2.p2	NM_008253|Hmgb3|15354|high mobility group box 3	AK032163|Hmgb3|15354|high mobility group box 3
mm9_v1_chr1_-_64167952_64168022	1.86702	SOX2.p2	BC019604|Klf7|93691|Kruppel-like factor 7 (ubiquitous)	NM_033563|Klf7|93691|Kruppel-like factor 7 (ubiquitous)	BC004700|Klf7|93691|Kruppel-like factor 7 (ubiquitous)	BC040794|Klf7|93691|Kruppel-like factor 7 (ubiquitous)	AF338369|Klf7|93691|Kruppel-like factor 7 (ubiquitous)	AK149362|Klf7|93691|Kruppel-like factor 7 (ubiquitous)
mm9_v1_chr7_+_105805420_105805457	1.8654	SOX2.p2	
mm9_v1_chr10_+_4978808_4978917	1.86251	SOX2.p2	AK148504|Syne1|64009|synaptic nuclear envelope 1
mm9_v1_chr5_-_137748882_137748932	1.86222	SOX2.p2	AK144300|Srrt|83701|serrate RNA effector molecule homolog (Arabidopsis)	NM_001109909|Srrt|83701|serrate RNA effector molecule homolog (Arabidopsis)	NM_001109910|Srrt|83701|serrate RNA effector molecule homolog (Arabidopsis)	NM_031405|Srrt|83701|serrate RNA effector molecule homolog (Arabidopsis)
mm9_v1_chr3_+_88125464_88125582	1.86215	SOX2.p2	
mm9_v1_chr1_-_53244460_53244460	1.86111	SOX2.p2	AK006101|1700019A02Rik|69397|RIKEN cDNA 1700019A02 gene	NM_027070|1700019A02Rik|69397|RIKEN cDNA 1700019A02 gene
mm9_v1_chrX_+_68809128_68809157	1.85897	SOX2.p2	BC011276|Hmgb3|15354|high mobility group box 3	BC158037|Hmgb3|15354|high mobility group box 3
mm9_v1_chr2_+_127164374_127164374	1.85817	SOX2.p2	AK033037|Astl|215095|astacin-like metalloendopeptidase (M12 family)	NM_172539|Astl|215095|astacin-like metalloendopeptidase (M12 family)
mm9_v1_chr4_+_111087610_111087629	1.85506	SOX2.p2	AK075885|Bend5|67621|BEN domain containing 5	NM_026279|Bend5|67621|BEN domain containing 5	AK014057|Bend5|67621|BEN domain containing 5
mm9_v1_chrX_+_68809092_68809096	1.8549	SOX2.p2	AK141399|Hmgb3|15354|high mobility group box 3	AK146795|Hmgb3|15354|high mobility group box 3
mm9_v1_chr10_+_74523775_74523878	1.85439	SOX2.p2	BC131682|Bcr|110279|breakpoint cluster region
mm9_v1_chr1_+_181891219_181891219	1.85108	SOX2.p2	BC158017|Cdc42bpa|226751|CDC42 binding protein kinase alpha	BC158095|Cdc42bpa|226751|CDC42 binding protein kinase alpha	NM_001033285|Cdc42bpa|226751|CDC42 binding protein kinase alpha
mm9_v1_chr6_+_86578269_86578294	1.8488	SOX2.p2	BC108357|Asprv1|67855|aspartic peptidase, retroviral-like 1
mm9_v1_chr5_-_112681521_112681539	1.84747	SOX2.p2	AJ272228|Cryba4|12959|crystallin, beta A4	BC058703|Cryba4|12959|crystallin, beta A4	NM_021351|Cryba4|12959|crystallin, beta A4	AK162018|Cryba4|12959|crystallin, beta A4	AK132591|Cryba4|12959|crystallin, beta A4
mm9_v1_chr7_+_148033703_148033814	1.84511	SOX2.p2	AK005883|Odf3|69287|outer dense fiber of sperm tails 3	AB067773|Odf3|69287|outer dense fiber of sperm tails 3	BC104105|Odf3|69287|outer dense fiber of sperm tails 3	BC104106|Odf3|69287|outer dense fiber of sperm tails 3	BC106806|Odf3|69287|outer dense fiber of sperm tails 3	NM_027019|Odf3|69287|outer dense fiber of sperm tails 3
mm9_v1_chrX_-_40627962_40627962	1.84321	SOX2.p2	AB025410|Odz1|23963|odd Oz/ten-m homolog 1 (Drosophila)	NM_011855|Odz1|23963|odd Oz/ten-m homolog 1 (Drosophila)
mm9_v1_chr18_+_37179802_37179999	1.84139	SOX2.p2	AY013759|Pcdha12|192164|protocadherin alpha 12	NM_138663|Pcdha12|192164|protocadherin alpha 12	AB008180|Pcdha12|192164|protocadherin alpha 12
mm9_v1_chr4_+_134024234_134024333	1.83714	SOX2.p2	NM_019641|Stmn1|16765|stathmin 1	AB064953|Stmn1|16765|stathmin 1	AK002606|Stmn1|16765|stathmin 1	AK012231|Stmn1|16765|stathmin 1	AK012347|Stmn1|16765|stathmin 1	AK014108|Stmn1|16765|stathmin 1	AK088628|Stmn1|16765|stathmin 1	AK013302|Stmn1|16765|stathmin 1	BC010581|Stmn1|16765|stathmin 1	BC031831|Stmn1|16765|stathmin 1	BC054396|Stmn1|16765|stathmin 1
mm9_v1_chr11_+_32355355_32355458	1.83538	SOX2.p2	AK076953|Ubtd2|327900|ubiquitin domain containing 2	BC057026|Ubtd2|327900|ubiquitin domain containing 2	NM_173784|Ubtd2|327900|ubiquitin domain containing 2
mm9_v1_chr19_+_4756524_4756619	1.83504	SOX2.p2	NM_025717|Rbm4b|66704|RNA binding motif protein 4B	AK006447|Rbm4b|66704|RNA binding motif protein 4B	AK032852|Rbm4b|66704|RNA binding motif protein 4B	AK019871|Rbm4b|66704|RNA binding motif protein 4B	AK142116|Rbm4b|66704|RNA binding motif protein 4B	AK160796|Rbm4b|66704|RNA binding motif protein 4B	AK014823|Rbm4b|66704|RNA binding motif protein 4B	AK028347|Rbm4b|66704|RNA binding motif protein 4B	BC019488|Rbm4b|66704|RNA binding motif protein 4B
mm9_v1_chr9_-_58218175_58218261	1.83119	SOX2.p2	BC132329|Tbc1d21|74286|TBC1 domain family, member 21	BC138332|Tbc1d21|74286|TBC1 domain family, member 21	BC145239|Tbc1d21|74286|TBC1 domain family, member 21	BC145240|Tbc1d21|74286|TBC1 domain family, member 21	NM_028854|Tbc1d21|74286|TBC1 domain family, member 21	BC100468|Tbc1d21|74286|TBC1 domain family, member 21	AK007086|Tbc1d21|74286|TBC1 domain family, member 21
mm9_v1_chr11_+_115243203_115243359	1.83057	SOX2.p2	NM_001080929|Cdr2l|237988|cerebellar degeneration-related protein 2-like	BC144823|Cdr2l|237988|cerebellar degeneration-related protein 2-like	BC150668|Cdr2l|237988|cerebellar degeneration-related protein 2-like
mm9_v1_chr7_+_25292201_25292230	1.82298	SOX2.p2	BC096675|Zfp428|232969|zinc finger protein 428	BC024802|Zfp428|232969|zinc finger protein 428	AK010415|Zfp428|232969|zinc finger protein 428
mm9_v1_chr2_+_154374639_154374777	1.82183	SOX2.p2	AK005633|1700003F12Rik|75480|RIKEN cDNA 1700003F12 gene	DQ080431|1700003F12Rik|75480|RIKEN cDNA 1700003F12 gene	NM_029305|1700003F12Rik|75480|RIKEN cDNA 1700003F12 gene	BC147532|1700003F12Rik|75480|RIKEN cDNA 1700003F12 gene	BC147533|1700003F12Rik|75480|RIKEN cDNA 1700003F12 gene	BC039797|1700003F12Rik|75480|RIKEN cDNA 1700003F12 gene
mm9_v1_chr1_-_166387998_166388161	1.82014	SOX2.p2	X16646|Atp1b1|11931|ATPase, Na+/K+ transporting, beta 1 polypeptide	BC094070|Atp1b1|11931|ATPase, Na+/K+ transporting, beta 1 polypeptide	BC027319|Atp1b1|11931|ATPase, Na+/K+ transporting, beta 1 polypeptide	AK005071|Atp1b1|11931|ATPase, Na+/K+ transporting, beta 1 polypeptide	AK140862|Atp1b1|11931|ATPase, Na+/K+ transporting, beta 1 polypeptide	AK160405|Atp1b1|11931|ATPase, Na+/K+ transporting, beta 1 polypeptide	AK161891|Atp1b1|11931|ATPase, Na+/K+ transporting, beta 1 polypeptide
mm9_v1_chr2_+_162762650_162762674	1.80979	SOX2.p2	
mm9_v1_chr4_-_120861138_120861138	1.80685	SOX2.p2	NM_001081013|Rlf|109263|rearranged L-myc fusion sequence
mm9_v1_chrX_+_111587911_111588212	1.80433	SOX2.p2	AK081448|Klhl4|237010|kelch-like 4 (Drosophila)	AK085099|Klhl4|237010|kelch-like 4 (Drosophila)	AK161786|Klhl4|237010|kelch-like 4 (Drosophila)	BC099954|Klhl4|237010|kelch-like 4 (Drosophila)	AK081937|Klhl4|237010|kelch-like 4 (Drosophila)	NM_172781|Klhl4|237010|kelch-like 4 (Drosophila)	BC141251|Klhl4|237010|kelch-like 4 (Drosophila)	BC057137|Klhl4|237010|kelch-like 4 (Drosophila)	AK044930|Klhl4|237010|kelch-like 4 (Drosophila)
mm9_v1_chr9_+_75159201_75159201	1.80374	SOX2.p2	NM_010313|Gnb5|14697|guanine nucleotide binding protein (G protein), beta 5	U69145|Gnb5|14697|guanine nucleotide binding protein (G protein), beta 5
mm9_v1_chr16_-_58928469_58928469	1.80294	SOX2.p2	NM_146999|Olfr181|259001|olfactory receptor 181
mm9_v1_chr10_+_84218792_84218938	1.80263	SOX2.p2	NM_001024918|Rfx4|71137|regulatory factor X, 4 (influences HLA class II expression)	AK034131|Rfx4|71137|regulatory factor X, 4 (influences HLA class II expression)	AK090309|Rfx4|71137|regulatory factor X, 4 (influences HLA class II expression)	AY102010|Rfx4|71137|regulatory factor X, 4 (influences HLA class II expression)	AY342003|Rfx4|71137|regulatory factor X, 4 (influences HLA class II expression)	AB086957|Rfx4|71137|regulatory factor X, 4 (influences HLA class II expression)
mm9_v1_chr4_+_132194931_132195032	1.80143	SOX2.p2	AK164591|Eya3|14050|eyes absent 3 homolog (Drosophila)	NM_210071|Eya3|14050|eyes absent 3 homolog (Drosophila)	NM_211357|Eya3|14050|eyes absent 3 homolog (Drosophila)	AK144653|Eya3|14050|eyes absent 3 homolog (Drosophila)	NM_010166|Eya3|14050|eyes absent 3 homolog (Drosophila)	BC052860|Eya3|14050|eyes absent 3 homolog (Drosophila)	U81604|Eya3|14050|eyes absent 3 homolog (Drosophila)	AK017913|5830409B07Rik|76020|RIKEN cDNA 5830409B07 gene	BC063259|Eya3|14050|eyes absent 3 homolog (Drosophila)
mm9_v1_chr2_+_69708777_69708824	1.80119	SOX2.p2	AK200405|Ssb|20823|Sjogren syndrome antigen B
mm9_v1_chr10_+_56107352_56107416	1.80094	SOX2.p2	CT010327|Gja1|14609|gap junction protein, alpha 1
mm9_v1_chr6_+_57652594_57652646	1.8004	SOX2.p2	BC016072|Lancl2|71835|LanC (bacterial lantibiotic synthetase component C)-like 2	AB035967|Lancl2|71835|LanC (bacterial lantibiotic synthetase component C)-like 2
mm9_v1_chr1_-_54983132_54983204	1.79991	SOX2.p2	AK157584|Ankrd44|329154|ankyrin repeat domain 44
mm9_v1_chr11_+_56825258_56825293	1.7976	SOX2.p2	X57497|Gria1|14799|glutamate receptor, ionotropic, AMPA1 (alpha 1)
mm9_v1_chr2_+_145068346_145068346	1.79397	SOX2.p2	BC017615|Slc24a3|94249|solute carrier family 24 (sodium/potassium/calcium exchanger), member 3	NM_053195|Slc24a3|94249|solute carrier family 24 (sodium/potassium/calcium exchanger), member 3
mm9_v1_chr17_-_56615875_56615935	1.7935	SOX2.p2	NM_011218|Ptprs|19280|protein tyrosine phosphatase, receptor type, S
mm9_v1_chr8_+_86520110_86520238	1.79247	SOX2.p2	AK131888|Prkaca|18747|protein kinase, cAMP dependent, catalytic, alpha
mm9_v1_chr5_-_71939438_71939443	1.78831	SOX2.p2	BC059709|Cox7b2|78174|cytochrome c oxidase subunit VIIb2	AK019665|Cox7b2|78174|cytochrome c oxidase subunit VIIb2	AK076833|Cox7b2|78174|cytochrome c oxidase subunit VIIb2	NM_030052|Cox7b2|78174|cytochrome c oxidase subunit VIIb2
mm9_v1_chr19_-_30623890_30624012	1.788	SOX2.p2	AF030433|Dkk1|13380|dickkopf homolog 1 (Xenopus laevis)	BC050189|Dkk1|13380|dickkopf homolog 1 (Xenopus laevis)	NM_010051|Dkk1|13380|dickkopf homolog 1 (Xenopus laevis)	AK141693|Dkk1|13380|dickkopf homolog 1 (Xenopus laevis)	AK144119|Dkk1|13380|dickkopf homolog 1 (Xenopus laevis)
mm9_v1_chr6_-_56319574_56319627	1.78036	SOX2.p2	AK077123|Pde1c|18575|phosphodiesterase 1C	AK015375|Pde1c|18575|phosphodiesterase 1C	AK014887|Pde1c|18575|phosphodiesterase 1C	AK133243|Pde1c|18575|phosphodiesterase 1C	AK029531|Pde1c|18575|phosphodiesterase 1C	NM_001159955|Pde1c|18575|phosphodiesterase 1C	NM_001159956|Pde1c|18575|phosphodiesterase 1C	NM_001159957|Pde1c|18575|phosphodiesterase 1C
mm9_v1_chr7_-_54389053_54389053	1.77964	SOX2.p2	NM_013643|Ptpn5|19259|protein tyrosine phosphatase, non-receptor type 5	U28217|Ptpn5|19259|protein tyrosine phosphatase, non-receptor type 5
mm9_v1_chr7_+_130114059_130114440	1.77909	SOX2.p2	NM_011247|Rbbp6|19647|retinoblastoma binding protein 6	NM_175023|Rbbp6|19647|retinoblastoma binding protein 6	AK081261|Rbbp6|19647|retinoblastoma binding protein 6	AK045635|Rbbp6|19647|retinoblastoma binding protein 6	BC025874|Rbbp6|19647|retinoblastoma binding protein 6
mm9_v1_chr4_-_77857594_77857662	1.77818	SOX2.p2	AK086248|Ptprd|19266|protein tyrosine phosphatase, receptor type, D
mm9_v1_chr2_+_43604343_43604389	1.77702	SOX2.p2	AK036520|Arhgap15|76117|Rho GTPase activating protein 15	NM_153820|Arhgap15|76117|Rho GTPase activating protein 15	AK170537|Arhgap15|76117|Rho GTPase activating protein 15	NM_001025377|Arhgap15|76117|Rho GTPase activating protein 15	AK041323|Arhgap15|76117|Rho GTPase activating protein 15	AK033620|Arhgap15|76117|Rho GTPase activating protein 15	AK040796|Arhgap15|76117|Rho GTPase activating protein 15	AK172407|Arhgap15|76117|Rho GTPase activating protein 15	BC034881|Arhgap15|76117|Rho GTPase activating protein 15	AK018058|Arhgap15|76117|Rho GTPase activating protein 15	AK031022|Arhgap15|76117|Rho GTPase activating protein 15	BC024887|Arhgap15|76117|Rho GTPase activating protein 15
mm9_v1_chr1_-_178737254_178737254	1.77334	SOX2.p2	NM_001099637|Cep170|545389|centrosomal protein 170
mm9_v1_chr5_+_81450617_81450617	1.76736	SOX2.p2	BC088989|Lphn3|319387|latrophilin 3	NM_198702|Lphn3|319387|latrophilin 3
mm9_v1_chr15_+_103070840_103070935	1.76484	SOX2.p2	AK131999|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	AK136113|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	AK146630|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	NM_001039129|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	NM_010447|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	AK168531|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	AK135391|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	AK152684|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	AK161730|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	AK166901|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	AK167161|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	AK167810|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	AK167811|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	AK168420|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	AK168733|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	AK169216|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	AK007802|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	AK088308|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	AK146126|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	AK166989|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	AK167820|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	AK167913|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	M99167|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	BC052723|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	BC080675|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	BC092395|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	BC089340|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	BC083136|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	D86728|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1	D86729|Hnrnpa1|15382|heterogeneous nuclear ribonucleoprotein A1
mm9_v1_chr5_-_100467945_100467960	1.76473	SOX2.p2	AB017020|Hnrpdl|50926|heterogeneous nuclear ribonucleoprotein D-like
mm9_v1_chr4_+_135841981_135841996	1.76336	SOX2.p2	AK053652|Zfp46|22704|zinc finger protein 46	NM_009557|Zfp46|22704|zinc finger protein 46	AK173240|Zfp46|22704|zinc finger protein 46
mm9_v1_chr5_-_52581705_52581765	1.76101	SOX2.p2	BC003745|Dhx15|13204|DEAH (Asp-Glu-Ala-His) box polypeptide 15	BC100343|Dhx15|13204|DEAH (Asp-Glu-Ala-His) box polypeptide 15	AK146441|Dhx15|13204|DEAH (Asp-Glu-Ala-His) box polypeptide 15	AK145983|Dhx15|13204|DEAH (Asp-Glu-Ala-His) box polypeptide 15	AK151015|Dhx15|13204|DEAH (Asp-Glu-Ala-His) box polypeptide 15	AK151757|Dhx15|13204|DEAH (Asp-Glu-Ala-His) box polypeptide 15	AK149869|Dhx15|13204|DEAH (Asp-Glu-Ala-His) box polypeptide 15	AK168323|Dhx15|13204|DEAH (Asp-Glu-Ala-His) box polypeptide 15	AK168835|Dhx15|13204|DEAH (Asp-Glu-Ala-His) box polypeptide 15	AK169174|Dhx15|13204|DEAH (Asp-Glu-Ala-His) box polypeptide 15	NM_001042620|Dhx15|13204|DEAH (Asp-Glu-Ala-His) box polypeptide 15	NM_007839|Dhx15|13204|DEAH (Asp-Glu-Ala-His) box polypeptide 15
mm9_v1_chr4_-_33010429_33010479	1.7582	SOX2.p2	BC065177|Ankrd6|140577|ankyrin repeat domain 6	NM_001012450|Ankrd6|140577|ankyrin repeat domain 6	NM_080471|Ankrd6|140577|ankyrin repeat domain 6
mm9_v1_chr4_+_107474842_107475017	1.75742	SOX2.p2	NM_001080926|Lrp8|16975|low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	D85463|Lrp8|16975|low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	BC127061|Lrp8|16975|low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	AJ312058|Lrp8|16975|low density lipoprotein receptor-related protein 8, apolipoprotein e receptor
mm9_v1_chr3_+_152009483_152009542	1.75288	SOX2.p2	BC005506|Usp33|170822|ubiquitin specific peptidase 33	AK053227|Usp33|170822|ubiquitin specific peptidase 33	BC089315|Usp33|170822|ubiquitin specific peptidase 33
mm9_v1_chr13_-_93346126_93346186	1.75107	SOX2.p2	BC050748|Spz1|79401|spermatogenic leucine zipper 1	AK006437|Spz1|79401|spermatogenic leucine zipper 1	NM_030237|Spz1|79401|spermatogenic leucine zipper 1
mm9_v1_chr5_-_121952988_121953080	1.75005	SOX2.p2	NM_172125|Adam1b|280667|a disintegrin and metallopeptidase domain 1b	BC140979|Adam1b|280667|a disintegrin and metallopeptidase domain 1b
mm9_v1_chr15_-_98780503_98780728	1.7478	SOX2.p2	AK199768|Tuba1a|22142|tubulin, alpha 1A	AK216974|Tuba1a|22142|tubulin, alpha 1A
mm9_v1_chr3_+_30645214_30645214	1.74354	SOX2.p2	AK044227|Samd7|75953|sterile alpha motif domain containing 7	NM_029489|Samd7|75953|sterile alpha motif domain containing 7
mm9_v1_chr16_-_29378636_29378817	1.7425	SOX2.p2	AK158355|Atp13a5|268878|ATPase type 13A5	BC115739|Atp13a5|268878|ATPase type 13A5	AK083102|Atp13a5|268878|ATPase type 13A5	AK083121|Atp13a5|268878|ATPase type 13A5	NM_175650|Atp13a5|268878|ATPase type 13A5
mm9_v1_chr11_-_41996141_41996431	1.74108	SOX2.p2	AK141596|Gabra1|14394|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1	AK034095|Gabra1|14394|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1	NM_010250|Gabra1|14394|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1
mm9_v1_chr2_-_25671355_25671362	1.73954	SOX2.p2	BC111823|Glt6d1|71103|glycosyltransferase 6 domain containing 1	NM_001039095|Glt6d1|71103|glycosyltransferase 6 domain containing 1	AK016765|Glt6d1|71103|glycosyltransferase 6 domain containing 1
mm9_v1_chr5_-_100588586_100588606	1.73538	SOX2.p2	AK044570|Tmem150c|231503|transmembrane protein 150C	BC062109|Tmem150c|231503|transmembrane protein 150C
mm9_v1_chr11_-_102786403_102786422	1.73304	SOX2.p2	AK156592|Kif18b|70218|kinesin family member 18B	BC057614|Kif18b|70218|kinesin family member 18B
mm9_v1_chr4_+_151573918_151573952	1.73267	SOX2.p2	AB088412|Acot7|70025|acyl-CoA thioesterase 7	NM_001146058|Acot7|70025|acyl-CoA thioesterase 7
mm9_v1_chr2_-_156754104_156754212	1.73215	SOX2.p2	AK183588|Ndrg3|29812|N-myc downstream regulated gene 3
mm9_v1_chr12_-_33777667_33777744	1.73214	SOX2.p2	BC138911|Cdhr3|68764|cadherin-related family member 3	AK047666|Cdhr3|68764|cadherin-related family member 3	AK049806|Cdhr3|68764|cadherin-related family member 3	NM_001024478|Cdhr3|68764|cadherin-related family member 3
mm9_v1_chr3_-_94240497_94240537	1.73036	SOX2.p2	AB045835|Oaz3|53814|ornithine decarboxylase antizyme 3	BC119339|Oaz3|53814|ornithine decarboxylase antizyme 3	BC119341|Oaz3|53814|ornithine decarboxylase antizyme 3	AK006116|Oaz3|53814|ornithine decarboxylase antizyme 3	AK006634|Oaz3|53814|ornithine decarboxylase antizyme 3	AK076942|Oaz3|53814|ornithine decarboxylase antizyme 3	AF175297|Oaz3|53814|ornithine decarboxylase antizyme 3	NM_016901|Oaz3|53814|ornithine decarboxylase antizyme 3
mm9_v1_chr19_-_28838026_28838038	1.72932	SOX2.p2	NM_001177391|Gm6788|627788|predicted gene 6788
mm9_v1_chr11_+_29642253_29642464	1.72748	SOX2.p2	AK186869|Rtn4|68585|reticulon 4	AK186438|Rtn4|68585|reticulon 4	AK047253|Rtn4|68585|reticulon 4
mm9_v1_chr1_+_108835529_108835558	1.7252	SOX2.p2	AK040697|Serpinb12|71869|serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 12	AK014669|Serpinb12|71869|serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 12	BC062134|Serpinb12|71869|serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 12
mm9_v1_chr1_-_73062445_73062472	1.72405	SOX2.p2	X12521|Tnp1|21958|transition protein 1	AK006495|Tnp1|21958|transition protein 1	BC061170|Tnp1|21958|transition protein 1	BC048494|Tnp1|21958|transition protein 1	NM_009407|Tnp1|21958|transition protein 1
mm9_v1_chr8_-_83263323_83263359	1.72171	SOX2.p2	AK153789|Smarca5|93762|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	BC053069|Smarca5|93762|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	NM_053124|Smarca5|93762|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5
mm9_v1_chr5_+_3928177_3928370	1.72153	SOX2.p2	AK031740|Akap9|100986|A kinase (PRKA) anchor protein (yotiao) 9	NM_194462|Akap9|100986|A kinase (PRKA) anchor protein (yotiao) 9	AK168404|Akap9|100986|A kinase (PRKA) anchor protein (yotiao) 9	AK008727|Akap9|100986|A kinase (PRKA) anchor protein (yotiao) 9	AK017707|Akap9|100986|A kinase (PRKA) anchor protein (yotiao) 9	AJ582913|Akap9|100986|A kinase (PRKA) anchor protein (yotiao) 9	AK080442|Akap9|100986|A kinase (PRKA) anchor protein (yotiao) 9
mm9_v1_chr10_+_66648458_66648510	1.71306	SOX2.p2	AK087621|Jmjd1c|108829|jumonji domain containing 1C	AK170460|Jmjd1c|108829|jumonji domain containing 1C	AK135461|Jmjd1c|108829|jumonji domain containing 1C	AK085500|Jmjd1c|108829|jumonji domain containing 1C	AK133016|Jmjd1c|108829|jumonji domain containing 1C
mm9_v1_chr1_-_33871261_33871282	1.71299	SOX2.p2	AK122541|Zfp451|98403|zinc finger protein 451	BC019546|Zfp451|98403|zinc finger protein 451	AK030088|Zfp451|98403|zinc finger protein 451	NM_133817|Zfp451|98403|zinc finger protein 451
mm9_v1_chr5_+_22252006_22252042	1.71166	SOX2.p2	NM_001081231|Lhfpl3|269629|lipoma HMGIC fusion partner-like 3	NM_029990|Lhfpl3|269629|lipoma HMGIC fusion partner-like 3	AK033906|Lhfpl3|269629|lipoma HMGIC fusion partner-like 3	AK020916|Lhfpl3|269629|lipoma HMGIC fusion partner-like 3
mm9_v1_chr1_-_36650176_36650176	1.71069	SOX2.p2	AK006300|Fam178b|381337|family with sequence similarity 178, member B	NM_027957|Fam178b|381337|family with sequence similarity 178, member B
mm9_v1_chr2_+_32087125_32087136	1.70799	SOX2.p2	AK161103|Prrc2b|227723|proline-rich coiled-coil 2B
mm9_v1_chr17_-_88464582_88464624	1.7073	SOX2.p2	BC117884|Fbxo11|225055|F-box protein 11	BC117885|Fbxo11|225055|F-box protein 11	BC128479|Fbxo11|225055|F-box protein 11	NM_001081034|Fbxo11|225055|F-box protein 11
mm9_v1_chr7_+_4734541_4734552	1.70632	SOX2.p2	NM_030028|Tmem190|78052|transmembrane protein 190	AK019807|Tmem190|78052|transmembrane protein 190
mm9_v1_chrX_+_46048180_46048269	1.70369	SOX2.p2	AK076115|Rbmx2|209003|RNA binding motif protein, X-linked 2	NM_173376|Rbmx2|209003|RNA binding motif protein, X-linked 2	AK160232|Rbmx2|209003|RNA binding motif protein, X-linked 2	BC026976|Rbmx2|209003|RNA binding motif protein, X-linked 2	AK168018|Rbmx2|209003|RNA binding motif protein, X-linked 2
mm9_v1_chr3_-_95862377_95862377	1.70329	SOX2.p2	NM_013841|Vps45|22365|vacuolar protein sorting 45 (yeast)	U66865|Vps45|22365|vacuolar protein sorting 45 (yeast)
mm9_v1_chr17_+_24551840_24552094	1.69732	SOX2.p2	X70067|Rnps1|19826|ribonucleic acid binding protein S1	AK206201|Rnps1|19826|ribonucleic acid binding protein S1
mm9_v1_chr2_+_29745239_29745414	1.69028	SOX2.p2	AF000968|Odf2|18286|outer dense fiber of sperm tails 2	NM_001113213|Odf2|18286|outer dense fiber of sperm tails 2	NM_001113214|Odf2|18286|outer dense fiber of sperm tails 2	NM_001177659|Odf2|18286|outer dense fiber of sperm tails 2	NM_001177661|Odf2|18286|outer dense fiber of sperm tails 2	AK148523|Odf2|18286|outer dense fiber of sperm tails 2	AK165588|Odf2|18286|outer dense fiber of sperm tails 2	AK143726|Odf2|18286|outer dense fiber of sperm tails 2	AK168415|Odf2|18286|outer dense fiber of sperm tails 2	AK162550|Odf2|18286|outer dense fiber of sperm tails 2	BC057001|Odf2|18286|outer dense fiber of sperm tails 2
mm9_v1_chr1_+_162836541_162836569	1.6889	SOX2.p2	NM_001024952|Rc3h1|381305|RING CCCH (C3H) domains 1	AK139648|Rc3h1|381305|RING CCCH (C3H) domains 1
mm9_v1_chr11_+_106078232_106078424	1.68753	SOX2.p2	AK049311|Ddx42|72047|DEAD (Asp-Glu-Ala-Asp) box polypeptide 42	NM_028074|Ddx42|72047|DEAD (Asp-Glu-Ala-Asp) box polypeptide 42	AK169816|Ddx42|72047|DEAD (Asp-Glu-Ala-Asp) box polypeptide 42	AK021013|Ddx42|72047|DEAD (Asp-Glu-Ala-Asp) box polypeptide 42	AK171730|Ddx42|72047|DEAD (Asp-Glu-Ala-Asp) box polypeptide 42	AK134182|Ddx42|72047|DEAD (Asp-Glu-Ala-Asp) box polypeptide 42
mm9_v1_chr9_-_7835107_7835268	1.68575	SOX2.p2	BC145985|Birc2|11797|baculoviral IAP repeat-containing 2	NM_007465|Birc2|11797|baculoviral IAP repeat-containing 2	U88909|Birc2|11797|baculoviral IAP repeat-containing 2	BC033480|Birc2|11797|baculoviral IAP repeat-containing 2
mm9_v1_chr11_-_46125777_46125868	1.68568	SOX2.p2	AK018280|Cyfip2|76884|cytoplasmic FMR1 interacting protein 2	AF334144|Cyfip2|76884|cytoplasmic FMR1 interacting protein 2	AK030397|Cyfip2|76884|cytoplasmic FMR1 interacting protein 2	AK147971|Cyfip2|76884|cytoplasmic FMR1 interacting protein 2	BC056974|Cyfip2|76884|cytoplasmic FMR1 interacting protein 2	AK147586|Cyfip2|76884|cytoplasmic FMR1 interacting protein 2	NM_133769|Cyfip2|76884|cytoplasmic FMR1 interacting protein 2
mm9_v1_chr2_+_67955769_67955862	1.68417	SOX2.p2	NM_020283|B3galt1|26877|UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1	BC094660|B3galt1|26877|UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1	BC132246|B3galt1|26877|UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1	BC132528|B3galt1|26877|UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1
mm9_v1_chr9_+_44215777_44215823	1.6821	SOX2.p2	AK169736|Rps25|75617|ribosomal protein S25	AK012696|Rps25|75617|ribosomal protein S25	BC079541|Rps25|75617|ribosomal protein S25	BC094392|Rps25|75617|ribosomal protein S25	NM_024266|Rps25|75617|ribosomal protein S25	BC092005|Rps25|75617|ribosomal protein S25	AK077450|Rps25|75617|ribosomal protein S25
mm9_v1_chr8_-_44662019_44662060	1.68035	SOX2.p2	AF167404|Adam26a|13525|a disintegrin and metallopeptidase domain 26A (testase 3)	AK015043|Adam26a|13525|a disintegrin and metallopeptidase domain 26A (testase 3)	AK029756|Adam26a|13525|a disintegrin and metallopeptidase domain 26A (testase 3)	NM_010085|Adam26a|13525|a disintegrin and metallopeptidase domain 26A (testase 3)
mm9_v1_chr7_-_85722668_85722860	1.67926	SOX2.p2	AY336094|Ntrk3|18213|neurotrophic tyrosine kinase, receptor, type 3	NM_008746|Ntrk3|18213|neurotrophic tyrosine kinase, receptor, type 3	NM_182809|Ntrk3|18213|neurotrophic tyrosine kinase, receptor, type 3	BC139764|Ntrk3|18213|neurotrophic tyrosine kinase, receptor, type 3	AF035399|Ntrk3|18213|neurotrophic tyrosine kinase, receptor, type 3	AF035400|Ntrk3|18213|neurotrophic tyrosine kinase, receptor, type 3
mm9_v1_chrX_-_133527570_133527593	1.67883	SOX2.p2	NM_001114179|Mcart6|67062|mitochondrial carrier triple repeat 6
mm9_v1_chr2_+_102546576_102546605	1.67828	SOX2.p2	AB007812|Slc1a2|20511|solute carrier family 1 (glial high affinity glutamate transporter), member 2	BC138255|Slc1a2|20511|solute carrier family 1 (glial high affinity glutamate transporter), member 2	BC138256|Slc1a2|20511|solute carrier family 1 (glial high affinity glutamate transporter), member 2	NM_001077515|Slc1a2|20511|solute carrier family 1 (glial high affinity glutamate transporter), member 2	NM_011393|Slc1a2|20511|solute carrier family 1 (glial high affinity glutamate transporter), member 2	AB007811|Slc1a2|20511|solute carrier family 1 (glial high affinity glutamate transporter), member 2
mm9_v1_chr6_-_51416921_51416984	1.67518	SOX2.p2	BC059107|Hnrnpa2b1|53379|heterogeneous nuclear ribonucleoprotein A2/B1
mm9_v1_chr17_+_12312128_12312218	1.66569	SOX2.p2	AK005139|Agpat4|68262|1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)	NM_026644|Agpat4|68262|1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)	AK166917|Agpat4|68262|1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)	BC047281|Agpat4|68262|1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)
mm9_v1_chr6_-_40469482_40469510	1.66118	SOX2.p2	AK029780|Prss37|67690|protease, serine, 37	AK006028|Prss37|67690|protease, serine, 37	NM_026317|Prss37|67690|protease, serine, 37	AK016088|Prss37|67690|protease, serine, 37
mm9_v1_chr2_-_14976498_14976510	1.65808	SOX2.p2	AK016629|Nsun6|74455|NOL1/NOP2/Sun domain family member 6	NM_001165941|Nsun6|74455|NOL1/NOP2/Sun domain family member 6	NM_001165943|Nsun6|74455|NOL1/NOP2/Sun domain family member 6	AK016811|Nsun6|74455|NOL1/NOP2/Sun domain family member 6
mm9_v1_chr3_-_80606704_80606756	1.65807	SOX2.p2	AK163941|Gria2|14800|glutamate receptor, ionotropic, AMPA2 (alpha 2)	AK046861|Gria2|14800|glutamate receptor, ionotropic, AMPA2 (alpha 2)	NM_001039195|Gria2|14800|glutamate receptor, ionotropic, AMPA2 (alpha 2)	NM_001083806|Gria2|14800|glutamate receptor, ionotropic, AMPA2 (alpha 2)	NM_013540|Gria2|14800|glutamate receptor, ionotropic, AMPA2 (alpha 2)	AK014389|Gria2|14800|glutamate receptor, ionotropic, AMPA2 (alpha 2)
mm9_v1_chr14_-_52935887_52935914	1.65736	SOX2.p2	AK077601|Sall2|50524|sal-like 2 (Drosophila)
mm9_v1_chr14_-_75991756_75991791	1.65382	SOX2.p2	AY092416|Spert|67926|spermatid associated	AK007022|Spert|67926|spermatid associated	BC109147|Spert|67926|spermatid associated	AK005703|Spert|67926|spermatid associated	NM_001164141|Spert|67926|spermatid associated	NM_026457|Spert|67926|spermatid associated
mm9_v1_chr5_-_137748860_137748870	1.65278	SOX2.p2	BC066831|Srrt|83701|serrate RNA effector molecule homolog (Arabidopsis)
mm9_v1_chr18_+_69753146_69753168	1.65163	SOX2.p2	AK151433|Tcf4|21413|transcription factor 4
mm9_v1_chr15_-_8273428_8273486	1.64894	SOX2.p2	AK135347|Nipbl|71175|Nipped-B homolog (Drosophila)
mm9_v1_chr7_+_25292105_25292148	1.64424	SOX2.p2	NM_146183|Zfp428|232969|zinc finger protein 428	AK080517|Zfp428|232969|zinc finger protein 428
mm9_v1_chr13_-_67162084_67162105	1.64252	SOX2.p2	AK019536|Zfp712|78251|zinc finger protein 712	NM_001166218|Zfp712|78251|zinc finger protein 712
mm9_v1_chr6_-_42643001_42643085	1.63703	SOX2.p2	AK076242|Fam115a|77574|family with sequence similarity 115, member A	AK013025|Fam115a|77574|family with sequence similarity 115, member A	AK148593|Fam115a|77574|family with sequence similarity 115, member A	AK053509|Fam115a|77574|family with sequence similarity 115, member A	NM_029930|Fam115a|77574|family with sequence similarity 115, member A	BC031718|Fam115a|77574|family with sequence similarity 115, member A
mm9_v1_chr9_-_57612906_57612972	1.63253	SOX2.p2	AK090215|Clk3|102414|CDC-like kinase 3	AK140015|Clk3|102414|CDC-like kinase 3	BC085084|Clk3|102414|CDC-like kinase 3	AK133936|Clk3|102414|CDC-like kinase 3	AK154003|Clk3|102414|CDC-like kinase 3	AK145880|Clk3|102414|CDC-like kinase 3	AK136481|Clk3|102414|CDC-like kinase 3
mm9_v1_chr7_-_97103461_97103540	1.6323	SOX2.p2	
mm9_v1_chr9_-_110018085_110018088	1.62967	SOX2.p2	AB047557|Dhx30|72831|DEAH (Asp-Glu-Ala-His) box polypeptide 30	NM_133347|Dhx30|72831|DEAH (Asp-Glu-Ala-His) box polypeptide 30	BC058331|Dhx30|72831|DEAH (Asp-Glu-Ala-His) box polypeptide 30
mm9_v1_chrX_+_133371611_133371673	1.62912	SOX2.p2	AK199492|Plp1|18823|proteolipid protein (myelin) 1
mm9_v1_chr4_+_13670425_13670448	1.62663	SOX2.p2	AK142006|Runx1t1|12395|runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	NM_001111026|Runx1t1|12395|runt-related transcription factor 1; translocated to, 1 (cyclin D-related)
mm9_v1_chr2_+_163843744_163843775	1.62119	SOX2.p2	
mm9_v1_chr19_-_37250472_37250552	1.62069	SOX2.p2	AK147243|Cpeb3|208922|cytoplasmic polyadenylation element binding protein 3
mm9_v1_chr4_+_6118235_6118245	1.62021	SOX2.p2	AK049018|Ubxn2b|68053|UBX domain protein 2B
mm9_v1_chr17_-_35972184_35972488	1.6097	SOX2.p2	M28732|Tubb5|22154|tubulin, beta 5	BC047993|Tubb5|22154|tubulin, beta 5
mm9_v1_chrX_+_7496899_7497045	1.60945	SOX2.p2	AF181560|Pcsk1n|30052|proprotein convertase subtilisin/kexin type 1 inhibitor	NM_013892|Pcsk1n|30052|proprotein convertase subtilisin/kexin type 1 inhibitor	AF293356|Pcsk1n|30052|proprotein convertase subtilisin/kexin type 1 inhibitor	AK076137|Pcsk1n|30052|proprotein convertase subtilisin/kexin type 1 inhibitor	AK002969|Pcsk1n|30052|proprotein convertase subtilisin/kexin type 1 inhibitor	BC012263|Pcsk1n|30052|proprotein convertase subtilisin/kexin type 1 inhibitor
mm9_v1_chr19_-_8963245_8963262	1.60736	SOX2.p2	BC027679|5730408K05Rik|67531|RIKEN cDNA 5730408K05 gene	AK019951|5730408K05Rik|67531|RIKEN cDNA 5730408K05 gene	AK017527|5730408K05Rik|67531|RIKEN cDNA 5730408K05 gene	AK043270|5730408K05Rik|67531|RIKEN cDNA 5730408K05 gene
mm9_v1_chr5_-_124170947_124171001	1.60453	SOX2.p2	AK017857|Zcchc8|70650|zinc finger, CCHC domain containing 8	AK167126|Zcchc8|70650|zinc finger, CCHC domain containing 8	AK166990|Zcchc8|70650|zinc finger, CCHC domain containing 8	AK167736|Zcchc8|70650|zinc finger, CCHC domain containing 8	AK033469|Zcchc8|70650|zinc finger, CCHC domain containing 8
mm9_v1_chr5_+_106305563_106305620	1.60399	SOX2.p2	AK017693|Zfp326|54367|zinc finger protein 326	AK032801|Zfp326|54367|zinc finger protein 326	BC039041|Zfp326|54367|zinc finger protein 326	NM_018759|Zfp326|54367|zinc finger protein 326	BC005567|Zfp326|54367|zinc finger protein 326	BC037055|Zfp326|54367|zinc finger protein 326	AK146438|Zfp326|54367|zinc finger protein 326	AB012725|Zfp326|54367|zinc finger protein 326
mm9_v1_chr11_+_75195846_75195864	1.60394	SOX2.p2	AK173306|Smyd4|319822|SET and MYND domain containing 4
mm9_v1_chr11_+_59476016_59476061	1.60389	SOX2.p2	BC063067|Mprip|26936|myosin phosphatase Rho interacting protein
mm9_v1_chr1_-_163748523_163748605	1.60144	SOX2.p2	AK033720|AI848100|226551|expressed sequence AI848100
mm9_v1_chr8_-_44613490_44613490	1.59658	SOX2.p2	AK015931|Adam26b|382007|a disintegrin and metallopeptidase domain 26B	NM_001009547|Adam26b|382007|a disintegrin and metallopeptidase domain 26B
mm9_v1_chr13_-_94269616_94269653	1.59555	SOX2.p2	BC069906|Jmy|57748|junction-mediating and regulatory protein	BC090835|Jmy|57748|junction-mediating and regulatory protein	NM_021310|Jmy|57748|junction-mediating and regulatory protein
mm9_v1_chr5_+_31014229_31014273	1.59493	SOX2.p2	AK044866|Dpysl5|65254|dihydropyrimidinase-like 5	BC065054|Dpysl5|65254|dihydropyrimidinase-like 5	NM_023047|Dpysl5|65254|dihydropyrimidinase-like 5	BC103789|Dpysl5|65254|dihydropyrimidinase-like 5
mm9_v1_chr18_+_37467108_37467135	1.59425	SOX2.p2	AK036169|Pcdhb4|93875|protocadherin beta 4	AK143280|Pcdhb4|93875|protocadherin beta 4	AK160730|Pcdhb4|93875|protocadherin beta 4	NM_053129|Pcdhb4|93875|protocadherin beta 4	AK029277|Pcdhb4|93875|protocadherin beta 4	BC053098|Pcdhb4|93875|protocadherin beta 4
mm9_v1_chr11_-_102786433_102786439	1.59128	SOX2.p2	NM_197959|Kif18b|70218|kinesin family member 18B
mm9_v1_chr1_-_141677744_141677835	1.58487	SOX2.p2	AJ871401|EG214403|214403|predicted gene, EG214403	AJ871402|EG214403|214403|predicted gene, EG214403	BC141136|EG214403|214403|predicted gene, EG214403	BC145444|EG214403|214403|predicted gene, EG214403	M29009|EG214403|214403|predicted gene, EG214403	NM_001029977|EG214403|214403|predicted gene, EG214403	NM_001160303|EG214403|214403|predicted gene, EG214403	NM_001160304|EG214403|214403|predicted gene, EG214403
mm9_v1_chr5_+_98609872_98610052	1.58262	SOX2.p2	AK050852|Prdm8|77630|PR domain containing 8	NM_029947|Prdm8|77630|PR domain containing 8	AK036202|Prdm8|77630|PR domain containing 8	AK044713|Prdm8|77630|PR domain containing 8	BC141020|Prdm8|77630|PR domain containing 8
mm9_v1_chr5_+_138882703_138882746	1.58232	SOX2.p2	NM_028130|Zfp157|72154|zinc finger protein 157	AK042470|Zfp157|72154|zinc finger protein 157	BC059261|Zfp157|72154|zinc finger protein 157	AK083851|Zfp157|72154|zinc finger protein 157	BC049676|Zfp157|72154|zinc finger protein 157	AK028290|Zfp157|72154|zinc finger protein 157
mm9_v1_chr9_-_44613544_44613680	1.58163	SOX2.p2	
mm9_v1_chr18_+_37974732_37974732	1.57807	SOX2.p2	BC064808|Pcdhgc4|93707|protocadherin gamma subfamily C, 4	NM_033582|Pcdhgc4|93707|protocadherin gamma subfamily C, 4
mm9_v1_chr4_+_120550473_120550605	1.57308	SOX2.p2	AY326953|Rims3|242662|regulating synaptic membrane exocytosis 3	BC115536|Rims3|242662|regulating synaptic membrane exocytosis 3	NM_182929|Rims3|242662|regulating synaptic membrane exocytosis 3	AK122226|Rims3|242662|regulating synaptic membrane exocytosis 3
mm9_v1_chr11_-_41996099_41996133	1.57271	SOX2.p2	M63436|Gabra1|14394|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1	BC132331|Gabra1|14394|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1	BC137733|Gabra1|14394|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1
mm9_v1_chr15_+_58731646_58731691	1.57147	SOX2.p2	AK016137|Rnf139|75841|ring finger protein 139
mm9_v1_chr18_+_37493599_37493681	1.56923	SOX2.p2	BC150716|Pcdhb6|93877|protocadherin beta 6	AY013788|Pcdhb6|93877|protocadherin beta 6	NM_053131|Pcdhb6|93877|protocadherin beta 6
mm9_v1_chr8_-_87538229_87538429	1.56769	SOX2.p2	BC036163|Best2|212989|bestrophin 2	NM_001130193|Best2|212989|bestrophin 2	BC036157|Best2|212989|bestrophin 2	NM_001130194|Best2|212989|bestrophin 2	NM_145388|Best2|212989|bestrophin 2	AY450428|Best2|212989|bestrophin 2
mm9_v1_chr11_-_58745825_58746102	1.55743	SOX2.p2	AK219828|Rnf187|108660|ring finger protein 187
mm9_v1_chr9_+_86360760_86360843	1.55391	SOX2.p2	NM_177208|Dopey1|320615|dopey family member 1	AK054511|Dopey1|320615|dopey family member 1	AK082462|Dopey1|320615|dopey family member 1	AK044820|Dopey1|320615|dopey family member 1	AK052544|Dopey1|320615|dopey family member 1	AK045873|Dopey1|320615|dopey family member 1
mm9_v1_chr14_-_11285927_11285966	1.54925	SOX2.p2	BC012662|Fhit|14198|fragile histidine triad gene
mm9_v1_chr18_+_37979199_37979219	1.54752	SOX2.p2	AF464163|Pcdhgc5|93708|protocadherin gamma subfamily C, 5	NM_033583|Pcdhgc5|93708|protocadherin gamma subfamily C, 5	AF464164|Pcdhgb4|93701|protocadherin gamma subfamily B, 4
mm9_v1_chr8_+_63702967_63703040	1.54195	SOX2.p2	NM_021506|Sh3rf1|59009|SH3 domain containing ring finger 1	BC060113|Sh3rf1|59009|SH3 domain containing ring finger 1	BC060696|Sh3rf1|59009|SH3 domain containing ring finger 1	AK088003|Sh3rf1|59009|SH3 domain containing ring finger 1	AK148137|Sh3rf1|59009|SH3 domain containing ring finger 1
mm9_v1_chr10_-_81090064_81090088	1.54053	SOX2.p2	AK145929|Sirt6|50721|sirtuin 6 (silent mating type information regulation 2, homolog) 6 (S. cerevisiae)	NM_001163430|Sirt6|50721|sirtuin 6 (silent mating type information regulation 2, homolog) 6 (S. cerevisiae)
mm9_v1_chr16_+_18877336_18877523	1.53886	SOX2.p2	X92590|Hira|15260|histone cell cycle regulation defective homolog A (S. cerevisiae)	X75295|Hira|15260|histone cell cycle regulation defective homolog A (S. cerevisiae)	X99712|Hira|15260|histone cell cycle regulation defective homolog A (S. cerevisiae)
mm9_v1_chr12_-_86480787_86480938	1.53352	SOX2.p2	AK036734|Rps6kl1|238323|ribosomal protein S6 kinase-like 1
mm9_v1_chr4_+_140257340_140257464	1.53138	SOX2.p2	NM_173867|Rcc2|108911|regulator of chromosome condensation 2	BC060624|Rcc2|108911|regulator of chromosome condensation 2	AK076040|Rcc2|108911|regulator of chromosome condensation 2	BC086666|Rcc2|108911|regulator of chromosome condensation 2
mm9_v1_chr11_+_100442831_100442963	1.52643	SOX2.p2	AK217119|Cnp|12799|2',3'-cyclic nucleotide 3' phosphodiesterase
mm9_v1_chrX_-_153929935_153930011	1.52577	SOX2.p2	AK017775|Sms|20603|spermine synthase	Y09419|Sms|20603|spermine synthase	BC046623|Sms|20603|spermine synthase	AF031486|Sms|20603|spermine synthase	AK049787|Sms|20603|spermine synthase	AK160637|Sms|20603|spermine synthase	AK149929|Sms|20603|spermine synthase	AK002687|Sms|20603|spermine synthase	AK049780|Sms|20603|spermine synthase	AK136798|Sms|20603|spermine synthase	AK011542|Sms|20603|spermine synthase	AK160659|Sms|20603|spermine synthase	NM_009214|Sms|20603|spermine synthase	AK166665|Sms|20603|spermine synthase
mm9_v1_chr11_-_94154354_94154488	1.52445	SOX2.p2	BC055921|Luc7l3|67684|LUC7-like 3 (S. cerevisiae)
mm9_v1_chr5_-_114280434_114280521	1.51788	SOX2.p2	AK089214|Selplg|20345|selectin, platelet (p-selectin) ligand	AK155762|Selplg|20345|selectin, platelet (p-selectin) ligand	AK156933|Selplg|20345|selectin, platelet (p-selectin) ligand	AK158134|Selplg|20345|selectin, platelet (p-selectin) ligand	BC003874|Selplg|20345|selectin, platelet (p-selectin) ligand	AK172077|Selplg|20345|selectin, platelet (p-selectin) ligand	AK171693|Selplg|20345|selectin, platelet (p-selectin) ligand	AK156551|Selplg|20345|selectin, platelet (p-selectin) ligand	AK089188|Selplg|20345|selectin, platelet (p-selectin) ligand	NM_009151|Selplg|20345|selectin, platelet (p-selectin) ligand
mm9_v1_chr12_-_35213738_35213753	1.51399	SOX2.p2	BC098187|Hdac9|79221|histone deacetylase 9	NM_024124|Hdac9|79221|histone deacetylase 9
mm9_v1_chr13_-_58228398_58228433	1.51361	SOX2.p2	AK172180|Hnrnpa0|77134|heterogeneous nuclear ribonucleoprotein A0
mm9_v1_chr18_-_43597640_43597708	1.50993	SOX2.p2	AK149024|Dpysl3|22240|dihydropyrimidinase-like 3
mm9_v1_chr11_+_87391881_87392001	1.50771	SOX2.p2	AK133933|Sept4|18952|septin 4	AK137299|Sept4|18952|septin 4	AK039859|Sept4|18952|septin 4
mm9_v1_chr5_+_31191349_31191378	1.5047	SOX2.p2	BC057349|Agbl5|231093|ATP/GTP binding protein-like 5	DQ867034|Agbl5|231093|ATP/GTP binding protein-like 5	DQ867035|Agbl5|231093|ATP/GTP binding protein-like 5	DQ867036|Agbl5|231093|ATP/GTP binding protein-like 5	DQ867037|Agbl5|231093|ATP/GTP binding protein-like 5	DQ867038|Agbl5|231093|ATP/GTP binding protein-like 5	NM_001048192|Agbl5|231093|ATP/GTP binding protein-like 5
mm9_v1_chr14_-_52723590_52723721	1.50353	SOX2.p2	AK214960|Hnrnpc|15381|heterogeneous nuclear ribonucleoprotein C	AK184811|Hnrnpc|15381|heterogeneous nuclear ribonucleoprotein C	BC095922|Hnrnpc|15381|heterogeneous nuclear ribonucleoprotein C	AF095257|Hnrnpc|15381|heterogeneous nuclear ribonucleoprotein C	AK012633|Hnrnpc|15381|heterogeneous nuclear ribonucleoprotein C	BC004706|Hnrnpc|15381|heterogeneous nuclear ribonucleoprotein C	AK011336|Hnrnpc|15381|heterogeneous nuclear ribonucleoprotein C	AK088678|Hnrnpc|15381|heterogeneous nuclear ribonucleoprotein C	AK169287|Hnrnpc|15381|heterogeneous nuclear ribonucleoprotein C	AK168802|Hnrnpc|15381|heterogeneous nuclear ribonucleoprotein C	AK010845|Hnrnpc|15381|heterogeneous nuclear ribonucleoprotein C	AK150399|Hnrnpc|15381|heterogeneous nuclear ribonucleoprotein C	AK019958|Hnrnpc|15381|heterogeneous nuclear ribonucleoprotein C	AK088245|Hnrnpc|15381|heterogeneous nuclear ribonucleoprotein C	AK151446|Hnrnpc|15381|heterogeneous nuclear ribonucleoprotein C	AK153053|Hnrnpc|15381|heterogeneous nuclear ribonucleoprotein C	AK089061|Hnrnpc|15381|heterogeneous nuclear ribonucleoprotein C	AK166590|Hnrnpc|15381|heterogeneous nuclear ribonucleoprotein C	NM_001170981|Hnrnpc|15381|heterogeneous nuclear ribonucleoprotein C	NM_001170982|Hnrnpc|15381|heterogeneous nuclear ribonucleoprotein C	NM_001170983|Hnrnpc|15381|heterogeneous nuclear ribonucleoprotein C	NM_001170984|Hnrnpc|15381|heterogeneous nuclear ribonucleoprotein C	NM_016884|Hnrnpc|15381|heterogeneous nuclear ribonucleoprotein C
mm9_v1_chr5_-_124171015_124171067	1.49626	SOX2.p2	AK156770|Zcchc8|70650|zinc finger, CCHC domain containing 8	AK032349|Zcchc8|70650|zinc finger, CCHC domain containing 8	NM_027494|Zcchc8|70650|zinc finger, CCHC domain containing 8
mm9_v1_chr15_+_88890519_88890533	1.49422	SOX2.p2	DQ093579|Panx2|406218|pannexin 2
mm9_v1_chr14_-_61664997_61665146	1.4935	SOX2.p2	AK028146|Tnfrsf19|29820|tumor necrosis factor receptor superfamily, member 19	AF167554|Tnfrsf19|29820|tumor necrosis factor receptor superfamily, member 19
mm9_v1_chr3_+_121129502_121129542	1.4926	SOX2.p2	AK081672|Cnn3|71994|calponin 3, acidic
mm9_v1_chr7_-_135020290_135020344	1.48652	SOX2.p2	BC028251|Zfp668|244219|zinc finger protein 668	AK047593|Zfp668|244219|zinc finger protein 668	AK081436|Zfp668|244219|zinc finger protein 668	AK053438|Zfp668|244219|zinc finger protein 668	NM_146259|Zfp668|244219|zinc finger protein 668	AK169556|Zfp668|244219|zinc finger protein 668
mm9_v1_chr16_-_38828843_38828861	1.48612	SOX2.p2	AK015321|4930435E12Rik|74663|RIKEN cDNA 4930435E12 gene	BC115688|4930435E12Rik|74663|RIKEN cDNA 4930435E12 gene	AK077164|4930435E12Rik|74663|RIKEN cDNA 4930435E12 gene	NM_029042|4930435E12Rik|74663|RIKEN cDNA 4930435E12 gene
mm9_v1_chr13_-_76081244_76081314	1.48508	SOX2.p2	BC005664|Rhobtb3|73296|Rho-related BTB domain containing 3	BC050836|Rhobtb3|73296|Rho-related BTB domain containing 3	NM_028493|Rhobtb3|73296|Rho-related BTB domain containing 3	AK129234|Rhobtb3|73296|Rho-related BTB domain containing 3
mm9_v1_chr7_-_81429262_81429274	1.48364	SOX2.p2	AK020010|Slco3a1|108116|solute carrier organic anion transporter family, member 3a1
mm9_v1_chr4_-_129012489_129012496	1.47999	SOX2.p2	AK141176|Rbbp4|19646|retinoblastoma binding protein 4
mm9_v1_chr2_-_30952019_30952019	1.46886	SOX2.p2	AK143512|Fnbp1|14269|formin binding protein 1	NM_001177650|Fnbp1|14269|formin binding protein 1
mm9_v1_chrX_-_109520387_109520387	1.46045	SOX2.p2	BC138009|Satl1|73809|spermidine/spermine N1-acetyl transferase-like 1	BC138011|Satl1|73809|spermidine/spermine N1-acetyl transferase-like 1	NM_028655|Satl1|73809|spermidine/spermine N1-acetyl transferase-like 1
mm9_v1_chr10_+_3323355_3323355	1.45731	SOX2.p2	NM_001033391|Ipcef1|320495|interaction protein for cytohesin exchange factors 1
mm9_v1_chr1_-_166388431_166388540	1.45449	SOX2.p2	AK010677|Atp1b1|11931|ATPase, Na+/K+ transporting, beta 1 polypeptide	NM_009721|Atp1b1|11931|ATPase, Na+/K+ transporting, beta 1 polypeptide
mm9_v1_chr14_+_55506625_55506792	1.45442	SOX2.p2	AK020321|Bcl2l2|12050|BCL2-like 2	AK020923|Bcl2l2|12050|BCL2-like 2
mm9_v1_chr16_-_18289209_18289363	1.45415	SOX2.p2	AK086233|Dgcr8|94223|DiGeorge syndrome critical region gene 8	AB086857|Dgcr8|94223|DiGeorge syndrome critical region gene 8	NM_033324|Dgcr8|94223|DiGeorge syndrome critical region gene 8	BC062919|Dgcr8|94223|DiGeorge syndrome critical region gene 8	BC066118|Dgcr8|94223|DiGeorge syndrome critical region gene 8
mm9_v1_chr12_-_113749361_113749362	1.45069	SOX2.p2	BC055014|Tmem179|104885|transmembrane protein 179
mm9_v1_chr1_-_65097587_65097736	1.45026	SOX2.p2	K02584|Cryge|12968|crystallin, gamma E	BC057012|Cryge|12968|crystallin, gamma E	BC078417|Cryge|12968|crystallin, gamma E	AK014301|Cryge|12968|crystallin, gamma E	BC132506|Cryge|12968|crystallin, gamma E	BC132508|Cryge|12968|crystallin, gamma E	NM_007777|Cryge|12968|crystallin, gamma E
mm9_v1_chr10_-_12587945_12588041	1.44958	SOX2.p2	BC062163|Utrn|22288|utrophin	BC011062|Utrn|22288|utrophin
mm9_v1_chr3_+_90280032_90280140	1.4471	SOX2.p2	AK135449|Ilf2|67781|interleukin enhancer binding factor 2	AK161127|Ilf2|67781|interleukin enhancer binding factor 2	AK031892|Ilf2|67781|interleukin enhancer binding factor 2	AK157129|Ilf2|67781|interleukin enhancer binding factor 2	AK013858|Ilf2|67781|interleukin enhancer binding factor 2	AK044885|Ilf2|67781|interleukin enhancer binding factor 2	AK161126|Ilf2|67781|interleukin enhancer binding factor 2	BC024718|Ilf2|67781|interleukin enhancer binding factor 2	NM_026374|Ilf2|67781|interleukin enhancer binding factor 2	AK012364|Ilf2|67781|interleukin enhancer binding factor 2	AK078003|Ilf2|67781|interleukin enhancer binding factor 2	AK135539|Ilf2|67781|interleukin enhancer binding factor 2
mm9_v1_chr14_-_67487226_67487503	1.44524	SOX2.p2	Y10339|Dpysl2|12934|dihydropyrimidinase-like 2	X87242|Dpysl2|12934|dihydropyrimidinase-like 2	BC062955|Dpysl2|12934|dihydropyrimidinase-like 2	NM_009955|Dpysl2|12934|dihydropyrimidinase-like 2
mm9_v1_chr5_-_147395979_147395979	1.44331	SOX2.p2	BC055746|Gpr12|14738|G-protein coupled receptor 12	NM_008151|Gpr12|14738|G-protein coupled receptor 12
mm9_v1_chr3_-_84284304_84284362	1.44266	SOX2.p2	BC042779|Fhdc1|229474|FH2 domain containing 1	AK145217|Fhdc1|229474|FH2 domain containing 1	NM_001033301|Fhdc1|229474|FH2 domain containing 1
mm9_v1_chr7_-_134758707_134758785	1.44247	SOX2.p2	BC035547|Zfp629|320683|zinc finger protein 629	AK172933|Zfp629|320683|zinc finger protein 629	AK034484|Zfp629|320683|zinc finger protein 629	AK031161|Zfp629|320683|zinc finger protein 629
mm9_v1_chr13_-_58227306_58227430	1.43977	SOX2.p2	BC048746|Hnrnpa0|77134|heterogeneous nuclear ribonucleoprotein A0
mm9_v1_chr2_+_102498798_102498825	1.43885	SOX2.p2	U75372|Slc1a2|20511|solute carrier family 1 (glial high affinity glutamate transporter), member 2
mm9_v1_chr17_-_88464225_88464367	1.43841	SOX2.p2	BC110686|Fbxo11|225055|F-box protein 11
mm9_v1_chr5_+_21049296_21049344	1.43569	SOX2.p2	NM_028977|Lrrc17|74511|leucine rich repeat containing 17
mm9_v1_chr3_+_64913289_64913311	1.43496	SOX2.p2	AK031362|Kcnab1|16497|potassium voltage-gated channel, shaker-related subfamily, beta member 1	AK138467|Kcnab1|16497|potassium voltage-gated channel, shaker-related subfamily, beta member 1	X97281|Kcnab1|16497|potassium voltage-gated channel, shaker-related subfamily, beta member 1
mm9_v1_chr17_+_33569840_33569843	1.43159	SOX2.p2	AK006498|Actl9|69481|actin-like 9	NM_183282|Actl9|69481|actin-like 9
mm9_v1_chr6_-_86683330_86683393	1.43072	SOX2.p2	BC054767|Gmcl1|23885|germ cell-less homolog 1 (Drosophila)	AK146964|Gmcl1|23885|germ cell-less homolog 1 (Drosophila)	AK004716|Gmcl1|23885|germ cell-less homolog 1 (Drosophila)	AK155238|Gmcl1|23885|germ cell-less homolog 1 (Drosophila)	NM_011818|Gmcl1|23885|germ cell-less homolog 1 (Drosophila)
mm9_v1_chr3_+_137806411_137806513	1.43064	SOX2.p2	AK089967|Rg9mtd2|108943|RNA (guanine-9-) methyltransferase domain containing 2	AK145681|Rg9mtd2|108943|RNA (guanine-9-) methyltransferase domain containing 2	BC098478|Rg9mtd2|108943|RNA (guanine-9-) methyltransferase domain containing 2	AK146481|Rg9mtd2|108943|RNA (guanine-9-) methyltransferase domain containing 2	BC090650|Rg9mtd2|108943|RNA (guanine-9-) methyltransferase domain containing 2	NM_175389|Rg9mtd2|108943|RNA (guanine-9-) methyltransferase domain containing 2	BC141035|Rg9mtd2|108943|RNA (guanine-9-) methyltransferase domain containing 2
mm9_v1_chr3_+_130320365_130320530	1.43009	SOX2.p2	AK049937|Agxt2l1|71760|alanine-glyoxylate aminotransferase 2-like 1	NM_001163587|Agxt2l1|71760|alanine-glyoxylate aminotransferase 2-like 1	AK030395|Agxt2l1|71760|alanine-glyoxylate aminotransferase 2-like 1	AK005060|Agxt2l1|71760|alanine-glyoxylate aminotransferase 2-like 1	NM_027907|Agxt2l1|71760|alanine-glyoxylate aminotransferase 2-like 1	BC043680|Agxt2l1|71760|alanine-glyoxylate aminotransferase 2-like 1	BC022644|Agxt2l1|71760|alanine-glyoxylate aminotransferase 2-like 1	BC058592|Agxt2l1|71760|alanine-glyoxylate aminotransferase 2-like 1
mm9_v1_chr11_-_102152310_102152512	1.42922	SOX2.p2	AK218190|Atxn7l3|217218|ataxin 7-like 3	AK053165|Atxn7l3|217218|ataxin 7-like 3
mm9_v1_chr11_-_69229653_69229709	1.42714	SOX2.p2	BC075632|Kdm6b|216850|KDM1 lysine (K)-specific demethylase 6B
mm9_v1_chr19_-_5799376_5799434	1.42518	SOX2.p2	AK020483|Malat1|72289|metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)
mm9_v1_chr10_-_52058305_52058381	1.42499	SOX2.p2	AK008806|Gopc|94221|golgi associated PDZ and coiled-coil motif containing
mm9_v1_chrX_-_91787317_91787335	1.42304	SOX2.p2	BC016438|Maged1|94275|melanoma antigen, family D, 1	AK017275|Maged1|94275|melanoma antigen, family D, 1	AK145872|Maged1|94275|melanoma antigen, family D, 1
mm9_v1_chr1_+_109258889_109258923	1.4218	SOX2.p2	AK009003|Serpinb11|66957|serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 11	AK009855|Serpinb11|66957|serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 11	NM_025867|Serpinb11|66957|serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 11	BC010313|Serpinb11|66957|serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 11
mm9_v1_chr1_-_5060365_5060365	1.42082	SOX2.p2	NM_001177795|Rgs20|58175|regulator of G-protein signaling 20
mm9_v1_chr7_+_117266253_117266328	1.41731	SOX2.p2	AK039572|Wee1|22390|WEE 1 homolog 1 (S. pombe)
mm9_v1_chr2_+_177876635_177876639	1.41695	SOX2.p2	AK135144|Phactr3|74189|phosphatase and actin regulator 3	NM_028806|Phactr3|74189|phosphatase and actin regulator 3
mm9_v1_chr6_-_98877291_98877410	1.41656	SOX2.p2	
mm9_v1_chr8_-_73223897_73223993	1.4159	SOX2.p2	AK135112|Gm11175|100303737|predicted gene 11175
mm9_v1_chr19_+_34035676_34035740	1.41236	SOX2.p2	AK009923|Lipf|67717|lipase, gastric	AK009428|Lipf|67717|lipase, gastric	AK009431|Lipf|67717|lipase, gastric	AK009546|Lipf|67717|lipase, gastric	AK075913|Lipf|67717|lipase, gastric	AK009300|Lipf|67717|lipase, gastric	AK009359|Lipf|67717|lipase, gastric	AK009413|Lipf|67717|lipase, gastric	AK009437|Lipf|67717|lipase, gastric	AK009459|Lipf|67717|lipase, gastric	AK009473|Lipf|67717|lipase, gastric	AK009474|Lipf|67717|lipase, gastric	AK009523|Lipf|67717|lipase, gastric	AK009525|Lipf|67717|lipase, gastric	AK009537|Lipf|67717|lipase, gastric	AK009560|Lipf|67717|lipase, gastric	AK009571|Lipf|67717|lipase, gastric	AK009573|Lipf|67717|lipase, gastric	AK009729|Lipf|67717|lipase, gastric	AK009773|Lipf|67717|lipase, gastric	AK009875|Lipf|67717|lipase, gastric	AK009990|Lipf|67717|lipase, gastric	AK010019|Lipf|67717|lipase, gastric	AK010026|Lipf|67717|lipase, gastric	AK010035|Lipf|67717|lipase, gastric	AK010036|Lipf|67717|lipase, gastric	AK010058|Lipf|67717|lipase, gastric	AK010061|Lipf|67717|lipase, gastric	AK010091|Lipf|67717|lipase, gastric	AK010093|Lipf|67717|lipase, gastric	AK010103|Lipf|67717|lipase, gastric	AK010106|Lipf|67717|lipase, gastric	AK010110|Lipf|67717|lipase, gastric	AK010116|Lipf|67717|lipase, gastric	AK010123|Lipf|67717|lipase, gastric	AK010125|Lipf|67717|lipase, gastric	AK010139|Lipf|67717|lipase, gastric	AK010148|Lipf|67717|lipase, gastric	AK010173|Lipf|67717|lipase, gastric	AK010203|Lipf|67717|lipase, gastric	AK010231|Lipf|67717|lipase, gastric	AK010236|Lipf|67717|lipase, gastric	BC061067|Lipf|67717|lipase, gastric	NM_026334|Lipf|67717|lipase, gastric	AK009479|Lipf|67717|lipase, gastric	AK009544|Lipf|67717|lipase, gastric
mm9_v1_chr2_-_143688908_143688908	1.40875	SOX2.p2	BC057580|Bfsp1|12075|beaded filament structural protein 1, in lens-CP94	NM_009751|Bfsp1|12075|beaded filament structural protein 1, in lens-CP94
mm9_v1_chr5_+_110425526_110425559	1.40488	SOX2.p2	AK009062|Zfp932|69504|zinc finger protein 932	NM_145563|Zfp932|69504|zinc finger protein 932	BC012405|Zfp932|69504|zinc finger protein 932
mm9_v1_chr5_-_92511942_92511942	1.40482	SOX2.p2	AK149427|G3bp2|23881|GTPase activating protein (SH3 domain) binding protein 2	NM_001080797|G3bp2|23881|GTPase activating protein (SH3 domain) binding protein 2
mm9_v1_chr14_+_58691522_58691522	1.40368	SOX2.p2	AK158782|Fgf9|14180|fibroblast growth factor 9	NM_013518|Fgf9|14180|fibroblast growth factor 9
mm9_v1_chr10_+_77505031_77505031	1.40307	SOX2.p2	EF051624|Dnmt3l|54427|DNA (cytosine-5-)-methyltransferase 3-like	NM_001081695|Dnmt3l|54427|DNA (cytosine-5-)-methyltransferase 3-like
mm9_v1_chr15_-_90880241_90880381	1.40097	SOX2.p2	AF202892|Kif21a|16564|kinesin family member 21A	BC060698|Kif21a|16564|kinesin family member 21A	BC062896|Kif21a|16564|kinesin family member 21A	AK163536|Kif21a|16564|kinesin family member 21A	AK047880|Kif21a|16564|kinesin family member 21A	AK147436|Kif21a|16564|kinesin family member 21A	AK008213|Kif21a|16564|kinesin family member 21A	AK047350|Kif21a|16564|kinesin family member 21A	NM_001109040|Kif21a|16564|kinesin family member 21A	NM_001109041|Kif21a|16564|kinesin family member 21A	NM_001109042|Kif21a|16564|kinesin family member 21A	NM_016705|Kif21a|16564|kinesin family member 21A	AK019525|Kif21a|16564|kinesin family member 21A
mm9_v1_chr9_+_108998083_108998108	1.39746	SOX2.p2	AB072381|Plxnb1|235611|plexin B1
mm9_v1_chr1_-_55084321_55084327	1.39742	SOX2.p2	NM_031179|Sf3b1|81898|splicing factor 3b, subunit 1	AB037890|Sf3b1|81898|splicing factor 3b, subunit 1	AK165992|Sf3b1|81898|splicing factor 3b, subunit 1
mm9_v1_chr1_-_170085798_170085873	1.39624	SOX2.p2	AK080184|Pbx1|18514|pre B-cell leukemia transcription factor 1	AK032161|Pbx1|18514|pre B-cell leukemia transcription factor 1	AK043495|Pbx1|18514|pre B-cell leukemia transcription factor 1	AK085198|Pbx1|18514|pre B-cell leukemia transcription factor 1
mm9_v1_chr10_-_121484248_121484370	1.39271	SOX2.p2	NM_001081037|Srgap1|117600|SLIT-ROBO Rho GTPase activating protein 1	BC120892|Srgap1|117600|SLIT-ROBO Rho GTPase activating protein 1	BC120893|Srgap1|117600|SLIT-ROBO Rho GTPase activating protein 1	AK138257|Srgap1|117600|SLIT-ROBO Rho GTPase activating protein 1
mm9_v1_chr2_-_77357674_77357722	1.39111	SOX2.p2	AK078551|Zfp385b|241494|zinc finger protein 385B	AK050293|Zfp385b|241494|zinc finger protein 385B	NM_001113400|Zfp385b|241494|zinc finger protein 385B
mm9_v1_chr13_-_76081142_76081219	1.38903	SOX2.p2	AK139158|Rhobtb3|73296|Rho-related BTB domain containing 3	AK020938|Rhobtb3|73296|Rho-related BTB domain containing 3
mm9_v1_chr6_+_51420581_51420714	1.38822	SOX2.p2	NM_007624|Cbx3|12417|chromobox homolog 3 (Drosophila HP1 gamma)	AK002910|Cbx3|12417|chromobox homolog 3 (Drosophila HP1 gamma)	AK017958|Cbx3|12417|chromobox homolog 3 (Drosophila HP1 gamma)	AK146376|Cbx3|12417|chromobox homolog 3 (Drosophila HP1 gamma)	BC003840|Cbx3|12417|chromobox homolog 3 (Drosophila HP1 gamma)	BC108370|Cbx3|12417|chromobox homolog 3 (Drosophila HP1 gamma)	AK083957|Cbx3|12417|chromobox homolog 3 (Drosophila HP1 gamma)	BC059831|Cbx3|12417|chromobox homolog 3 (Drosophila HP1 gamma)
mm9_v1_chr9_+_69855789_69855998	1.38487	SOX2.p2	AF071429|Bnip2|12175|BCL2/adenovirus E1B interacting protein 2	AK161900|Bnip2|12175|BCL2/adenovirus E1B interacting protein 2
mm9_v1_chr2_+_28048779_28048916	1.38382	SOX2.p2	AF028740|Olfm1|56177|olfactomedin 1
mm9_v1_chr14_+_45119792_45119792	1.38367	SOX2.p2	BC061237|BC061237|385138|cDNA sequence BC061237	NM_198677|BC061237|385138|cDNA sequence BC061237
mm9_v1_chr1_-_93829376_93829378	1.3835	SOX2.p2	AK170461|Hdac4|208727|histone deacetylase 4
mm9_v1_chr3_+_101266000_101266048	1.38016	SOX2.p2	AK012857|Igsf3|78908|immunoglobulin superfamily, member 3
mm9_v1_chr12_+_111805938_111806039	1.37942	SOX2.p2	AK047089|Ppp2r5c|26931|protein phosphatase 2, regulatory subunit B (B56), gamma isoform	AK178752|Ppp2r5c|26931|protein phosphatase 2, regulatory subunit B (B56), gamma isoform	AK196801|Ppp2r5c|26931|protein phosphatase 2, regulatory subunit B (B56), gamma isoform	AK201559|Ppp2r5c|26931|protein phosphatase 2, regulatory subunit B (B56), gamma isoform	AK211769|Ppp2r5c|26931|protein phosphatase 2, regulatory subunit B (B56), gamma isoform
mm9_v1_chr3_+_101180976_101181070	1.37893	SOX2.p2	AK083000|Igsf3|78908|immunoglobulin superfamily, member 3	AK084011|Igsf3|78908|immunoglobulin superfamily, member 3	AK129151|Igsf3|78908|immunoglobulin superfamily, member 3	NM_207205|Igsf3|78908|immunoglobulin superfamily, member 3
mm9_v1_chr14_-_37911383_37911496	1.37411	SOX2.p2	AF426393|Cdhr1|170677|cadherin-related family member 1	BC042454|Cdhr1|170677|cadherin-related family member 1	AK143151|Cdhr1|170677|cadherin-related family member 1	BC058270|Cdhr1|170677|cadherin-related family member 1	NM_130878|Cdhr1|170677|cadherin-related family member 1
mm9_v1_chr11_-_106646226_106646242	1.37074	SOX2.p2	AK013106|Ddx5|13207|DEAD (Asp-Glu-Ala-Asp) box polypeptide 5
mm9_v1_chr16_+_92086695_92086827	1.36761	SOX2.p2	AK133105|Slc5a3|53881|solute carrier family 5 (inositol transporters), member 3
mm9_v1_chr10_-_10802102_10802153	1.3671	SOX2.p2	BC067057|Grm1|14816|glutamate receptor, metabotropic 1	NM_001114333|Grm1|14816|glutamate receptor, metabotropic 1	NM_016976|Grm1|14816|glutamate receptor, metabotropic 1	AF320126|Grm1|14816|glutamate receptor, metabotropic 1
mm9_v1_chr8_+_84239098_84239098	1.36614	SOX2.p2	BC064813|Inpp4b|234515|inositol polyphosphate-4-phosphatase, type II	NM_001024617|Inpp4b|234515|inositol polyphosphate-4-phosphatase, type II
mm9_v1_chr9_+_105303117_105303117	1.35604	SOX2.p2	AK006153|Aste1|66595|asteroid homolog 1 (Drosophila)	NM_001164828|Aste1|66595|asteroid homolog 1 (Drosophila)
mm9_v1_chr14_+_22318991_22319040	1.35529	SOX2.p2	AK147509|Myst4|54169|MYST histone acetyltransferase monocytic leukemia 4
mm9_v1_chr2_+_25036524_25036678	1.35387	SOX2.p2	BC069891|Nrarp|67122|Notch-regulated ankyrin repeat protein	AK012426|Nrarp|67122|Notch-regulated ankyrin repeat protein
mm9_v1_chr13_+_55471165_55471252	1.35381	SOX2.p2	AK154944|Rgs14|51791|regulator of G-protein signaling 14	U85055|Rgs14|51791|regulator of G-protein signaling 14
mm9_v1_chr2_+_153956082_153956082	1.35299	SOX2.p2	AK006829|1700058C13Rik|73388|RIKEN cDNA 1700058C13 gene	BC049691|1700058C13Rik|73388|RIKEN cDNA 1700058C13 gene	NM_028528|1700058C13Rik|73388|RIKEN cDNA 1700058C13 gene
mm9_v1_chr7_-_28231535_28231646	1.35229	SOX2.p2	AK006254|Spnb4|80297|spectrin beta 4	AB055618|Spnb4|80297|spectrin beta 4	NM_032610|Spnb4|80297|spectrin beta 4	AK147558|Spnb4|80297|spectrin beta 4
mm9_v1_chr6_-_129610573_129610706	1.34985	SOX2.p2	AF109785|Klrc2|16642|killer cell lectin-like receptor subfamily C, member 2	NM_010653|Klrc2|16642|killer cell lectin-like receptor subfamily C, member 2	AK036555|Klrc2|16642|killer cell lectin-like receptor subfamily C, member 2	AF106011|Klrc2|16642|killer cell lectin-like receptor subfamily C, member 2	NM_001098669|Klrc2|16642|killer cell lectin-like receptor subfamily C, member 2	AK040721|Klrc2|16642|killer cell lectin-like receptor subfamily C, member 2	AF106010|Klrc2|16642|killer cell lectin-like receptor subfamily C, member 2
mm9_v1_chr12_-_15823536_15823550	1.34903	SOX2.p2	BC037387|Trib2|217410|tribbles homolog 2 (Drosophila)	AK044747|Trib2|217410|tribbles homolog 2 (Drosophila)
mm9_v1_chr16_+_91270009_91270054	1.34814	SOX2.p2	NM_016968|Olig1|50914|oligodendrocyte transcription factor 1	AK144435|Olig1|50914|oligodendrocyte transcription factor 1	AB038696|Olig1|50914|oligodendrocyte transcription factor 1	BC046316|Olig1|50914|oligodendrocyte transcription factor 1
mm9_v1_chr10_+_127162447_127162481	1.3444	SOX2.p2	NM_009312|Tac2|21334|tachykinin 2	BC031348|Tac2|21334|tachykinin 2	BC051476|Tac2|21334|tachykinin 2	AF186116|Tac2|21334|tachykinin 2
mm9_v1_chr4_+_126698539_126698547	1.34224	SOX2.p2	NM_023603|Sfpq|71514|splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
mm9_v1_chr1_-_180259336_180259529	1.34191	SOX2.p2	AK049375|Hnrnpu|51810|heterogeneous nuclear ribonucleoprotein U	AK080656|Hnrnpu|51810|heterogeneous nuclear ribonucleoprotein U
mm9_v1_chr17_+_53618542_53618596	1.34185	SOX2.p2	AK081999|Rab5a|271457|RAB5A, member RAS oncogene family	NM_025887|Rab5a|271457|RAB5A, member RAS oncogene family	AK076093|Rab5a|271457|RAB5A, member RAS oncogene family	BC096481|Rab5a|271457|RAB5A, member RAS oncogene family
mm9_v1_chr6_+_64992810_64992853	1.34027	SOX2.p2	AK134442|Smarcad1|13990|SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	AK011724|Smarcad1|13990|SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	AK122454|Smarcad1|13990|SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1
mm9_v1_chr14_-_64606614_64606626	1.33985	SOX2.p2	AK005778|4930578I06Rik|67750|RIKEN cDNA 4930578I06 gene	BC048583|4930578I06Rik|67750|RIKEN cDNA 4930578I06 gene	NM_026359|4930578I06Rik|67750|RIKEN cDNA 4930578I06 gene	AK016302|4930578I06Rik|67750|RIKEN cDNA 4930578I06 gene
mm9_v1_chr13_+_20564928_20564972	1.33918	SOX2.p2	AK053306|Elmo1|140580|engulfment and cell motility 1, ced-12 homolog (C. elegans)	AK032085|Elmo1|140580|engulfment and cell motility 1, ced-12 homolog (C. elegans)	BC024727|Elmo1|140580|engulfment and cell motility 1, ced-12 homolog (C. elegans)	NM_198093|Elmo1|140580|engulfment and cell motility 1, ced-12 homolog (C. elegans)
mm9_v1_chr16_-_5132502_5132606	1.33849	SOX2.p2	BC057152|Ppl|19041|periplakin	AF126834|Ppl|19041|periplakin	AK142562|Ppl|19041|periplakin	NM_008909|Ppl|19041|periplakin
mm9_v1_chr10_-_62254978_62254996	1.33804	SOX2.p2	BC079652|Ccar1|67500|cell division cycle and apoptosis regulator 1	BC010199|Ccar1|67500|cell division cycle and apoptosis regulator 1
mm9_v1_chr10_+_90039435_90039495	1.33744	SOX2.p2	AK032211|Anks1b|77531|ankyrin repeat and sterile alpha motif domain containing 1B	NM_001177396|Anks1b|77531|ankyrin repeat and sterile alpha motif domain containing 1B	NM_001177398|Anks1b|77531|ankyrin repeat and sterile alpha motif domain containing 1B	NM_181398|Anks1b|77531|ankyrin repeat and sterile alpha motif domain containing 1B	AK163750|Anks1b|77531|ankyrin repeat and sterile alpha motif domain containing 1B	AK132228|Anks1b|77531|ankyrin repeat and sterile alpha motif domain containing 1B	AK019361|Ipw|16353|imprinted gene in the Prader-Willi syndrome region	AK049899|Anks1b|77531|ankyrin repeat and sterile alpha motif domain containing 1B
mm9_v1_chr1_-_167564449_167564681	1.33548	SOX2.p2	AK192253|Mpzl1|68481|myelin protein zero-like 1	AK192408|Mpzl1|68481|myelin protein zero-like 1	AK193736|Mpzl1|68481|myelin protein zero-like 1	AK197743|Mpzl1|68481|myelin protein zero-like 1	AY764248|Mpzl1|68481|myelin protein zero-like 1	BC072563|Mpzl1|68481|myelin protein zero-like 1	AK090278|Mpzl1|68481|myelin protein zero-like 1	AK169385|Mpzl1|68481|myelin protein zero-like 1	AY764247|Mpzl1|68481|myelin protein zero-like 1	NM_001001880|Mpzl1|68481|myelin protein zero-like 1	NM_001083897|Mpzl1|68481|myelin protein zero-like 1
mm9_v1_chr18_+_67247984_67247998	1.33531	SOX2.p2	AK045484|Gnal|14680|guanine nucleotide binding protein, alpha stimulating, olfactory type	BC078439|Gnal|14680|guanine nucleotide binding protein, alpha stimulating, olfactory type	NM_177137|Gnal|14680|guanine nucleotide binding protein, alpha stimulating, olfactory type
mm9_v1_chr10_-_62254998_62255005	1.3292	SOX2.p2	AF465615|Ccar1|67500|cell division cycle and apoptosis regulator 1	AK012111|Ccar1|67500|cell division cycle and apoptosis regulator 1	BC060130|Ccar1|67500|cell division cycle and apoptosis regulator 1	BC039939|Ccar1|67500|cell division cycle and apoptosis regulator 1
mm9_v1_chr11_-_41995688_41995930	1.32786	SOX2.p2	X61430|Gabra1|14394|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1	AK039496|Gabra1|14394|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1	M86566|Gabra1|14394|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1
mm9_v1_chr11_-_98859189_98859196	1.32724	SOX2.p2	U01915|Top2a|21973|topoisomerase (DNA) II alpha
mm9_v1_chr12_+_105339322_105339359	1.32639	SOX2.p2	AK077160|Serpina5|268591|serine (or cysteine) peptidase inhibitor, clade A, member 5	NM_172953|Serpina5|268591|serine (or cysteine) peptidase inhibitor, clade A, member 5	AK087714|Serpina5|268591|serine (or cysteine) peptidase inhibitor, clade A, member 5	BC090981|Serpina5|268591|serine (or cysteine) peptidase inhibitor, clade A, member 5
mm9_v1_chr3_-_116126853_116126921	1.32604	SOX2.p2	AK048250|Cdc14a|229776|CDC14 cell division cycle 14 homolog A (S. cerevisiae)	AK032515|Cdc14a|229776|CDC14 cell division cycle 14 homolog A (S. cerevisiae)	BC072644|Cdc14a|229776|CDC14 cell division cycle 14 homolog A (S. cerevisiae)
mm9_v1_chr4_-_132848450_132848516	1.32548	SOX2.p2	
mm9_v1_chr4_-_147533696_147533703	1.32509	SOX2.p2	NM_001161851|Fbxo44|230903|F-box protein 44
mm9_v1_chr9_-_44543245_44543320	1.31924	SOX2.p2	BC058712|Phldb1|102693|pleckstrin homology-like domain, family B, member 1	NM_153537|Phldb1|102693|pleckstrin homology-like domain, family B, member 1
mm9_v1_chr11_-_109159357_109159494	1.3164	SOX2.p2	BC129899|Rgs9|19739|regulator of G-protein signaling 9	BC129898|Rgs9|19739|regulator of G-protein signaling 9	AF011358|Rgs9|19739|regulator of G-protein signaling 9	AK138159|Rgs9|19739|regulator of G-protein signaling 9	AK085443|Rgs9|19739|regulator of G-protein signaling 9	AF125046|Rgs9|19739|regulator of G-protein signaling 9	AK164961|Rgs9|19739|regulator of G-protein signaling 9	NM_001165934|Rgs9|19739|regulator of G-protein signaling 9	NM_011268|Rgs9|19739|regulator of G-protein signaling 9
mm9_v1_chr2_+_32006651_32006708	1.31611	SOX2.p2	AK147271|Prrc2b|227723|proline-rich coiled-coil 2B	AK147677|Prrc2b|227723|proline-rich coiled-coil 2B	NM_001159634|Prrc2b|227723|proline-rich coiled-coil 2B	NM_172661|Prrc2b|227723|proline-rich coiled-coil 2B	BC055116|Prrc2b|227723|proline-rich coiled-coil 2B
mm9_v1_chr12_-_12948513_12948641	1.31477	SOX2.p2	BC005453|Mycn|18109|v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)	AK144126|Mycn|18109|v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)	AK146913|Mycn|18109|v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)	AK146696|Mycn|18109|v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)	NM_008709|Mycn|18109|v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)
mm9_v1_chr7_-_133727793_133727820	1.30827	SOX2.p2	NM_001146311|Cln3|12752|ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	BC047120|Cln3|12752|ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)
mm9_v1_chr2_+_69877182_69877182	1.30645	SOX2.p2	NM_177376|Myo3b|329421|myosin IIIB
mm9_v1_chr1_-_188529867_188529872	1.30586	SOX2.p2	X57413|Tgfb2|21808|transforming growth factor, beta 2	NM_009367|Tgfb2|21808|transforming growth factor, beta 2
mm9_v1_chr15_-_24957039_24957112	1.30415	SOX2.p2	AK033069|Gm2824|100040529|predicted gene 2824	AK083927|Gm2824|100040529|predicted gene 2824
mm9_v1_chr4_+_6118252_6118258	1.30284	SOX2.p2	AK012822|Ubxn2b|68053|UBX domain protein 2B	AB120715|Ubxn2b|68053|UBX domain protein 2B	AK013985|Ubxn2b|68053|UBX domain protein 2B
mm9_v1_chr12_-_81537261_81537482	1.30062	SOX2.p2	BC042567|Dcaf5|320808|DDB1 and CUL4 associated factor 5	AK122561|Dcaf5|320808|DDB1 and CUL4 associated factor 5
mm9_v1_chr5_-_115750998_115751012	1.30007	SOX2.p2	NM_019682|Dynll1|56455|dynein light chain LC8-type 1
mm9_v1_chr15_-_77949709_77949709	1.29795	SOX2.p2	AF077739|Cacng2|12300|calcium channel, voltage-dependent, gamma subunit 2	NM_007583|Cacng2|12300|calcium channel, voltage-dependent, gamma subunit 2
mm9_v1_chr7_-_150734696_150734742	1.29372	SOX2.p2	AK090112|Nap1l4|17955|nucleosome assembly protein 1-like 4
mm9_v1_chr14_+_70930491_70930682	1.29354	SOX2.p2	AK087125|Lgi3|213469|leucine-rich repeat LGI family, member 3	NM_145219|Lgi3|213469|leucine-rich repeat LGI family, member 3	AK132296|Lgi3|213469|leucine-rich repeat LGI family, member 3	AF515590|Lgi3|213469|leucine-rich repeat LGI family, member 3	AY174077|Lgi3|213469|leucine-rich repeat LGI family, member 3	AK049831|Lgi3|213469|leucine-rich repeat LGI family, member 3	AK163664|Lgi3|213469|leucine-rich repeat LGI family, member 3	AK047495|Lgi3|213469|leucine-rich repeat LGI family, member 3
mm9_v1_chr2_+_80479420_80479420	1.2921	SOX2.p2	NM_001190179|Nup35|69482|nucleoporin 35
mm9_v1_chr15_-_79085177_79085186	1.29062	SOX2.p2	BC018216|Slc16a8|57274|solute carrier family 16 (monocarboxylic acid transporters), member 8	NM_020516|Slc16a8|57274|solute carrier family 16 (monocarboxylic acid transporters), member 8	AF019111|Slc16a8|57274|solute carrier family 16 (monocarboxylic acid transporters), member 8
mm9_v1_chr11_-_68635236_68635451	1.2897	SOX2.p2	AK194070|Ndel1|83431|nuclear distribution gene E-like homolog 1 (A. nidulans)
mm9_v1_chr2_+_61642509_61642690	1.28637	SOX2.p2	BC052737|Tbr1|21375|T-box brain gene 1	NM_009322|Tbr1|21375|T-box brain gene 1	AK158835|Tbr1|21375|T-box brain gene 1	BC058399|Tbr1|21375|T-box brain gene 1	U49251|Tbr1|21375|T-box brain gene 1
mm9_v1_chr11_+_43534658_43534687	1.28379	SOX2.p2	AK086604|Pwwp2a|70802|PWWP domain containing 2A	AK039984|Pwwp2a|70802|PWWP domain containing 2A
mm9_v1_chr6_+_116123984_116124113	1.2809	SOX2.p2	AK210116|Gm8203|666634|predicted pseudogene 8203
mm9_v1_chr11_+_56825192_56825257	1.27615	SOX2.p2	NM_001113325|Gria1|14799|glutamate receptor, ionotropic, AMPA1 (alpha 1)	NM_008165|Gria1|14799|glutamate receptor, ionotropic, AMPA1 (alpha 1)
mm9_v1_chr16_+_43762333_43762354	1.27553	SOX2.p2	BC119286|Drd3|13490|dopamine receptor D3	BC137819|Drd3|13490|dopamine receptor D3	NM_007877|Drd3|13490|dopamine receptor D3	X67274|Drd3|13490|dopamine receptor D3
mm9_v1_chr5_-_75098910_75098927	1.27503	SOX2.p2	AF034745|Lnx1|16924|ligand of numb-protein X 1	NM_001159577|Lnx1|16924|ligand of numb-protein X 1
mm9_v1_chr2_+_154262114_154262265	1.27295	SOX2.p2	AK148027|Cbfa2t2|12396|core-binding factor, runt domain, alpha subunit 2, translocated to, 2 (human)	NM_009823|Cbfa2t2|12396|core-binding factor, runt domain, alpha subunit 2, translocated to, 2 (human)	NM_172860|Cbfa2t2|12396|core-binding factor, runt domain, alpha subunit 2, translocated to, 2 (human)	AK040403|Cbfa2t2|12396|core-binding factor, runt domain, alpha subunit 2, translocated to, 2 (human)	DQ213025|Cbfa2t2|12396|core-binding factor, runt domain, alpha subunit 2, translocated to, 2 (human)	BC064679|Cbfa2t2|12396|core-binding factor, runt domain, alpha subunit 2, translocated to, 2 (human)	AK049206|Cbfa2t2|12396|core-binding factor, runt domain, alpha subunit 2, translocated to, 2 (human)
mm9_v1_chr2_+_76244603_76244617	1.26959	SOX2.p2	AK037703|Osbpl6|99031|oxysterol binding protein-like 6	AK157944|Osbpl6|99031|oxysterol binding protein-like 6	AK220498|Osbpl6|99031|oxysterol binding protein-like 6
mm9_v1_chr15_+_44259636_44259698	1.26816	SOX2.p2	AK007877|Eny2|223527|enhancer of yellow 2 homolog (Drosophila)	AF173297|Eny2|223527|enhancer of yellow 2 homolog (Drosophila)	BC048361|Eny2|223527|enhancer of yellow 2 homolog (Drosophila)	NM_175009|Eny2|223527|enhancer of yellow 2 homolog (Drosophila)	AK032957|Eny2|223527|enhancer of yellow 2 homolog (Drosophila)	AK162511|Eny2|223527|enhancer of yellow 2 homolog (Drosophila)	AK160628|Eny2|223527|enhancer of yellow 2 homolog (Drosophila)	AK016562|Eny2|223527|enhancer of yellow 2 homolog (Drosophila)	AK087816|Eny2|223527|enhancer of yellow 2 homolog (Drosophila)
mm9_v1_chr5_-_86802390_86802444	1.26776	SOX2.p2	AF448809|Tmprss11d|231382|transmembrane protease, serine 11d	BC020151|Tmprss11d|231382|transmembrane protease, serine 11d	NM_145561|Tmprss11d|231382|transmembrane protease, serine 11d	AB053953|Tmprss11d|231382|transmembrane protease, serine 11d
mm9_v1_chr3_+_59533707_59533707	1.2664	SOX2.p2	NM_001101531|Gm5538|433597|predicted gene 5538
mm9_v1_chr2_-_7002287_7002310	1.26332	SOX2.p2	AK137292|Celf2|14007|CUGBP, Elav-like family member 2	AK164914|Celf2|14007|CUGBP, Elav-like family member 2
mm9_v1_chr5_-_73729789_73729885	1.26296	SOX2.p2	BC044883|Ociad2|433904|OCIA domain containing 2	AK007617|Ociad2|433904|OCIA domain containing 2	NM_026950|Ociad2|433904|OCIA domain containing 2
mm9_v1_chr2_+_180332926_180333016	1.26127	SOX2.p2	NM_009936|Col9a3|12841|collagen, type IX, alpha 3	AK030350|Col9a3|12841|collagen, type IX, alpha 3	AF349718|Col9a3|12841|collagen, type IX, alpha 3
mm9_v1_chr14_+_65885454_65885579	1.26032	SOX2.p2	AK164657|Fbxo16|50759|F-box protein 16	AK081947|Fbxo16|50759|F-box protein 16	AF176531|Fbxo16|50759|F-box protein 16	NM_015795|Fbxo16|50759|F-box protein 16	AK043554|Fbxo16|50759|F-box protein 16	BC086690|Fbxo16|50759|F-box protein 16	BC115890|Fbxo16|50759|F-box protein 16
mm9_v1_chr1_-_39777833_39777833	1.25894	SOX2.p2	AK133372|Rfx8|619289|regulatory factor X 8	NM_001145660|Rfx8|619289|regulatory factor X 8
mm9_v1_chr15_+_80453912_80453951	1.25871	SOX2.p2	AF055465|Grap2|17444|GRB2-related adaptor protein 2	NM_010815|Grap2|17444|GRB2-related adaptor protein 2	AK156939|Grap2|17444|GRB2-related adaptor protein 2	AJ011735|Grap2|17444|GRB2-related adaptor protein 2	AF129477|Grap2|17444|GRB2-related adaptor protein 2	AF236118|Grap2|17444|GRB2-related adaptor protein 2
mm9_v1_chr18_-_36855578_36855578	1.25804	SOX2.p2	AK087618|E230025N22Rik|240216|Riken cDNA E230025N22 gene	NM_172831|E230025N22Rik|240216|Riken cDNA E230025N22 gene
mm9_v1_chr7_+_134376574_134376794	1.25501	SOX2.p2	AK049208|Zfp553|233887|zinc finger protein 553	AK144911|Zfp553|233887|zinc finger protein 553	AK146581|Zfp553|233887|zinc finger protein 553	AK140924|Zfp553|233887|zinc finger protein 553
mm9_v1_chr3_+_9250566_9250566	1.25409	SOX2.p2	NM_177660|Zbtb10|229055|zinc finger and BTB domain containing 10
mm9_v1_chr12_+_53955707_53955717	1.24845	SOX2.p2	DQ233646|Akap6|238161|A kinase (PRKA) anchor protein 6
mm9_v1_chr7_-_140793797_140793840	1.24831	SOX2.p2	BC100509|4930404H21Rik|73808|RIKEN cDNA 4930404H21 gene	NM_028654|4930404H21Rik|73808|RIKEN cDNA 4930404H21 gene	AK015080|4930404H21Rik|73808|RIKEN cDNA 4930404H21 gene
mm9_v1_chr8_+_3587791_3587801	1.24823	SOX2.p2	BC043081|2310057J16Rik|69697|RIKEN cDNA 2310057J16 gene	BC048787|2310057J16Rik|69697|RIKEN cDNA 2310057J16 gene
mm9_v1_chr1_+_59969845_59969868	1.24792	SOX2.p2	AK154812|Fam117b|72750|family with sequence similarity 117, member B	NM_001037725|Fam117b|72750|family with sequence similarity 117, member B
mm9_v1_chr12_+_88367442_88367513	1.24502	SOX2.p2	AK034410|Tmem63c|217733|transmembrane protein 63c	AK043536|Tmem63c|217733|transmembrane protein 63c	BC056936|Tmem63c|217733|transmembrane protein 63c	BC057088|Tmem63c|217733|transmembrane protein 63c	NM_172583|Tmem63c|217733|transmembrane protein 63c
mm9_v1_chr2_+_25074264_25074265	1.24248	SOX2.p2	AK016459|Fam166a|68222|family with sequence similarity 166, member A	NM_026624|Fam166a|68222|family with sequence similarity 166, member A	BC061039|Fam166a|68222|family with sequence similarity 166, member A
mm9_v1_chr5_-_135391315_135391362	1.24242	SOX2.p2	BC115481|Cldn13|57255|claudin 13	BC115482|Cldn13|57255|claudin 13
mm9_v1_chr12_+_52449216_52449372	1.24233	SOX2.p2	NM_001015099|G2e3|217558|G2/M-phase specific E3 ubiquitin ligase	NM_001167963|G2e3|217558|G2/M-phase specific E3 ubiquitin ligase	NM_001167964|G2e3|217558|G2/M-phase specific E3 ubiquitin ligase	AK033513|G2e3|217558|G2/M-phase specific E3 ubiquitin ligase	AK129332|G2e3|217558|G2/M-phase specific E3 ubiquitin ligase	BC086455|G2e3|217558|G2/M-phase specific E3 ubiquitin ligase	AK084256|G2e3|217558|G2/M-phase specific E3 ubiquitin ligase	AK031333|G2e3|217558|G2/M-phase specific E3 ubiquitin ligase
mm9_v1_chr1_-_192803077_192803174	1.23889	SOX2.p2	BC024141|Vash2|226841|vasohibin 2	AK163193|Vash2|226841|vasohibin 2	AK045261|Vash2|226841|vasohibin 2	AK078596|Vash2|226841|vasohibin 2
mm9_v1_chr19_+_41904459_41904605	1.23797	SOX2.p2	NM_008043|Frat1|14296|frequently rearranged in advanced T-cell lymphomas	AK015680|Frat1|14296|frequently rearranged in advanced T-cell lymphomas	BC140987|Frat1|14296|frequently rearranged in advanced T-cell lymphomas	U58974|Frat1|14296|frequently rearranged in advanced T-cell lymphomas
mm9_v1_chr13_+_44826700_44826834	1.23762	SOX2.p2	BC050129|Jarid2|16468|jumonji, AT rich interactive domain 2	AK044888|Jarid2|16468|jumonji, AT rich interactive domain 2	BC051010|Jarid2|16468|jumonji, AT rich interactive domain 2	BC026056|Jarid2|16468|jumonji, AT rich interactive domain 2	AK045214|Jarid2|16468|jumonji, AT rich interactive domain 2
mm9_v1_chr3_+_138189154_138189154	1.23754	SOX2.p2	NM_007917|Eif4e|13684|eukaryotic translation initiation factor 4E
mm9_v1_chr15_-_95485136_95485201	1.23678	SOX2.p2	AK034882|Dbx2|223843|developing brain homeobox 2	NM_207533|Dbx2|223843|developing brain homeobox 2
mm9_v1_chr17_+_25325344_25325353	1.23638	SOX2.p2	NM_001197024|Unkl|74154|unkempt-like (Drosophila)
mm9_v1_chr15_+_97962651_97962722	1.23589	SOX2.p2	
mm9_v1_chr17_+_85025830_85025873	1.23529	SOX2.p2	BC030450|Dync2li1|213575|dynein cytoplasmic 2 light intermediate chain 1	BC039070|Dync2li1|213575|dynein cytoplasmic 2 light intermediate chain 1	NM_172256|Dync2li1|213575|dynein cytoplasmic 2 light intermediate chain 1	AK008822|Dync2li1|213575|dynein cytoplasmic 2 light intermediate chain 1
mm9_v1_chr14_+_76354807_76354815	1.23482	SOX2.p2	AK004465|Kctd4|67516|potassium channel tetramerisation domain containing 4	NM_026214|Kctd4|67516|potassium channel tetramerisation domain containing 4	AK008741|Kctd4|67516|potassium channel tetramerisation domain containing 4
mm9_v1_chr4_-_110024513_110024515	1.23444	SOX2.p2	AF041341|Elavl4|15572|ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	NM_001163397|Elavl4|15572|ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)
mm9_v1_chr5_-_52581615_52581700	1.23376	SOX2.p2	BC144759|Dhx15|13204|DEAH (Asp-Glu-Ala-His) box polypeptide 15	AF017153|Dhx15|13204|DEAH (Asp-Glu-Ala-His) box polypeptide 15	AK167927|Dhx15|13204|DEAH (Asp-Glu-Ala-His) box polypeptide 15
mm9_v1_chr13_+_77274778_77274859	1.23344	SOX2.p2	NM_001081353|2210408I21Rik|72371|RIKEN cDNA 2210408I21 gene	NM_001145676|2210408I21Rik|72371|RIKEN cDNA 2210408I21 gene	AK165312|2210408I21Rik|72371|RIKEN cDNA 2210408I21 gene	AK050886|2210408I21Rik|72371|RIKEN cDNA 2210408I21 gene	AK008859|2210408I21Rik|72371|RIKEN cDNA 2210408I21 gene	BC089469|2210408I21Rik|72371|RIKEN cDNA 2210408I21 gene	BC151066|2210408I21Rik|72371|RIKEN cDNA 2210408I21 gene	BC157949|2210408I21Rik|72371|RIKEN cDNA 2210408I21 gene	AK143619|2210408I21Rik|72371|RIKEN cDNA 2210408I21 gene
mm9_v1_chr18_+_23468655_23468725	1.2329	SOX2.p2	X95227|Dtna|13527|dystrobrevin alpha
mm9_v1_chr5_+_125343060_125343124	1.23038	SOX2.p2	AK143192|Zfp664|269704|zinc finger protein 664	AK086580|Zfp664|269704|zinc finger protein 664	AK039671|Zfp664|269704|zinc finger protein 664	NM_001081750|Zfp664|269704|zinc finger protein 664	AK165974|Zfp664|269704|zinc finger protein 664
mm9_v1_chr5_-_136849232_136849238	1.22991	SOX2.p2	AF004225|Cux1|13047|cut-like homeobox 1
mm9_v1_chr1_-_141755209_141755302	1.22893	SOX2.p2	AJ565908|BC026782|545366|cDNA sequence BC026782	M29007|BC026782|545366|cDNA sequence BC026782	AK149511|BC026782|545366|cDNA sequence BC026782	NM_001025575|BC026782|545366|cDNA sequence BC026782
mm9_v1_chr4_-_142718290_142718420	1.22269	SOX2.p2	AK136099|Prdm2|110593|PR domain containing 2, with ZNF domain
mm9_v1_chr1_-_166371638_166371729	1.22253	SOX2.p2	AK162938|Atp1b1|11931|ATPase, Na+/K+ transporting, beta 1 polypeptide
mm9_v1_chr17_+_3326513_3326683	1.21952	SOX2.p2	BC067048|Tiam2|24001|T-cell lymphoma invasion and metastasis 2	NM_001122998|Tiam2|24001|T-cell lymphoma invasion and metastasis 2	BC079600|Tiam2|24001|T-cell lymphoma invasion and metastasis 2
mm9_v1_chr18_+_82753560_82753917	1.21842	SOX2.p2	AK205832|Mbp|17196|myelin basic protein	AK195683|Mbp|17196|myelin basic protein	AK198099|Mbp|17196|myelin basic protein
mm9_v1_chr11_-_113571330_113571330	1.21681	SOX2.p2	AK005072|Cpsf4l|52670|cleavage and polyadenylation specific factor 4-like	NM_029794|Cpsf4l|52670|cleavage and polyadenylation specific factor 4-like
mm9_v1_chrX_-_105143713_105143774	1.21545	SOX2.p2	BC147603|Gm732|213450|predicted gene 732	BC147609|Gm732|213450|predicted gene 732	AK132985|Gm732|213450|predicted gene 732	NM_001033252|Gm732|213450|predicted gene 732
mm9_v1_chr6_+_133479206_133479206	1.21478	SOX2.p2	NM_001185040|Gm5885|545884|predicted gene 5885
mm9_v1_chr16_+_36277233_36277264	1.21028	SOX2.p2	NM_001082543|Stfa1|20861|stefin A1	M92417|Stfa1|20861|stefin A1
mm9_v1_chr10_-_74495269_74495330	1.20962	SOX2.p2	BC147792|Rtdr1|71236|rhabdoid tumor deletion region gene 1	BC147801|Rtdr1|71236|rhabdoid tumor deletion region gene 1	NM_001163534|Rtdr1|71236|rhabdoid tumor deletion region gene 1	NM_001163535|Rtdr1|71236|rhabdoid tumor deletion region gene 1	AK017008|Rtdr1|71236|rhabdoid tumor deletion region gene 1	AK077078|Rtdr1|71236|rhabdoid tumor deletion region gene 1	NM_001163533|Rtdr1|71236|rhabdoid tumor deletion region gene 1	NM_027730|Rtdr1|71236|rhabdoid tumor deletion region gene 1
mm9_v1_chr17_-_36046961_36047023	1.20951	SOX2.p2	AK049682|Atat1|73242|alpha tubulin acetyltransferase 1	AK014265|Atat1|73242|alpha tubulin acetyltransferase 1	AK011750|Atat1|73242|alpha tubulin acetyltransferase 1	AK034725|Atat1|73242|alpha tubulin acetyltransferase 1	AK133694|Atat1|73242|alpha tubulin acetyltransferase 1	BC030669|Atat1|73242|alpha tubulin acetyltransferase 1	AK011350|Atat1|73242|alpha tubulin acetyltransferase 1	BC028847|Atat1|73242|alpha tubulin acetyltransferase 1	AK011838|Atat1|73242|alpha tubulin acetyltransferase 1	AK028297|Atat1|73242|alpha tubulin acetyltransferase 1	NM_001142744|Atat1|73242|alpha tubulin acetyltransferase 1	NM_001142745|Atat1|73242|alpha tubulin acetyltransferase 1	NM_028476|Atat1|73242|alpha tubulin acetyltransferase 1
mm9_v1_chr14_+_55551531_55551607	1.20941	SOX2.p2	BC120568|Il25|140806|interleukin 25	BC125524|Il25|140806|interleukin 25	BC144962|Il25|140806|interleukin 25	NM_080729|Il25|140806|interleukin 25	AF458060|Il25|140806|interleukin 25
mm9_v1_chr3_-_132754703_132754778	1.20806	SOX2.p2	BC047136|Gstcd|67553|glutathione S-transferase, C-terminal domain containing	NM_026231|Gstcd|67553|glutathione S-transferase, C-terminal domain containing	AK044441|Gstcd|67553|glutathione S-transferase, C-terminal domain containing	AK033409|Gstcd|67553|glutathione S-transferase, C-terminal domain containing	AK037169|Gstcd|67553|glutathione S-transferase, C-terminal domain containing
mm9_v1_chr1_+_133737686_133737717	1.20657	SOX2.p2	BC037033|Slc41a1|98396|solute carrier family 41, member 1
mm9_v1_chr7_-_91558468_91558528	1.20414	SOX2.p2	BC054546|Arnt2|11864|aryl hydrocarbon receptor nuclear translocator 2	NM_007488|Arnt2|11864|aryl hydrocarbon receptor nuclear translocator 2
mm9_v1_chr8_+_3587675_3587681	1.20398	SOX2.p2	AK081728|2310057J16Rik|69697|RIKEN cDNA 2310057J16 gene
mm9_v1_chr1_+_172238933_172238992	1.20315	SOX2.p2	AK005990|1700015E13Rik|76925|RIKEN cDNA 1700015E13 gene	BC099563|1700015E13Rik|76925|RIKEN cDNA 1700015E13 gene	NM_001039593|1700015E13Rik|76925|RIKEN cDNA 1700015E13 gene	BC132313|1700015E13Rik|76925|RIKEN cDNA 1700015E13 gene	BC132315|1700015E13Rik|76925|RIKEN cDNA 1700015E13 gene
mm9_v1_chr4_+_59639079_59639315	1.20054	SOX2.p2	AK047478|E130308A19Rik|230259|RIKEN cDNA E130308A19 gene	AK087509|E130308A19Rik|230259|RIKEN cDNA E130308A19 gene	NM_153158|E130308A19Rik|230259|RIKEN cDNA E130308A19 gene	AK047601|E130308A19Rik|230259|RIKEN cDNA E130308A19 gene	AK081604|E130308A19Rik|230259|RIKEN cDNA E130308A19 gene	NM_001015681|E130308A19Rik|230259|RIKEN cDNA E130308A19 gene	BC037070|E130308A19Rik|230259|RIKEN cDNA E130308A19 gene	BC017649|E130308A19Rik|230259|RIKEN cDNA E130308A19 gene
mm9_v1_chr16_-_64786146_64786199	1.19966	SOX2.p2	BC068018|Zfp654|72020|zinc finger protein 654	NM_028059|Zfp654|72020|zinc finger protein 654	AK005508|Zfp654|72020|zinc finger protein 654
mm9_v1_chr4_+_135842003_135842015	1.19922	SOX2.p2	AK051031|Zfp46|22704|zinc finger protein 46
mm9_v1_chrX_-_16488889_16488889	1.19408	SOX2.p2	BC090623|Ndp|17986|Norrie disease (pseudoglioma) (human)	NM_010883|Ndp|17986|Norrie disease (pseudoglioma) (human)
mm9_v1_chr8_+_32222291_32222336	1.19269	SOX2.p2	AK077856|Rnf122|68867|ring finger protein 122	AK171823|Rnf122|68867|ring finger protein 122	AK136206|Rnf122|68867|ring finger protein 122	AK162034|Rnf122|68867|ring finger protein 122	BC038399|Rnf122|68867|ring finger protein 122	NM_175136|Rnf122|68867|ring finger protein 122	AK085376|Rnf122|68867|ring finger protein 122
mm9_v1_chr13_+_35016277_35016322	1.19256	SOX2.p2	AK016838|4933417A18Rik|66761|RIKEN cDNA 4933417A18 gene	NM_025750|4933417A18Rik|66761|RIKEN cDNA 4933417A18 gene	BC100450|4933417A18Rik|66761|RIKEN cDNA 4933417A18 gene	AK016778|4933417A18Rik|66761|RIKEN cDNA 4933417A18 gene	BC145747|4933417A18Rik|66761|RIKEN cDNA 4933417A18 gene
mm9_v1_chr18_+_37925233_37925233	1.1905	SOX2.p2	BC056998|Pcdhga12|93724|protocadherin gamma subfamily A, 12	NM_033595|Pcdhga12|93724|protocadherin gamma subfamily A, 12
mm9_v1_chr16_-_90144013_90144100	1.18912	SOX2.p2	BC065126|Tiam1|21844|T-cell lymphoma invasion and metastasis 1	AK043966|Tiam1|21844|T-cell lymphoma invasion and metastasis 1
mm9_v1_chr11_+_23978110_23978267	1.18789	SOX2.p2	AK140949|Bcl11a|14025|B-cell CLL/lymphoma 11A (zinc finger protein)	AF051525|Bcl11a|14025|B-cell CLL/lymphoma 11A (zinc finger protein)	AF169036|Bcl11a|14025|B-cell CLL/lymphoma 11A (zinc finger protein)	AF169037|Bcl11a|14025|B-cell CLL/lymphoma 11A (zinc finger protein)	AK122557|Bcl11a|14025|B-cell CLL/lymphoma 11A (zinc finger protein)	AF186018|Bcl11a|14025|B-cell CLL/lymphoma 11A (zinc finger protein)	AK004395|Bcl11a|14025|B-cell CLL/lymphoma 11A (zinc finger protein)	AK043677|Bcl11a|14025|B-cell CLL/lymphoma 11A (zinc finger protein)	BC051418|Bcl11a|14025|B-cell CLL/lymphoma 11A (zinc finger protein)
mm9_v1_chr13_+_55471092_55471131	1.18656	SOX2.p2	NM_016758|Rgs14|51791|regulator of G-protein signaling 14	BC030321|Rgs14|51791|regulator of G-protein signaling 14
mm9_v1_chrX_-_91787338_91787350	1.18636	SOX2.p2	AK220150|Maged1|94275|melanoma antigen, family D, 1	AK132248|Maged1|94275|melanoma antigen, family D, 1
mm9_v1_chr3_-_38349112_38349206	1.18341	SOX2.p2	BC051515|Ankrd50|99696|ankyrin repeat domain 50
mm9_v1_chr17_+_85025803_85025818	1.18109	SOX2.p2	AK160259|Dync2li1|213575|dynein cytoplasmic 2 light intermediate chain 1
mm9_v1_chr17_+_81343933_81344010	1.18096	SOX2.p2	AK013110|Tmem178|68027|transmembrane protein 178	AK014196|Tmem178|68027|transmembrane protein 178	NM_026516|Tmem178|68027|transmembrane protein 178
mm9_v1_chr9_+_36500804_36500844	1.1731	SOX2.p2	AK005705|Acrv1|11451|acrosomal vesicle protein 1	BC100459|Acrv1|11451|acrosomal vesicle protein 1	NM_007391|Acrv1|11451|acrosomal vesicle protein 1	U31992|Acrv1|11451|acrosomal vesicle protein 1	AK030129|Acrv1|11451|acrosomal vesicle protein 1	BC139101|Acrv1|11451|acrosomal vesicle protein 1	BC139103|Acrv1|11451|acrosomal vesicle protein 1
mm9_v1_chr9_-_71332764_71332764	1.17238	SOX2.p2	AK002571|Grinl1a|28015|glutamate receptor, ionotropic, N-methyl D-aspartate-like 1A	NM_001164793|Grinl1a|28015|glutamate receptor, ionotropic, N-methyl D-aspartate-like 1A
mm9_v1_chr2_-_140485267_140485302	1.17169	SOX2.p2	AK017456|Flrt3|71436|fibronectin leucine rich transmembrane protein 3
mm9_v1_chr9_-_57966613_57966629	1.17166	SOX2.p2	AK166434|Ccdc33|382077|coiled-coil domain containing 33	AK145264|Ccdc33|382077|coiled-coil domain containing 33	NM_001166282|Ccdc33|382077|coiled-coil domain containing 33
mm9_v1_chr19_-_47036782_47036852	1.17125	SOX2.p2	AK008045|Nt5c2|76952|5'-nucleotidase, cytosolic II	AK030786|Nt5c2|76952|5'-nucleotidase, cytosolic II	AK036730|Nt5c2|76952|5'-nucleotidase, cytosolic II	AK038326|Nt5c2|76952|5'-nucleotidase, cytosolic II	AK132384|Nt5c2|76952|5'-nucleotidase, cytosolic II	AK147901|Nt5c2|76952|5'-nucleotidase, cytosolic II	AK169616|Nt5c2|76952|5'-nucleotidase, cytosolic II	NM_029810|Nt5c2|76952|5'-nucleotidase, cytosolic II
mm9_v1_chr7_+_4866810_4866885	1.17055	SOX2.p2	AK155214|Zfp628|232816|zinc finger protein 628	NM_170759|Zfp628|232816|zinc finger protein 628	AK048291|Zfp628|232816|zinc finger protein 628	BC056945|Zfp628|232816|zinc finger protein 628	BC062973|Zfp628|232816|zinc finger protein 628
mm9_v1_chr17_+_53618611_53618848	1.16933	SOX2.p2	AK036011|Rab5a|271457|RAB5A, member RAS oncogene family	BC004842|Rab5a|271457|RAB5A, member RAS oncogene family	AK010495|Rab5a|271457|RAB5A, member RAS oncogene family	AK150405|Rab5a|271457|RAB5A, member RAS oncogene family	AK002631|Rab5a|271457|RAB5A, member RAS oncogene family	AK150296|Rab5a|271457|RAB5A, member RAS oncogene family	AK151066|Rab5a|271457|RAB5A, member RAS oncogene family	AK153131|Rab5a|271457|RAB5A, member RAS oncogene family	AK159706|Rab5a|271457|RAB5A, member RAS oncogene family	AK150346|Rab5a|271457|RAB5A, member RAS oncogene family	BC034370|Rab5a|271457|RAB5A, member RAS oncogene family	AK008198|Rab5a|271457|RAB5A, member RAS oncogene family
mm9_v1_chr9_-_64869349_64869525	1.16929	SOX2.p2	Z97207|Ptplad1|57874|protein tyrosine phosphatase-like A domain containing 1	AK051735|Ptplad1|57874|protein tyrosine phosphatase-like A domain containing 1	AK159494|Ptplad1|57874|protein tyrosine phosphatase-like A domain containing 1	BC057023|Ptplad1|57874|protein tyrosine phosphatase-like A domain containing 1	BC031755|Ptplad1|57874|protein tyrosine phosphatase-like A domain containing 1	AK050556|Ptplad1|57874|protein tyrosine phosphatase-like A domain containing 1	AK052865|Ptplad1|57874|protein tyrosine phosphatase-like A domain containing 1	NM_021345|Ptplad1|57874|protein tyrosine phosphatase-like A domain containing 1
mm9_v1_chr1_-_20608010_20608144	1.16865	SOX2.p2	AY438374|Pkhd1|241035|polycystic kidney and hepatic disease 1	AK143992|Pkhd1|241035|polycystic kidney and hepatic disease 1	AY130764|Pkhd1|241035|polycystic kidney and hepatic disease 1	NM_153179|Pkhd1|241035|polycystic kidney and hepatic disease 1	AK052698|Pkhd1|241035|polycystic kidney and hepatic disease 1
mm9_v1_chr5_-_123439064_123439107	1.16839	SOX2.p2	BC065090|Kdm2b|30841|lysine (K)-specific demethylase 2B	AK043352|Kdm2b|30841|lysine (K)-specific demethylase 2B	NM_001003953|Kdm2b|30841|lysine (K)-specific demethylase 2B	AK136625|Kdm2b|30841|lysine (K)-specific demethylase 2B
mm9_v1_chr2_-_180689380_180689413	1.16705	SOX2.p2	BC061107|Nkain4|58237|Na+/K+ transporting ATPase interacting 4	AK021096|Nkain4|58237|Na+/K+ transporting ATPase interacting 4	NM_001141933|Nkain4|58237|Na+/K+ transporting ATPase interacting 4	NM_021426|Nkain4|58237|Na+/K+ transporting ATPase interacting 4
mm9_v1_chr8_+_94192087_94192089	1.16371	SOX2.p2	
mm9_v1_chr6_-_115788429_115788481	1.16225	SOX2.p2	BC060267|BC060267|212516|cDNA sequence BC060267	NM_001110506|BC060267|212516|cDNA sequence BC060267
mm9_v1_chr5_+_77020738_77020827	1.16054	SOX2.p2	BC062951|Cep135|381644|centrosomal protein 135	NM_199032|Cep135|381644|centrosomal protein 135	AK172988|Cep135|381644|centrosomal protein 135
mm9_v1_chr19_+_56536148_56536166	1.15959	SOX2.p2	BC090250|9930023K05Rik|226245|RIKEN cDNA 9930023K05 gene
mm9_v1_chr1_+_55462764_55462802	1.15888	SOX2.p2	AK083136|Plcl1|227120|phospholipase C-like 1	AK161943|Plcl1|227120|phospholipase C-like 1	NM_001114663|Plcl1|227120|phospholipase C-like 1	AK135610|Plcl1|227120|phospholipase C-like 1
mm9_v1_chr5_-_122822329_122822391	1.15782	SOX2.p2	BC019498|1500011H22Rik|68948|RIKEN cDNA 1500011H22 gene	AK005211|1500011H22Rik|68948|RIKEN cDNA 1500011H22 gene	AK150218|1500011H22Rik|68948|RIKEN cDNA 1500011H22 gene
mm9_v1_chr5_-_100465086_100465197	1.15676	SOX2.p2	AK011143|Hnrpdl|50926|heterogeneous nuclear ribonucleoprotein D-like
mm9_v1_chr9_-_117539030_117539030	1.15342	SOX2.p2	AK046197|Rbms3|207181|RNA binding motif, single stranded interacting protein	NM_001172121|Rbms3|207181|RNA binding motif, single stranded interacting protein
mm9_v1_chrX_-_91787351_91787352	1.15237	SOX2.p2	BC031461|Maged1|94275|melanoma antigen, family D, 1
mm9_v1_chr8_+_107951514_107951547	1.15179	SOX2.p2	AK133042|Lrrc36|270091|leucine rich repeat containing 36	NM_001033371|Lrrc36|270091|leucine rich repeat containing 36	NM_001170789|Lrrc36|270091|leucine rich repeat containing 36	BC150957|Lrrc36|270091|leucine rich repeat containing 36	BC172120|Lrrc36|270091|leucine rich repeat containing 36
mm9_v1_chr2_+_177876858_177876930	1.1513	SOX2.p2	BC059869|Phactr3|74189|phosphatase and actin regulator 3	AK032242|Phactr3|74189|phosphatase and actin regulator 3	AY501387|Phactr3|74189|phosphatase and actin regulator 3
mm9_v1_chr7_-_52381569_52381578	1.15023	SOX2.p2	BC034450|Rpl13a|22121|ribosomal protein L13A	BC042392|Rpl13a|22121|ribosomal protein L13A
mm9_v1_chr3_-_107734481_107734662	1.14869	SOX2.p2	AK162441|Gstm7|68312|glutathione S-transferase, mu 7	AK002213|Gstm7|68312|glutathione S-transferase, mu 7	BC051924|Gstm7|68312|glutathione S-transferase, mu 7	NM_026672|Gstm7|68312|glutathione S-transferase, mu 7
mm9_v1_chr6_-_23605087_23605135	1.1479	SOX2.p2	AY155440|Rnf148|71300|ring finger protein 148	AK017027|Rnf148|71300|ring finger protein 148	NM_027754|Rnf148|71300|ring finger protein 148
mm9_v1_chr11_-_97490456_97490494	1.14688	SOX2.p2	BC006054|E130012A19Rik|103551|RIKEN cDNA E130012A19 gene
mm9_v1_chr5_-_135164426_135164540	1.1436	SOX2.p2	BC063768|Limk1|16885|LIM-domain containing, protein kinase	AK141813|Limk1|16885|LIM-domain containing, protein kinase	AK164484|Limk1|16885|LIM-domain containing, protein kinase	U15159|Limk1|16885|LIM-domain containing, protein kinase	NM_010717|Limk1|16885|LIM-domain containing, protein kinase	U14166|Limk1|16885|LIM-domain containing, protein kinase
mm9_v1_chr6_+_83187368_83187368	1.1433	SOX2.p2	NM_001166067|Slc4a5|232156|solute carrier family 4, sodium bicarbonate cotransporter, member 5
mm9_v1_chr12_+_72237834_72237834	1.14132	SOX2.p2	BC043104|2700049A03Rik|76967|RIKEN cDNA 2700049A03 gene	NM_001163378|2700049A03Rik|76967|RIKEN cDNA 2700049A03 gene	NM_029818|2700049A03Rik|76967|RIKEN cDNA 2700049A03 gene
mm9_v1_chr5_-_23953594_23953663	1.14066	SOX2.p2	AY603379|Tmub1|64295|transmembrane and ubiquitin-like domain containing 1	AK008109|Tmub1|64295|transmembrane and ubiquitin-like domain containing 1	BC019547|Tmub1|64295|transmembrane and ubiquitin-like domain containing 1	AB030183|Tmub1|64295|transmembrane and ubiquitin-like domain containing 1	NM_022418|Tmub1|64295|transmembrane and ubiquitin-like domain containing 1
mm9_v1_chr11_-_97490978_97491083	1.14034	SOX2.p2	AK087411|E130012A19Rik|103551|RIKEN cDNA E130012A19 gene	BC055770|E130012A19Rik|103551|RIKEN cDNA E130012A19 gene	NM_175332|E130012A19Rik|103551|RIKEN cDNA E130012A19 gene
mm9_v1_chr2_+_180716817_180716845	1.13943	SOX2.p2	
mm9_v1_chr4_+_21775172_21775224	1.13725	SOX2.p2	AK162695|Sfrs18|66625|serine/arginine-rich splicing factor 18	AK012036|Sfrs18|66625|serine/arginine-rich splicing factor 18	AK031964|Sfrs18|66625|serine/arginine-rich splicing factor 18	AK017507|Sfrs18|66625|serine/arginine-rich splicing factor 18	AK020035|Sfrs18|66625|serine/arginine-rich splicing factor 18	AK081407|Sfrs18|66625|serine/arginine-rich splicing factor 18	AK083021|Sfrs18|66625|serine/arginine-rich splicing factor 18	AK160288|Sfrs18|66625|serine/arginine-rich splicing factor 18	BC060111|Sfrs18|66625|serine/arginine-rich splicing factor 18
mm9_v1_chr5_+_73882264_73882364	1.13569	SOX2.p2	NM_001190733|Dcun1d4|100737|DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)	NM_178896|Dcun1d4|100737|DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)	AK033559|Dcun1d4|100737|DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)	BC137627|Dcun1d4|100737|DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)	BC137628|Dcun1d4|100737|DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)	BC144794|Dcun1d4|100737|DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)	BC060213|Dcun1d4|100737|DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)	BC108346|Dcun1d4|100737|DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)
mm9_v1_chr2_+_90620127_90620146	1.13489	SOX2.p2	BC039616|Fnbp4|55935|formin binding protein 4
mm9_v1_chr7_-_26506741_26506878	1.13433	SOX2.p2	
mm9_v1_chr15_-_93166789_93166977	1.13286	SOX2.p2	AK184096|Yaf2|67057|YY1 associated factor 2	AK012787|Yaf2|67057|YY1 associated factor 2
mm9_v1_chr19_+_56536126_56536129	1.13102	SOX2.p2	NM_001164263|9930023K05Rik|226245|RIKEN cDNA 9930023K05 gene	NM_172641|9930023K05Rik|226245|RIKEN cDNA 9930023K05 gene	AK036908|9930023K05Rik|226245|RIKEN cDNA 9930023K05 gene	AK053921|9930023K05Rik|226245|RIKEN cDNA 9930023K05 gene
mm9_v1_chrX_-_161765324_161765332	1.12988	SOX2.p2	AK139335|Glra2|237213|glycine receptor, alpha 2 subunit
mm9_v1_chr16_+_19760300_19760490	1.12982	SOX2.p2	AK037166|B3gnt5|108105|UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	AK083839|B3gnt5|108105|UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	NM_001159407|B3gnt5|108105|UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	NM_001159408|B3gnt5|108105|UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	NM_054052|B3gnt5|108105|UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	AK032911|B3gnt5|108105|UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	AK048010|B3gnt5|108105|UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	BC063076|B3gnt5|108105|UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5
mm9_v1_chr7_+_128089656_128089684	1.12869	SOX2.p2	AK162059|Polr3e|26939|polymerase (RNA) III (DNA directed) polypeptide E
mm9_v1_chr2_-_155979971_155980032	1.12693	SOX2.p2	AK046526|Rbm39|170791|RNA binding motif protein 39
mm9_v1_chr4_+_135842056_135842075	1.12629	SOX2.p2	AK136405|Zfp46|22704|zinc finger protein 46
mm9_v1_chr5_-_24781987_24782111	1.12578	SOX2.p2	AK077567|Mll3|231051|myeloid/lymphoid or mixed-lineage leukemia 3
mm9_v1_chr4_+_17780628_17780643	1.12509	SOX2.p2	BC057926|Mmp16|17389|matrix metallopeptidase 16	NM_019724|Mmp16|17389|matrix metallopeptidase 16
mm9_v1_chr18_+_37454493_37454629	1.12457	SOX2.p2	NM_053127|Pcdhb2|93873|protocadherin beta 2	BC021789|Pcdhb2|93873|protocadherin beta 2	BC141154|Pcdhb2|93873|protocadherin beta 2	AY013781|Pcdhb2|93873|protocadherin beta 2
mm9_v1_chr9_+_70390703_70390723	1.11882	SOX2.p2	AK162780|Sltm|66660|SAFB-like, transcription modulator	AK017839|Sltm|66660|SAFB-like, transcription modulator
mm9_v1_chr9_+_55388955_55389013	1.11881	SOX2.p2	NM_027397|Isl2|104360|insulin related protein 2 (islet 2)	AK013964|Isl2|104360|insulin related protein 2 (islet 2)	BC120880|Isl2|104360|insulin related protein 2 (islet 2)	BC148307|Isl2|104360|insulin related protein 2 (islet 2)
mm9_v1_chr2_-_131855937_131856045	1.11869	SOX2.p2	AK172906|Rassf2|215653|Ras association (RalGDS/AF-6) domain family member 2
mm9_v1_chr17_-_59130757_59130797	1.11827	SOX2.p2	BC034642|2610034M16Rik|69239|RIKEN cDNA 2610034M16 gene	BC033350|2610034M16Rik|69239|RIKEN cDNA 2610034M16 gene	NM_027001|2610034M16Rik|69239|RIKEN cDNA 2610034M16 gene
mm9_v1_chr8_+_95425293_95425305	1.11535	SOX2.p2	NM_027112|Capns2|69543|calpain, small subunit 2	AK009171|Capns2|69543|calpain, small subunit 2
mm9_v1_chr11_+_102254949_102254989	1.115	SOX2.p2	U73941|Rundc3a|51799|RUN domain containing 3A
mm9_v1_chr7_+_116154373_116154494	1.11407	SOX2.p2	AK165720|Tub|22141|tubby candidate gene	NM_021885|Tub|22141|tubby candidate gene	U52433|Tub|22141|tubby candidate gene	BC096554|Tub|22141|tubby candidate gene	U54643|Tub|22141|tubby candidate gene
mm9_v1_chr4_-_45097427_45097496	1.1136	SOX2.p2	AK153358|Fbxo10|269529|F-box protein 10	BC054731|Fbxo10|269529|F-box protein 10	AK150292|Fbxo10|269529|F-box protein 10	AK142389|Fbxo10|269529|F-box protein 10	NM_001024142|Fbxo10|269529|F-box protein 10
mm9_v1_chr17_-_40931024_40931046	1.11188	SOX2.p2	AK018856|Crisp2|22024|cysteine-rich secretory protein 2	M25533|Crisp2|22024|cysteine-rich secretory protein 2	NM_009420|Crisp2|22024|cysteine-rich secretory protein 2	BC049615|Crisp2|22024|cysteine-rich secretory protein 2
mm9_v1_chr10_+_74523633_74523640	1.11124	SOX2.p2	NM_001081412|Bcr|110279|breakpoint cluster region
mm9_v1_chr18_+_34932278_34932429	1.11114	SOX2.p2	AK012724|Fam53c|66306|family with sequence similarity 53, member C	AK205811|Fam53c|66306|family with sequence similarity 53, member C
mm9_v1_chr1_-_136700389_136700428	1.1106	SOX2.p2	AK035285|Ppp1r12b|329251|protein phosphatase 1, regulatory (inhibitor) subunit 12B
mm9_v1_chr17_-_47551659_47551659	1.11039	SOX2.p2	AK005579|1700001C19Rik|75462|RIKEN cDNA 1700001C19 gene	NM_001172091|1700001C19Rik|75462|RIKEN cDNA 1700001C19 gene
mm9_v1_chr8_-_8666771_8666782	1.10954	SOX2.p2	AK038412|Arglu1|234023|arginine and glutamate rich 1
mm9_v1_chr17_+_47767638_47767638	1.10869	SOX2.p2	BC060712|Usp49|224836|ubiquitin specific peptidase 49	NM_198421|Usp49|224836|ubiquitin specific peptidase 49
mm9_v1_chr9_-_16182674_16182674	1.10719	SOX2.p2	NM_001080814|Fat3|270120|FAT tumor suppressor homolog 3 (Drosophila)
mm9_v1_chr6_-_29330414_29330512	1.10709	SOX2.p2	U49720|Opn1sw|12057|opsin 1 (cone pigments), short-wave-sensitive (color blindness, tritan)	BC050002|Opn1sw|12057|opsin 1 (cone pigments), short-wave-sensitive (color blindness, tritan)	BC058267|Opn1sw|12057|opsin 1 (cone pigments), short-wave-sensitive (color blindness, tritan)	AF190670|Opn1sw|12057|opsin 1 (cone pigments), short-wave-sensitive (color blindness, tritan)	BC026021|Opn1sw|12057|opsin 1 (cone pigments), short-wave-sensitive (color blindness, tritan)	NM_007538|Opn1sw|12057|opsin 1 (cone pigments), short-wave-sensitive (color blindness, tritan)
mm9_v1_chr5_-_115750649_115750671	1.10569	SOX2.p2	BC085492|Dynll1|56455|dynein light chain LC8-type 1
mm9_v1_chr10_+_80643263_80643395	1.10503	SOX2.p2	AK189998|Eef2|13629|eukaryotic translation elongation factor 2	AK190198|Eef2|13629|eukaryotic translation elongation factor 2	AK190350|Eef2|13629|eukaryotic translation elongation factor 2	AK190868|Eef2|13629|eukaryotic translation elongation factor 2	AK191552|Eef2|13629|eukaryotic translation elongation factor 2	AK191881|Eef2|13629|eukaryotic translation elongation factor 2	AK192244|Eef2|13629|eukaryotic translation elongation factor 2	AK192889|Eef2|13629|eukaryotic translation elongation factor 2	AK192915|Eef2|13629|eukaryotic translation elongation factor 2	AK193101|Eef2|13629|eukaryotic translation elongation factor 2	AK193468|Eef2|13629|eukaryotic translation elongation factor 2	AK193703|Eef2|13629|eukaryotic translation elongation factor 2	AK193872|Eef2|13629|eukaryotic translation elongation factor 2	AK194719|Eef2|13629|eukaryotic translation elongation factor 2	AK195368|Eef2|13629|eukaryotic translation elongation factor 2	AK195633|Eef2|13629|eukaryotic translation elongation factor 2	AK195893|Eef2|13629|eukaryotic translation elongation factor 2	AK196946|Eef2|13629|eukaryotic translation elongation factor 2	AK197219|Eef2|13629|eukaryotic translation elongation factor 2	AK197725|Eef2|13629|eukaryotic translation elongation factor 2	AK198008|Eef2|13629|eukaryotic translation elongation factor 2	AK198317|Eef2|13629|eukaryotic translation elongation factor 2	AK198429|Eef2|13629|eukaryotic translation elongation factor 2	AK199118|Eef2|13629|eukaryotic translation elongation factor 2	AK200031|Eef2|13629|eukaryotic translation elongation factor 2	AK200070|Eef2|13629|eukaryotic translation elongation factor 2	AK200383|Eef2|13629|eukaryotic translation elongation factor 2	AK201054|Eef2|13629|eukaryotic translation elongation factor 2	AK201169|Eef2|13629|eukaryotic translation elongation factor 2	AK201226|Eef2|13629|eukaryotic translation elongation factor 2	AK201313|Eef2|13629|eukaryotic translation elongation factor 2	AK201376|Eef2|13629|eukaryotic translation elongation factor 2	AK202006|Eef2|13629|eukaryotic translation elongation factor 2	AK202706|Eef2|13629|eukaryotic translation elongation factor 2	AK202834|Eef2|13629|eukaryotic translation elongation factor 2	AK203709|Eef2|13629|eukaryotic translation elongation factor 2	AK203838|Eef2|13629|eukaryotic translation elongation factor 2	AK204069|Eef2|13629|eukaryotic translation elongation factor 2	AK204359|Eef2|13629|eukaryotic translation elongation factor 2	AK204850|Eef2|13629|eukaryotic translation elongation factor 2	AK207898|Eef2|13629|eukaryotic translation elongation factor 2	AK215864|Eef2|13629|eukaryotic translation elongation factor 2	AK215877|Eef2|13629|eukaryotic translation elongation factor 2
mm9_v1_chr18_+_45719101_45719122	1.1034	SOX2.p2	AK149082|Kcnn2|140492|potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	AK039033|Kcnn2|140492|potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2
mm9_v1_chr5_-_92512683_92512782	1.1033	SOX2.p2	AF145285|G3bp2|23881|GTPase activating protein (SH3 domain) binding protein 2	U65313|G3bp2|23881|GTPase activating protein (SH3 domain) binding protein 2	AK151965|G3bp2|23881|GTPase activating protein (SH3 domain) binding protein 2	AK152792|G3bp2|23881|GTPase activating protein (SH3 domain) binding protein 2	AK172256|G3bp2|23881|GTPase activating protein (SH3 domain) binding protein 2	BC048176|G3bp2|23881|GTPase activating protein (SH3 domain) binding protein 2	AK145697|G3bp2|23881|GTPase activating protein (SH3 domain) binding protein 2	AK076117|G3bp2|23881|GTPase activating protein (SH3 domain) binding protein 2	AK167186|G3bp2|23881|GTPase activating protein (SH3 domain) binding protein 2	NM_001080795|G3bp2|23881|GTPase activating protein (SH3 domain) binding protein 2	NM_011816|G3bp2|23881|GTPase activating protein (SH3 domain) binding protein 2
mm9_v1_chr3_-_27795287_27795289	1.10118	SOX2.p2	AK053134|Tmem212|208613|transmembrane protein 212	BC119391|Tmem212|208613|transmembrane protein 212	BC119393|Tmem212|208613|transmembrane protein 212	NM_001164437|Tmem212|208613|transmembrane protein 212
mm9_v1_chr9_+_21420612_21420824	1.10111	SOX2.p2	BC079560|Smarca4|20586|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	NM_001174078|Smarca4|20586|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	NM_001174079|Smarca4|20586|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	NM_011417|Smarca4|20586|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	AK147285|Smarca4|20586|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	AK166837|Smarca4|20586|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	AK160825|Smarca4|20586|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	AK135308|Smarca4|20586|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	AK142137|Smarca4|20586|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	BC061214|Smarca4|20586|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	BC060229|Smarca4|20586|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	BC023830|Smarca4|20586|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	BC032162|Smarca4|20586|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	BC054056|Smarca4|20586|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	BC014760|Smarca4|20586|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	AK051530|Smarca4|20586|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4
mm9_v1_chr4_+_109088251_109088289	1.10087	SOX2.p2	NM_001145948|Ttc39a|230603|tetratricopeptide repeat domain 39A	AK076720|Ttc39a|230603|tetratricopeptide repeat domain 39A	AK076641|Ttc39a|230603|tetratricopeptide repeat domain 39A	AK076772|Ttc39a|230603|tetratricopeptide repeat domain 39A
mm9_v1_chrX_-_91787372_91787452	1.10048	SOX2.p2	AB029448|Maged1|94275|melanoma antigen, family D, 1	NM_019791|Maged1|94275|melanoma antigen, family D, 1
mm9_v1_chr11_+_59475986_59476013	1.09968	SOX2.p2	AK154807|Mprip|26936|myosin phosphatase Rho interacting protein	NM_012027|Mprip|26936|myosin phosphatase Rho interacting protein	NM_201245|Mprip|26936|myosin phosphatase Rho interacting protein	AK158296|Mprip|26936|myosin phosphatase Rho interacting protein	AK171089|Mprip|26936|myosin phosphatase Rho interacting protein	AK170849|Mprip|26936|myosin phosphatase Rho interacting protein
mm9_v1_chr6_-_120314373_120314396	1.09737	SOX2.p2	AK031590|Ccdc77|67200|coiled-coil domain containing 77
mm9_v1_chr15_+_10994444_10994583	1.09652	SOX2.p2	AK145096|Adamts12|239337|a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 12	AK135354|Adamts12|239337|a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 12	NM_175501|Adamts12|239337|a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 12	AK054015|Adamts12|239337|a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 12	AK048612|Adamts12|239337|a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 12
mm9_v1_chr2_-_14970818_14970938	1.09556	SOX2.p2	AK077778|Nsun6|74455|NOL1/NOP2/Sun domain family member 6	AK132428|Nsun6|74455|NOL1/NOP2/Sun domain family member 6	BC053751|Nsun6|74455|NOL1/NOP2/Sun domain family member 6	AK042750|Nsun6|74455|NOL1/NOP2/Sun domain family member 6	NM_001165942|Nsun6|74455|NOL1/NOP2/Sun domain family member 6	NM_028950|Nsun6|74455|NOL1/NOP2/Sun domain family member 6
mm9_v1_chr9_+_43552046_43552085	1.09452	SOX2.p2	AK147479|Pvrl1|58235|poliovirus receptor-related 1
mm9_v1_chr2_-_37502738_37502804	1.09397	SOX2.p2	X84692|Strbp|20744|spermatid perinuclear RNA binding protein	NM_009261|Strbp|20744|spermatid perinuclear RNA binding protein
mm9_v1_chr17_-_47537384_47537532	1.09357	SOX2.p2	L36860|Guca1a|14913|guanylate cyclase activator 1a (retina)	BC031810|Guca1a|14913|guanylate cyclase activator 1a (retina)	BC026834|Guca1a|14913|guanylate cyclase activator 1a (retina)	NM_008189|Guca1a|14913|guanylate cyclase activator 1a (retina)
mm9_v1_chrX_+_130722039_130722141	1.09304	SOX2.p2	AK016872|Arl13a|74448|ADP-ribosylation factor-like 13A	NM_028947|Arl13a|74448|ADP-ribosylation factor-like 13A	BC100522|Arl13a|74448|ADP-ribosylation factor-like 13A
mm9_v1_chr3_-_19595395_19595395	1.09143	SOX2.p2	NM_205769|Crh|12918|corticotropin releasing hormone
mm9_v1_chr7_-_107663293_107663468	1.09116	SOX2.p2	AK139680|Dnajb13|69387|DnaJ (Hsp40) related, subfamily B, member 13	BC048501|Dnajb13|69387|DnaJ (Hsp40) related, subfamily B, member 13	NM_153527|Dnajb13|69387|DnaJ (Hsp40) related, subfamily B, member 13	AF419292|Dnajb13|69387|DnaJ (Hsp40) related, subfamily B, member 13
mm9_v1_chrX_+_7367116_7367152	1.09107	SOX2.p2	AK156165|Gripap1|54645|GRIP1 associated protein 1	AK172623|Gripap1|54645|GRIP1 associated protein 1	AK172699|Gripap1|54645|GRIP1 associated protein 1	AK172590|Gripap1|54645|GRIP1 associated protein 1	NM_207670|Gripap1|54645|GRIP1 associated protein 1	BC138523|Gripap1|54645|GRIP1 associated protein 1	BC145310|Gripap1|54645|GRIP1 associated protein 1	AK158098|Gripap1|54645|GRIP1 associated protein 1	X97571|Gripap1|54645|GRIP1 associated protein 1
mm9_v1_chr1_-_132526172_132526182	1.09082	SOX2.p2	BC119121|Zp3r|22789|zona pellucida 3 receptor	BC119123|Zp3r|22789|zona pellucida 3 receptor	U17108|Zp3r|22789|zona pellucida 3 receptor	NM_009581|Zp3r|22789|zona pellucida 3 receptor
mm9_v1_chr16_+_13780778_13780842	1.09081	SOX2.p2	NM_001039521|Rrn3|106298|RRN3 RNA polymerase I transcription factor homolog (yeast)	AK021410|Rrn3|106298|RRN3 RNA polymerase I transcription factor homolog (yeast)	AK165676|Rrn3|106298|RRN3 RNA polymerase I transcription factor homolog (yeast)	AK080680|Rrn3|106298|RRN3 RNA polymerase I transcription factor homolog (yeast)	BC138774|Rrn3|106298|RRN3 RNA polymerase I transcription factor homolog (yeast)	BC138776|Rrn3|106298|RRN3 RNA polymerase I transcription factor homolog (yeast)	AK080397|Rrn3|106298|RRN3 RNA polymerase I transcription factor homolog (yeast)
mm9_v1_chr1_-_155334737_155334791	1.08956	SOX2.p2	U91922|Dhx9|13211|DEAH (Asp-Glu-Ala-His) box polypeptide 9	BC064082|Dhx9|13211|DEAH (Asp-Glu-Ala-His) box polypeptide 9	BC089159|Dhx9|13211|DEAH (Asp-Glu-Ala-His) box polypeptide 9	AK141824|Dhx9|13211|DEAH (Asp-Glu-Ala-His) box polypeptide 9	AK148423|Dhx9|13211|DEAH (Asp-Glu-Ala-His) box polypeptide 9	AK169735|Dhx9|13211|DEAH (Asp-Glu-Ala-His) box polypeptide 9	AK013423|Dhx9|13211|DEAH (Asp-Glu-Ala-His) box polypeptide 9	BC033911|Dhx9|13211|DEAH (Asp-Glu-Ala-His) box polypeptide 9	NM_007842|Dhx9|13211|DEAH (Asp-Glu-Ala-His) box polypeptide 9
mm9_v1_chr5_+_28492235_28492251	1.08707	SOX2.p2	AK157766|En2|13799|engrailed 2	NM_010134|En2|13799|engrailed 2
mm9_v1_chr12_-_81861527_81861701	1.08643	SOX2.p2	AK147473|Gm1568|380768|predicted gene 1568	BC067044|Gm1568|380768|predicted gene 1568	NM_001008423|Gm1568|380768|predicted gene 1568
mm9_v1_chr13_+_95793012_95793015	1.08479	SOX2.p2	
mm9_v1_chr3_-_8666930_8666974	1.08311	SOX2.p2	AB041590|Hey1|15213|hairy/enhancer-of-split related with YRPW motif 1
mm9_v1_chr12_-_77896481_77896489	1.08277	SOX2.p2	BC066825|Gpx2|14776|glutathione peroxidase 2	BC039658|Gpx2|14776|glutathione peroxidase 2
mm9_v1_chr8_+_97605076_97605133	1.08155	SOX2.p2	NM_028805|Katnb1|74187|katanin p80 (WD40-containing) subunit B 1	AK054173|Katnb1|74187|katanin p80 (WD40-containing) subunit B 1
mm9_v1_chr11_-_99250663_99250679	1.07847	SOX2.p2	AK014360|Krt10|16661|keratin 10	V00830|Krt10|16661|keratin 10	AK076508|Krt10|16661|keratin 10	AK081914|Krt10|16661|keratin 10	AK081402|Krt10|16661|keratin 10	NM_010660|Krt10|16661|keratin 10
mm9_v1_chr1_-_136700174_136700333	1.07827	SOX2.p2	AK051953|Ppp1r12b|329251|protein phosphatase 1, regulatory (inhibitor) subunit 12B	AK161046|Ppp1r12b|329251|protein phosphatase 1, regulatory (inhibitor) subunit 12B
mm9_v1_chr18_-_36925819_36925867	1.07607	SOX2.p2	AY321066|Dnd1|213236|dead end homolog 1 (zebrafish)	AK141343|Dnd1|213236|dead end homolog 1 (zebrafish)	BC034897|Dnd1|213236|dead end homolog 1 (zebrafish)	NM_173383|Dnd1|213236|dead end homolog 1 (zebrafish)
mm9_v1_chr19_-_7877065_7877081	1.07538	SOX2.p2	AJ132857|BC014805|236149|cDNA sequence BC014805
mm9_v1_chr7_+_128061257_128061281	1.07448	SOX2.p2	AK005034|Polr3e|26939|polymerase (RNA) III (DNA directed) polypeptide E	NM_001164096|Polr3e|26939|polymerase (RNA) III (DNA directed) polypeptide E	NM_025298|Polr3e|26939|polymerase (RNA) III (DNA directed) polypeptide E
mm9_v1_chr5_+_21049368_21049436	1.07429	SOX2.p2	AK014767|Lrrc17|74511|leucine rich repeat containing 17	AK018071|Lrrc17|74511|leucine rich repeat containing 17	BC030317|Lrrc17|74511|leucine rich repeat containing 17
mm9_v1_chr18_+_69753035_69753127	1.06896	SOX2.p2	AK014343|Tcf4|21413|transcription factor 4	U16321|Tcf4|21413|transcription factor 4	AK132140|Tcf4|21413|transcription factor 4	BC014293|Tcf4|21413|transcription factor 4
mm9_v1_chr17_+_36053855_36053941	1.0688	SOX2.p2	NM_175934|Ppp1r10|52040|protein phosphatase 1, regulatory subunit 10	AK004266|Ppp1r10|52040|protein phosphatase 1, regulatory subunit 10	AK011552|Ppp1r10|52040|protein phosphatase 1, regulatory subunit 10	AK079389|Ppp1r10|52040|protein phosphatase 1, regulatory subunit 10	AK031654|Ppp1r10|52040|protein phosphatase 1, regulatory subunit 10	AK053183|Ppp1r10|52040|protein phosphatase 1, regulatory subunit 10	AK079918|Ppp1r10|52040|protein phosphatase 1, regulatory subunit 10	BC030903|Ppp1r10|52040|protein phosphatase 1, regulatory subunit 10
mm9_v1_chr11_+_78312784_78312851	1.0673	SOX2.p2	X63003|Vtn|22370|vitronectin	BC012690|Vtn|22370|vitronectin	AF440693|Vtn|22370|vitronectin	M77123|Vtn|22370|vitronectin
mm9_v1_chrX_-_9793578_9793578	1.06695	SOX2.p2	AK138977|Rpgr|19893|retinitis pigmentosa GTPase regulator	NM_001177952|Rpgr|19893|retinitis pigmentosa GTPase regulator
mm9_v1_chr8_+_11840520_11840520	1.06672	SOX2.p2	AK006092|1700018L24Rik|75528|RIKEN cDNA 1700018L24 gene	BC049746|1700018L24Rik|75528|RIKEN cDNA 1700018L24 gene	NM_029326|1700018L24Rik|75528|RIKEN cDNA 1700018L24 gene
mm9_v1_chr2_+_156138184_156138368	1.06651	SOX2.p2	AK014912|4921517L17Rik|70873|RIKEN cDNA 4921517L17 gene	NM_027585|4921517L17Rik|70873|RIKEN cDNA 4921517L17 gene	BC140978|4921517L17Rik|70873|RIKEN cDNA 4921517L17 gene	AK162372|4921517L17Rik|70873|RIKEN cDNA 4921517L17 gene	AK017330|4921517L17Rik|70873|RIKEN cDNA 4921517L17 gene	AK158271|4921517L17Rik|70873|RIKEN cDNA 4921517L17 gene	BC027204|4921517L17Rik|70873|RIKEN cDNA 4921517L17 gene
mm9_v1_chr16_-_78576898_78576912	1.06571	SOX2.p2	AK009258|D16Ertd472e|67102|DNA segment, Chr 16, ERATO Doi 472, expressed	NM_025967|D16Ertd472e|67102|DNA segment, Chr 16, ERATO Doi 472, expressed
mm9_v1_chr13_-_94269762_94269770	1.06393	SOX2.p2	AK141957|Jmy|57748|junction-mediating and regulatory protein
mm9_v1_chrX_+_149993135_149993155	1.06289	SOX2.p2	AK005674|Cypt3|69361|cysteine-rich perinuclear theca 3	BC048527|Cypt3|69361|cysteine-rich perinuclear theca 3	NM_173367|Cypt3|69361|cysteine-rich perinuclear theca 3	AM040452|Cypt3|69361|cysteine-rich perinuclear theca 3	AF463500|Cypt3|69361|cysteine-rich perinuclear theca 3
mm9_v1_chr5_-_121614560_121614637	1.06205	SOX2.p2	AK163809|Ptpn11|19247|protein tyrosine phosphatase, non-receptor type 11
mm9_v1_chr6_-_142271469_142271500	1.05691	SOX2.p2	AF240694|Slco1a5|108096|solute carrier organic anion transporter family, member 1a5	NM_130861|Slco1a5|108096|solute carrier organic anion transporter family, member 1a5	AK029706|Slco1a5|108096|solute carrier organic anion transporter family, member 1a5
mm9_v1_chr10_-_33344405_33344571	1.05617	SOX2.p2	AK039308|Clvs2|215890|clavesin 2	NM_175448|Clvs2|215890|clavesin 2	BC058539|Clvs2|215890|clavesin 2	AK163214|Clvs2|215890|clavesin 2	AK053797|Clvs2|215890|clavesin 2	AK139868|Clvs2|215890|clavesin 2	AK139409|Clvs2|215890|clavesin 2	AK169009|Clvs2|215890|clavesin 2
mm9_v1_chr4_-_63064369_63064478	1.05601	SOX2.p2	AK170885|Akna|100182|AT-hook transcription factor	AK129468|Akna|100182|AT-hook transcription factor	AK089194|Akna|100182|AT-hook transcription factor	AK159547|Akna|100182|AT-hook transcription factor	NM_001045514|Akna|100182|AT-hook transcription factor
mm9_v1_chr3_+_51299646_51299685	1.05542	SOX2.p2	
mm9_v1_chr2_-_85359091_85359185	1.05299	SOX2.p2	BC120879|4833423E24Rik|228151|RIKEN cDNA 4833423E24 gene	NM_001081664|4833423E24Rik|228151|RIKEN cDNA 4833423E24 gene	AK076485|4833423E24Rik|228151|RIKEN cDNA 4833423E24 gene
mm9_v1_chr12_-_82669460_82669460	1.05243	SOX2.p2	AK014827|Adam21|56622|a disintegrin and metallopeptidase domain 21	NM_020330|Adam21|56622|a disintegrin and metallopeptidase domain 21
mm9_v1_chr5_+_150921233_150921280	1.05187	SOX2.p2	AK157981|Fry|320365|furry homolog (Drosophila)
mm9_v1_chr14_-_44026325_44026343	1.04794	SOX2.p2	BC061060|1700001F09Rik|71826|RIKEN cDNA 1700001F09 gene	AK005587|1700001F09Rik|71826|RIKEN cDNA 1700001F09 gene	NM_027940|1700001F09Rik|71826|RIKEN cDNA 1700001F09 gene
mm9_v1_chr18_+_32056465_32056564	1.04499	SOX2.p2	BC003939|Wdr33|74320|WD repeat domain 33
mm9_v1_chr14_-_125076242_125076348	1.04326	SOX2.p2	BC107003|Fgf14|14169|fibroblast growth factor 14	BC107004|Fgf14|14169|fibroblast growth factor 14	AK079100|Fgf14|14169|fibroblast growth factor 14	NM_207667|Fgf14|14169|fibroblast growth factor 14
mm9_v1_chrX_+_98624989_98625073	1.04325	SOX2.p2	NM_023144|Nono|53610|non-POU-domain-containing, octamer binding protein	AK161152|Nono|53610|non-POU-domain-containing, octamer binding protein	AK169303|Nono|53610|non-POU-domain-containing, octamer binding protein	AK145179|Nono|53610|non-POU-domain-containing, octamer binding protein	AK028338|Nono|53610|non-POU-domain-containing, octamer binding protein	AK004830|Nono|53610|non-POU-domain-containing, octamer binding protein	AK169202|Nono|53610|non-POU-domain-containing, octamer binding protein	AK165855|Nono|53610|non-POU-domain-containing, octamer binding protein	BC005465|Nono|53610|non-POU-domain-containing, octamer binding protein	S64860|Nono|53610|non-POU-domain-containing, octamer binding protein	AK167297|Nono|53610|non-POU-domain-containing, octamer binding protein	AK033201|Nono|53610|non-POU-domain-containing, octamer binding protein	AK013444|Nono|53610|non-POU-domain-containing, octamer binding protein
mm9_v1_chr3_-_10197187_10197261	1.04291	SOX2.p2	AK161314|Fabp9|21884|fatty acid binding protein 9, testis	AK005745|Fabp9|21884|fatty acid binding protein 9, testis	BC048437|Fabp9|21884|fatty acid binding protein 9, testis	NM_011598|Fabp9|21884|fatty acid binding protein 9, testis
mm9_v1_chr6_-_113451922_113451926	1.04264	SOX2.p2	AK031947|Prrt3|210673|proline-rich transmembrane protein 3
mm9_v1_chr7_-_88049882_88049956	1.04166	SOX2.p2	BC028490|Nmb|68039|neuromedin B	AK011929|Nmb|68039|neuromedin B	AK014077|Nmb|68039|neuromedin B	NM_026523|Nmb|68039|neuromedin B
mm9_v1_chr16_-_78576914_78576958	1.04098	SOX2.p2	AK044670|D16Ertd472e|67102|DNA segment, Chr 16, ERATO Doi 472, expressed
mm9_v1_chr15_-_36700634_36700638	1.0405	SOX2.p2	AK003664|Ywhaz|22631|tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide
mm9_v1_chr10_-_24919916_24919967	1.04048	SOX2.p2	AK086696|Akap7|432442|A kinase (PRKA) anchor protein 7	AK085630|Akap7|432442|A kinase (PRKA) anchor protein 7	AK139238|Akap7|432442|A kinase (PRKA) anchor protein 7
mm9_v1_chrX_-_91787353_91787369	1.03935	SOX2.p2	AK135452|Maged1|94275|melanoma antigen, family D, 1	AK146867|Maged1|94275|melanoma antigen, family D, 1	AK146908|Maged1|94275|melanoma antigen, family D, 1	AK049660|Maged1|94275|melanoma antigen, family D, 1	AK087937|Maged1|94275|melanoma antigen, family D, 1
mm9_v1_chr5_-_100407805_100407989	1.03791	SOX2.p2	U11273|Hnrnpd|11991|heterogeneous nuclear ribonucleoprotein D	AK135733|Hnrnpd|11991|heterogeneous nuclear ribonucleoprotein D	AK077409|Hnrnpd|11991|heterogeneous nuclear ribonucleoprotein D	BC049098|Hnrnpd|11991|heterogeneous nuclear ribonucleoprotein D	NM_001077265|Hnrnpd|11991|heterogeneous nuclear ribonucleoprotein D	NM_001077266|Hnrnpd|11991|heterogeneous nuclear ribonucleoprotein D	NM_001077267|Hnrnpd|11991|heterogeneous nuclear ribonucleoprotein D	NM_007516|Hnrnpd|11991|heterogeneous nuclear ribonucleoprotein D
mm9_v1_chr5_-_100588826_100588826	1.03738	SOX2.p2	BC055321|Tmem150c|231503|transmembrane protein 150C	NM_182841|Tmem150c|231503|transmembrane protein 150C
mm9_v1_chr8_-_63433528_63433596	1.03654	SOX2.p2	BC057133|Clcn3|12725|chloride channel 3	NM_173876|Clcn3|12725|chloride channel 3
mm9_v1_chr5_-_72049479_72049546	1.03617	SOX2.p2	AK141571|Gabra4|14397|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 4	AK159299|Gabra4|14397|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 4	AK013727|Gabra4|14397|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 4	NM_010251|Gabra4|14397|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 4
mm9_v1_chr9_+_110034489_110034583	1.03573	SOX2.p2	NM_009211|Smarcc1|20588|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	AK143485|Smarcc1|20588|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	AK144122|Smarcc1|20588|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	AK133922|Smarcc1|20588|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	U85614|Smarcc1|20588|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	AK144631|Smarcc1|20588|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	AK145352|Smarcc1|20588|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	AK042194|Smarcc1|20588|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	BC056375|Smarcc1|20588|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	BC052423|Smarcc1|20588|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	BC053064|Smarcc1|20588|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	BC022173|Smarcc1|20588|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1
mm9_v1_chr11_-_33893151_33893192	1.03471	SOX2.p2	AK048178|Kcnip1|70357|Kv channel-interacting protein 1	AK081845|Kcnip1|70357|Kv channel-interacting protein 1	DQ148494|Kcnip1|70357|Kv channel-interacting protein 1	NM_001190886|Kcnip1|70357|Kv channel-interacting protein 1
mm9_v1_chr7_+_128061297_128061331	1.03414	SOX2.p2	AK012184|Polr3e|26939|polymerase (RNA) III (DNA directed) polypeptide E	AK144721|Polr3e|26939|polymerase (RNA) III (DNA directed) polypeptide E	AK146279|Polr3e|26939|polymerase (RNA) III (DNA directed) polypeptide E	AK159723|Polr3e|26939|polymerase (RNA) III (DNA directed) polypeptide E	BC037637|Polr3e|26939|polymerase (RNA) III (DNA directed) polypeptide E	BC028924|Polr3e|26939|polymerase (RNA) III (DNA directed) polypeptide E
mm9_v1_chr18_-_50728323_50728377	1.02934	SOX2.p2	AK014922|Hdhd1a|67365|haloacid dehalogenase-like hydrolase domain containing 1A	BC048447|Hdhd1a|67365|haloacid dehalogenase-like hydrolase domain containing 1A	NM_026108|Hdhd1a|67365|haloacid dehalogenase-like hydrolase domain containing 1A	AK007231|Hdhd1a|67365|haloacid dehalogenase-like hydrolase domain containing 1A
mm9_v1_chr15_+_38148957_38148957	1.02898	SOX2.p2	BC145758|Odf1|18285|outer dense fiber of sperm tails 1	EU791469|Odf1|18285|outer dense fiber of sperm tails 1	NM_008757|Odf1|18285|outer dense fiber of sperm tails 1	X79446|Odf1|18285|outer dense fiber of sperm tails 1
mm9_v1_chr9_-_100386803_100386891	1.02859	SOX2.p2	BC107263|Il20rb|213208|interleukin 20 receptor beta	BC107264|Il20rb|213208|interleukin 20 receptor beta	BC148190|Il20rb|213208|interleukin 20 receptor beta	NM_001033543|Il20rb|213208|interleukin 20 receptor beta
mm9_v1_chr12_+_109572514_109572610	1.02843	SOX2.p2	BC018307|Cyp46a1|13116|cytochrome P450, family 46, subfamily a, polypeptide 1	AK140740|Cyp46a1|13116|cytochrome P450, family 46, subfamily a, polypeptide 1	AF094479|Cyp46a1|13116|cytochrome P450, family 46, subfamily a, polypeptide 1	NM_010010|Cyp46a1|13116|cytochrome P450, family 46, subfamily a, polypeptide 1
mm9_v1_chr1_-_36614370_36614401	1.0276	SOX2.p2	AK173247|Sema4c|20353|sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C	AK090073|Sema4c|20353|sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C
mm9_v1_chr17_+_47863790_47863799	1.02671	SOX2.p2	AK008886|Pgc|109820|progastricsin (pepsinogen C)	AK008959|Pgc|109820|progastricsin (pepsinogen C)	AK160474|Pgc|109820|progastricsin (pepsinogen C)	NM_025973|Pgc|109820|progastricsin (pepsinogen C)	BC099409|Pgc|109820|progastricsin (pepsinogen C)
mm9_v1_chr3_+_17848443_17848443	1.02597	SOX2.p2	AK005586|Cypt12|75439|cysteine-rich perinuclear theca 12	NM_029289|Cypt12|75439|cysteine-rich perinuclear theca 12
mm9_v1_chr13_+_27149438_27149473	1.02519	SOX2.p2	NM_001163530|Prl|19109|prolactin	NM_011164|Prl|19109|prolactin	AK017547|Prl|19109|prolactin	AK161619|Prl|19109|prolactin	AK077493|Prl|19109|prolactin	AK017520|Prl|19109|prolactin	X04418|Prl|19109|prolactin	AK017521|Prl|19109|prolactin	AK017579|Prl|19109|prolactin	AK017584|Prl|19109|prolactin	AK133645|Prl|19109|prolactin	AK133736|Prl|19109|prolactin	AK133752|Prl|19109|prolactin	AK161553|Prl|19109|prolactin	AK161557|Prl|19109|prolactin	AK161565|Prl|19109|prolactin	AK161594|Prl|19109|prolactin	BC061141|Prl|19109|prolactin	X02892|Prl|19109|prolactin	AK017562|Prl|19109|prolactin
mm9_v1_chr14_-_61665691_61665691	1.02404	SOX2.p2	NM_013869|Tnfrsf19|29820|tumor necrosis factor receptor superfamily, member 19
mm9_v1_chr1_+_136078939_136079071	1.02214	SOX2.p2	NM_007695|Chi3l1|12654|chitinase 3-like 1	AK051475|Chi3l1|12654|chitinase 3-like 1	AK155412|Chi3l1|12654|chitinase 3-like 1	BC003780|Chi3l1|12654|chitinase 3-like 1	BC004734|Chi3l1|12654|chitinase 3-like 1	BC005611|Chi3l1|12654|chitinase 3-like 1
mm9_v1_chr10_+_79611013_79611064	1.02173	SOX2.p2	AK164324|Midn|59090|midnolin	AK164651|Midn|59090|midnolin	AB036882|Midn|59090|midnolin	NM_021565|Midn|59090|midnolin	BC034719|Midn|59090|midnolin
mm9_v1_chr6_-_38075416_38075515	1.02153	SOX2.p2	AK141785|D630045J12Rik|330286|RIKEN cDNA D630045J12 gene
mm9_v1_chr6_+_147995935_147995985	1.02033	SOX2.p2	AK043388|Far2|330450|fatty acyl CoA reductase 2	AK043589|Far2|330450|fatty acyl CoA reductase 2	AK137298|Far2|330450|fatty acyl CoA reductase 2	NM_178797|Far2|330450|fatty acyl CoA reductase 2	BC055759|Far2|330450|fatty acyl CoA reductase 2	AK161201|Far2|330450|fatty acyl CoA reductase 2	AK038584|Far2|330450|fatty acyl CoA reductase 2
mm9_v1_chr7_-_29086780_29086803	1.01724	SOX2.p2	BC052002|Dll3|13389|delta-like 3 (Drosophila)	AB013440|Dll3|13389|delta-like 3 (Drosophila)	AK144282|Dll3|13389|delta-like 3 (Drosophila)	NM_007866|Dll3|13389|delta-like 3 (Drosophila)
mm9_v1_chr4_+_6118247_6118251	1.01612	SOX2.p2	AK028268|Ubxn2b|68053|UBX domain protein 2B	AK018273|Ubxn2b|68053|UBX domain protein 2B	AK032332|Ubxn2b|68053|UBX domain protein 2B	BC076632|Ubxn2b|68053|UBX domain protein 2B	NM_026534|Ubxn2b|68053|UBX domain protein 2B
mm9_v1_chr7_-_54707508_54707537	1.01362	SOX2.p2	BC064040|Mrgpra2a|668727|MAS-related GPR, member A2A	NM_001172588|Mrgpra2a|668727|MAS-related GPR, member A2A	AK156116|Mrgpra2b|235712|MAS-related GPR, member A2B
mm9_v1_chr17_-_46624611_46624627	1.01312	SOX2.p2	NM_001162864|Ttbk1|106763|tau tubulin kinase 1
mm9_v1_chr8_-_89269853_89269958	1.0125	SOX2.p2	BC046317|Siah1a|20437|seven in absentia 1A	NM_009172|Siah1a|20437|seven in absentia 1A
mm9_v1_chr6_-_23600205_23600304	1.0117	SOX2.p2	BC116423|Rnf133|386611|ring finger protein 133	BC116424|Rnf133|386611|ring finger protein 133	AK028082|Rnf133|386611|ring finger protein 133	NM_198251|Rnf133|386611|ring finger protein 133
mm9_v1_chr7_+_30088984_30089023	1.01125	SOX2.p2	BC052348|Dpf1|29861|D4, zinc and double PHD fingers family 1	NM_013874|Dpf1|29861|D4, zinc and double PHD fingers family 1	U48238|Dpf1|29861|D4, zinc and double PHD fingers family 1
mm9_v1_chr18_+_69843588_69843609	1.00977	SOX2.p2	AK017365|Tcf4|21413|transcription factor 4
mm9_v1_chr17_-_56615784_56615852	1.00899	SOX2.p2	D28530|Ptprs|19280|protein tyrosine phosphatase, receptor type, S	D28531|Ptprs|19280|protein tyrosine phosphatase, receptor type, S	AK032604|Ptprs|19280|protein tyrosine phosphatase, receptor type, S	BC052462|Ptprs|19280|protein tyrosine phosphatase, receptor type, S
mm9_v1_chr6_-_49214015_49214054	0.999899	SOX2.p2	AK170599|Tra2a|101214|transformer 2 alpha homolog (Drosophila)	AK076230|Tra2a|101214|transformer 2 alpha homolog (Drosophila)	AK089980|Tra2a|101214|transformer 2 alpha homolog (Drosophila)	AK171708|Tra2a|101214|transformer 2 alpha homolog (Drosophila)	AK005187|Tra2a|101214|transformer 2 alpha homolog (Drosophila)	NM_198102|Tra2a|101214|transformer 2 alpha homolog (Drosophila)	AK148552|Tra2a|101214|transformer 2 alpha homolog (Drosophila)
mm9_v1_chr5_+_31191728_31191729	0.99962	SOX2.p2	AK034894|Agbl5|231093|ATP/GTP binding protein-like 5
mm9_v1_chr14_-_56143799_56143817	0.999458	SOX2.p2	AK044316|Nrl|18185|neural retina leucine zipper gene	BC031440|Nrl|18185|neural retina leucine zipper gene	NM_001136074|Nrl|18185|neural retina leucine zipper gene	AK044244|Nrl|18185|neural retina leucine zipper gene
mm9_v1_chr14_+_26942094_26942094	0.999398	SOX2.p2	NM_001177538|Gm10394|100039227|predicted gene 10394	NM_001177539|Gm10391|100039293|predicted gene 10391
mm9_v1_chr3_+_115711207_115711327	0.99838	SOX2.p2	NM_001163514|Extl2|58193|exostoses (multiple)-like 2	AF200973|Extl2|58193|exostoses (multiple)-like 2	AK019370|Extl2|58193|exostoses (multiple)-like 2
mm9_v1_chr2_+_29925959_29926154	0.997546	SOX2.p2	BC012508|Set|56086|SET nuclear oncogene
mm9_v1_chr14_-_57190668_57190714	0.997217	SOX2.p2	BC092399|Cenpj|219103|centromere protein J	AK077045|Cenpj|219103|centromere protein J	NM_001014996|Cenpj|219103|centromere protein J
mm9_v1_chr8_+_97605137_97605189	0.997129	SOX2.p2	AK010364|Katnb1|74187|katanin p80 (WD40-containing) subunit B 1	AK037858|Katnb1|74187|katanin p80 (WD40-containing) subunit B 1	AK034103|Katnb1|74187|katanin p80 (WD40-containing) subunit B 1	AK136322|Katnb1|74187|katanin p80 (WD40-containing) subunit B 1	AK031630|Katnb1|74187|katanin p80 (WD40-containing) subunit B 1	AK049345|Katnb1|74187|katanin p80 (WD40-containing) subunit B 1	AK087973|Katnb1|74187|katanin p80 (WD40-containing) subunit B 1	BC045200|Katnb1|74187|katanin p80 (WD40-containing) subunit B 1
mm9_v1_chr15_-_101403190_101403258	0.996214	SOX2.p2	AF343088|Krt75|109052|keratin 75
mm9_v1_chr1_-_192988695_192988695	0.995518	SOX2.p2	AK133412|Fam71a|619288|family with sequence similarity 71, member A	NM_001109759|Fam71a|619288|family with sequence similarity 71, member A
mm9_v1_chr10_+_98478207_98478246	0.993309	SOX2.p2	BC025199|Atp2b1|67972|ATPase, Ca++ transporting, plasma membrane 1
mm9_v1_chr11_+_59953583_59953674	0.992938	SOX2.p2	NM_001037764|Rai1|19377|retinoic acid induced 1	AY548172|Rai1|19377|retinoic acid induced 1	D29801|Rai1|19377|retinoic acid induced 1
mm9_v1_chr16_+_90831052_90831391	0.988195	SOX2.p2	AK037486|4931408A02Rik|70967|RIKEN cDNA 4931408A02 gene	BC132305|4931408A02Rik|70967|RIKEN cDNA 4931408A02 gene	BC144751|4931408A02Rik|70967|RIKEN cDNA 4931408A02 gene	BC157969|4931408A02Rik|70967|RIKEN cDNA 4931408A02 gene	BC100350|4931408A02Rik|70967|RIKEN cDNA 4931408A02 gene	NM_027627|4931408A02Rik|70967|RIKEN cDNA 4931408A02 gene	AF358257|4931408A02Rik|70967|RIKEN cDNA 4931408A02 gene
mm9_v1_chr1_-_13117243_13117243	0.986982	SOX2.p2	AK134292|Prdm14|383491|PR domain containing 14	NM_001081209|Prdm14|383491|PR domain containing 14
mm9_v1_chr5_-_83783923_83784219	0.98533	SOX2.p2	AK052302|Tecrl|243078|trans-2,3-enoyl-CoA reductase-like	AK052378|Tecrl|243078|trans-2,3-enoyl-CoA reductase-like	AK052276|Tecrl|243078|trans-2,3-enoyl-CoA reductase-like	BC107366|Tecrl|243078|trans-2,3-enoyl-CoA reductase-like	BC107367|Tecrl|243078|trans-2,3-enoyl-CoA reductase-like	AF548365|Tecrl|243078|trans-2,3-enoyl-CoA reductase-like	AK052284|Tecrl|243078|trans-2,3-enoyl-CoA reductase-like	NM_153801|Tecrl|243078|trans-2,3-enoyl-CoA reductase-like
mm9_v1_chr6_+_47404312_47404467	0.985118	SOX2.p2	BC029260|Cul1|26965|cullin 1	NM_012042|Cul1|26965|cullin 1	AK147004|Cul1|26965|cullin 1	AK165978|Cul1|26965|cullin 1	AK040053|Cul1|26965|cullin 1	AF176910|Cul1|26965|cullin 1	AF136441|Cul1|26965|cullin 1
mm9_v1_chr15_+_97942484_97942592	0.982923	SOX2.p2	D21868|Pfkm|18642|phosphofructokinase, muscle	NM_021514|Pfkm|18642|phosphofructokinase, muscle	BC005526|Pfkm|18642|phosphofructokinase, muscle	AF249894|Pfkm|18642|phosphofructokinase, muscle	D21865|Pfkm|18642|phosphofructokinase, muscle
mm9_v1_chr8_+_127316918_127316991	0.981308	SOX2.p2	AK051455|Trim67|330863|tripartite motif-containing 67	NM_198632|Trim67|330863|tripartite motif-containing 67	BC094596|Trim67|330863|tripartite motif-containing 67
mm9_v1_chr8_-_44784840_44784846	0.981096	SOX2.p2	BC132102|Adam34|252866|a disintegrin and metallopeptidase domain 34	BC132292|Adam34|252866|a disintegrin and metallopeptidase domain 34	BC141203|Adam34|252866|a disintegrin and metallopeptidase domain 34	BC141204|Adam34|252866|a disintegrin and metallopeptidase domain 34	NM_001079931|Gm5347|384814|predicted gene 5347	AK029590|Adam34|252866|a disintegrin and metallopeptidase domain 34
mm9_v1_chr17_-_35971652_35971809	0.98013	SOX2.p2	AK080778|Tubb5|22154|tubulin, beta 5	AK088137|Tubb5|22154|tubulin, beta 5
mm9_v1_chr4_+_88481428_88481428	0.980029	SOX2.p2	BC120910|Ifna5|15968|interferon alpha 5	BC120911|Ifna5|15968|interferon alpha 5	NM_010505|Ifna5|15968|interferon alpha 5
mm9_v1_chr15_-_44259852_44259852	0.979087	SOX2.p2	AF521132|Nudcd1|67429|NudC domain containing 1	AK014996|Nudcd1|67429|NudC domain containing 1	NM_001113554|Nudcd1|67429|NudC domain containing 1	NM_026149|Nudcd1|67429|NudC domain containing 1
mm9_v1_chr12_-_101397818_101397862	0.978267	SOX2.p2	AK036688|BC002230|217827|cDNA sequence BC002230	AK032800|BC002230|217827|cDNA sequence BC002230	NM_183155|BC002230|217827|cDNA sequence BC002230
mm9_v1_chr14_-_66211842_66211926	0.977692	SOX2.p2	NM_028811|Elp3|74195|elongation protein 3 homolog (S. cerevisiae)	AK012072|Elp3|74195|elongation protein 3 homolog (S. cerevisiae)	AK150058|Elp3|74195|elongation protein 3 homolog (S. cerevisiae)	BC057453|Elp3|74195|elongation protein 3 homolog (S. cerevisiae)	AK088457|Elp3|74195|elongation protein 3 homolog (S. cerevisiae)
mm9_v1_chr17_-_37727295_37727325	0.97743	SOX2.p2	NM_146287|Olfr114|258284|olfactory receptor 114	BC132209|Olfr114|258284|olfactory receptor 114	BC132573|Olfr114|258284|olfactory receptor 114
mm9_v1_chr1_-_33871349_33871443	0.97528	SOX2.p2	AK015797|Zfp451|98403|zinc finger protein 451
mm9_v1_chr13_+_43711165_43711165	0.974926	SOX2.p2	NM_183204|Rnf182|328234|ring finger protein 182
mm9_v1_chr4_-_45024999_45025283	0.97368	SOX2.p2	AK160003|Zbtb5|230119|zinc finger and BTB domain containing 5	BC054551|Zbtb5|230119|zinc finger and BTB domain containing 5	AK031172|Zbtb5|230119|zinc finger and BTB domain containing 5	AY635051|Zbtb5|230119|zinc finger and BTB domain containing 5	BC057545|Zbtb5|230119|zinc finger and BTB domain containing 5	NM_001163283|Zbtb5|230119|zinc finger and BTB domain containing 5	NM_001163284|Zbtb5|230119|zinc finger and BTB domain containing 5	NM_173399|Zbtb5|230119|zinc finger and BTB domain containing 5
mm9_v1_chr4_-_153534748_153534817	0.973643	SOX2.p2	BC019544|Tprgl|67808|transformation related protein 63 regulated like	AK004777|Tprgl|67808|transformation related protein 63 regulated like	AK155413|Tprgl|67808|transformation related protein 63 regulated like	NM_026388|Tprgl|67808|transformation related protein 63 regulated like
mm9_v1_chr2_+_109739389_109739489	0.972052	SOX2.p2	AK078903|Lin7c|22343|lin-7 homolog C (C. elegans)	AK049807|Lin7c|22343|lin-7 homolog C (C. elegans)
mm9_v1_chr19_-_40588255_40588287	0.969615	SOX2.p2	AK166943|Sorbs1|20411|sorbin and SH3 domain containing 1
mm9_v1_chr14_+_31948038_31948038	0.969483	SOX2.p2	BC011230|Nt5dc2|70021|5'-nucleotidase domain containing 2	NM_027289|Nt5dc2|70021|5'-nucleotidase domain containing 2
mm9_v1_chr2_+_138104219_138104260	0.96935	SOX2.p2	AB093275|Btbd3|228662|BTB (POZ) domain containing 3	NM_145534|Btbd3|228662|BTB (POZ) domain containing 3	BC018174|Btbd3|228662|BTB (POZ) domain containing 3
mm9_v1_chr8_-_122346577_122346634	0.967893	SOX2.p2	
mm9_v1_chr12_-_82881995_82882183	0.964962	SOX2.p2	AK053843|Map3k9|338372|mitogen-activated protein kinase kinase kinase 9	AK155677|Map3k9|338372|mitogen-activated protein kinase kinase kinase 9	NM_001174107|Map3k9|338372|mitogen-activated protein kinase kinase kinase 9	NM_177395|Map3k9|338372|mitogen-activated protein kinase kinase kinase 9
mm9_v1_chr3_+_103664214_103664288	0.963697	SOX2.p2	M90388|Ptpn22|19260|protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	NM_008979|Ptpn22|19260|protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	AK169559|Ptpn22|19260|protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	BC055377|Ptpn22|19260|protein tyrosine phosphatase, non-receptor type 22 (lymphoid)
mm9_v1_chr10_-_17954752_17954810	0.961686	SOX2.p2	AK028075|Ccdc28a|215814|coiled-coil domain containing 28A	BC013553|Ccdc28a|215814|coiled-coil domain containing 28A	BC027759|Ccdc28a|215814|coiled-coil domain containing 28A	AK148447|Ccdc28a|215814|coiled-coil domain containing 28A	NM_144820|Ccdc28a|215814|coiled-coil domain containing 28A
mm9_v1_chr8_+_91220965_91221031	0.958553	SOX2.p2	AK147426|Cyld|74256|cylindromatosis (turban tumor syndrome)	BC042438|Cyld|74256|cylindromatosis (turban tumor syndrome)	AK039054|Cyld|74256|cylindromatosis (turban tumor syndrome)
mm9_v1_chr3_+_103718466_103718512	0.957996	SOX2.p2	AK138603|Rsbn1|229675|rosbin, round spermatid basic protein 1	BC069993|Rsbn1|229675|rosbin, round spermatid basic protein 1	AK122577|Rsbn1|229675|rosbin, round spermatid basic protein 1	BC094667|Rsbn1|229675|rosbin, round spermatid basic protein 1
mm9_v1_chr10_+_18127443_18127504	0.957405	SOX2.p2	AK041760|Nhsl1|215819|NHS-like 1	AK017530|Nhsl1|215819|NHS-like 1	NM_173390|Nhsl1|215819|NHS-like 1	AK038892|Nhsl1|215819|NHS-like 1
mm9_v1_chr17_+_32185229_32185229	0.957255	SOX2.p2	AK129078|Rrp1b|72462|ribosomal RNA processing 1 homolog B (S. cerevisiae)	NM_001163734|Rrp1b|72462|ribosomal RNA processing 1 homolog B (S. cerevisiae)
mm9_v1_chr7_-_54744926_54744955	0.956196	SOX2.p2	BC064040|Mrgpra2a|668727|MAS-related GPR, member A2A	NM_153101|Mrgpra2b|235712|MAS-related GPR, member A2B	AK156116|Mrgpra2b|235712|MAS-related GPR, member A2B
mm9_v1_chr7_-_108080671_108080707	0.956147	SOX2.p2	NM_001081116|Arhgef17|207212|Rho guanine nucleotide exchange factor (GEF) 17
mm9_v1_chr16_-_88826362_88826389	0.955455	SOX2.p2	BC104263|Krtap14|23927|keratin associated protein 14	BC104262|Krtap14|23927|keratin associated protein 14	AF003691|Krtap14|23927|keratin associated protein 14	D85925|Krtap14|23927|keratin associated protein 14	NM_013707|Krtap14|23927|keratin associated protein 14
mm9_v1_chr5_-_134713853_134713859	0.955387	SOX2.p2	
mm9_v1_chr13_+_88961161_88961261	0.954643	SOX2.p2	AK045839|Edil3|13612|EGF-like repeats and discoidin I-like domains 3	AK084810|Edil3|13612|EGF-like repeats and discoidin I-like domains 3	BC056386|Edil3|13612|EGF-like repeats and discoidin I-like domains 3	AK044978|Edil3|13612|EGF-like repeats and discoidin I-like domains 3	AK084215|Edil3|13612|EGF-like repeats and discoidin I-like domains 3	AK081003|Edil3|13612|EGF-like repeats and discoidin I-like domains 3	AK045088|Edil3|13612|EGF-like repeats and discoidin I-like domains 3
mm9_v1_chr12_-_32893074_32893513	0.954266	SOX2.p2	BC051246|Pik3cg|30955|phosphoinositide-3-kinase, catalytic, gamma polypeptide	AK137620|Pik3cg|30955|phosphoinositide-3-kinase, catalytic, gamma polypeptide	NM_001146201|Pik3cg|30955|phosphoinositide-3-kinase, catalytic, gamma polypeptide	AJ249280|Pik3cg|30955|phosphoinositide-3-kinase, catalytic, gamma polypeptide	NM_020272|Pik3cg|30955|phosphoinositide-3-kinase, catalytic, gamma polypeptide	AK137470|Pik3cg|30955|phosphoinositide-3-kinase, catalytic, gamma polypeptide	AK040543|Pik3cg|30955|phosphoinositide-3-kinase, catalytic, gamma polypeptide	AK132553|Pik3cg|30955|phosphoinositide-3-kinase, catalytic, gamma polypeptide	NM_001146200|Pik3cg|30955|phosphoinositide-3-kinase, catalytic, gamma polypeptide
mm9_v1_chr12_-_97285329_97285431	0.949257	SOX2.p2	DQ309695|1700019M22Rik|69423|RIKEN cDNA 1700019M22 gene	AK006132|1700019M22Rik|69423|RIKEN cDNA 1700019M22 gene	BC050791|1700019M22Rik|69423|RIKEN cDNA 1700019M22 gene	NM_027076|1700019M22Rik|69423|RIKEN cDNA 1700019M22 gene
mm9_v1_chrX_-_130696466_130696502	0.947624	SOX2.p2	AY534249|Xkrx|331524|X Kell blood group precursor related X linked	NM_183319|Xkrx|331524|X Kell blood group precursor related X linked	BC150896|Xkrx|331524|X Kell blood group precursor related X linked	BC150897|Xkrx|331524|X Kell blood group precursor related X linked
mm9_v1_chr3_-_50247306_50247534	0.946269	SOX2.p2	AK162233|Slc7a11|26570|solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	AK170568|Slc7a11|26570|solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	BC141402|Slc7a11|26570|solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	BC141408|Slc7a11|26570|solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	AB022345|Slc7a11|26570|solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	AY766236|Slc7a11|26570|solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	AY766237|Slc7a11|26570|solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	AK165599|Slc7a11|26570|solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	AK089202|Slc7a11|26570|solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	AK037742|Slc7a11|26570|solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	AK076322|Slc7a11|26570|solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	AK163168|Slc7a11|26570|solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	AK171252|Slc7a11|26570|solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	AK171327|Slc7a11|26570|solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	AK089283|Slc7a11|26570|solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	AK171192|Slc7a11|26570|solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	AK037490|Slc7a11|26570|solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	NM_011990|Slc7a11|26570|solute carrier family 7 (cationic amino acid transporter, y+ system), member 11
mm9_v1_chr18_-_70301202_70301243	0.944445	SOX2.p2	AK045312|Rab27b|80718|RAB27b, member RAS oncogene family	AK086987|Rab27b|80718|RAB27b, member RAS oncogene family	AK049854|Rab27b|80718|RAB27b, member RAS oncogene family	NM_001082553|Rab27b|80718|RAB27b, member RAS oncogene family
mm9_v1_chr6_-_86683191_86683319	0.943944	SOX2.p2	AF186095|Gmcl1|23885|germ cell-less homolog 1 (Drosophila)	AK132788|Gmcl1|23885|germ cell-less homolog 1 (Drosophila)	AF282322|Gmcl1|23885|germ cell-less homolog 1 (Drosophila)	AF163665|Gmcl1|23885|germ cell-less homolog 1 (Drosophila)
mm9_v1_chr2_-_119613164_119613274	0.94373	SOX2.p2	BC117973|Rpap1|68925|RNA polymerase II associated protein 1	BC117974|Rpap1|68925|RNA polymerase II associated protein 1	AK190910|Rpap1|68925|RNA polymerase II associated protein 1	AK122505|Rpap1|68925|RNA polymerase II associated protein 1	BC088899|Rpap1|68925|RNA polymerase II associated protein 1	AK171233|Rpap1|68925|RNA polymerase II associated protein 1	AK042776|Rpap1|68925|RNA polymerase II associated protein 1	AK154007|Rpap1|68925|RNA polymerase II associated protein 1	AK161487|Rpap1|68925|RNA polymerase II associated protein 1	AK164658|Rpap1|68925|RNA polymerase II associated protein 1	AK166232|Rpap1|68925|RNA polymerase II associated protein 1	AK167589|Rpap1|68925|RNA polymerase II associated protein 1	NM_001163701|Rpap1|68925|RNA polymerase II associated protein 1	NM_177294|Rpap1|68925|RNA polymerase II associated protein 1
mm9_v1_chr9_-_38455101_38455106	0.942853	SOX2.p2	BC111098|Olfr915|258781|olfactory receptor 915	NM_146785|Olfr915|258781|olfactory receptor 915
mm9_v1_chr7_-_138473006_138473012	0.939796	SOX2.p2	AK005730|1700007K09Rik|69318|RIKEN cDNA 1700007K09 gene	BC048596|1700007K09Rik|69318|RIKEN cDNA 1700007K09 gene	NM_027037|1700007K09Rik|69318|RIKEN cDNA 1700007K09 gene
mm9_v1_chr4_-_83919835_83919836	0.939683	SOX2.p2	AK018429|Bnc2|242509|basonuclin 2
mm9_v1_chr16_-_10790997_10791006	0.939309	SOX2.p2	BC049598|Prm3|19120|protamine 3	BC061127|Prm3|19120|protamine 3	AK132894|Prm3|19120|protamine 3	NM_013638|Prm3|19120|protamine 3
mm9_v1_chr18_+_37874471_37874595	0.939166	SOX2.p2	AK034910|Pcdhga7|93715|protocadherin gamma subfamily A, 7	BC077712|Pcdhga7|93715|protocadherin gamma subfamily A, 7	NM_033590|Pcdhga7|93715|protocadherin gamma subfamily A, 7	AY013801|Pcdhga7|93715|protocadherin gamma subfamily A, 7
mm9_v1_chr5_+_31191224_31191333	0.937319	SOX2.p2	AK029676|Agbl5|231093|ATP/GTP binding protein-like 5	NM_174849|Agbl5|231093|ATP/GTP binding protein-like 5	AK044195|Agbl5|231093|ATP/GTP binding protein-like 5	AK083656|Agbl5|231093|ATP/GTP binding protein-like 5
mm9_v1_chr11_-_31571811_31571918	0.936368	SOX2.p2	NM_001024919|Bod1|69556|biorientation of chromosomes in cell division 1	BC116435|Bod1|69556|biorientation of chromosomes in cell division 1	BC116436|Bod1|69556|biorientation of chromosomes in cell division 1	BC128508|Bod1|69556|biorientation of chromosomes in cell division 1	BC128509|Bod1|69556|biorientation of chromosomes in cell division 1
mm9_v1_chr7_+_13983480_13983656	0.935824	SOX2.p2	BC018253|Cabp5|29865|calcium binding protein 5	AK044544|Cabp5|29865|calcium binding protein 5	NM_013877|Cabp5|29865|calcium binding protein 5	AF169161|Cabp5|29865|calcium binding protein 5	AK087416|Cabp5|29865|calcium binding protein 5	AB079605|Cabp5|29865|calcium binding protein 5
mm9_v1_chr17_-_5418711_5418766	0.935521	SOX2.p2	AK077089|Ldhal6b|106557|lactate dehydrogenase A-like 6B	BC061193|Ldhal6b|106557|lactate dehydrogenase A-like 6B	AY280363|Ldhal6b|106557|lactate dehydrogenase A-like 6B	NM_175349|Ldhal6b|106557|lactate dehydrogenase A-like 6B
mm9_v1_chr4_+_136166351_136166390	0.933361	SOX2.p2	AK016074|4930549C01Rik|67663|RIKEN cDNA 4930549C01 gene	NM_026300|4930549C01Rik|67663|RIKEN cDNA 4930549C01 gene	BC048442|4930549C01Rik|67663|RIKEN cDNA 4930549C01 gene	AK015053|4930549C01Rik|67663|RIKEN cDNA 4930549C01 gene
mm9_v1_chr3_-_88893885_88893966	0.932505	SOX2.p2	AK170210|Rusc1|72296|RUN and SH3 domain containing 1	NM_001083808|Rusc1|72296|RUN and SH3 domain containing 1	AK170012|Rusc1|72296|RUN and SH3 domain containing 1
mm9_v1_chr15_+_57817333_57817464	0.932471	SOX2.p2	NM_173862|Fam83a|239463|family with sequence similarity 83, member A	BC030396|Fam83a|239463|family with sequence similarity 83, member A
mm9_v1_chr9_-_44215391_44215460	0.93215	SOX2.p2	AK032168|Trappc4|60409|trafficking protein particle complex 4	AK005276|Trappc4|60409|trafficking protein particle complex 4
mm9_v1_chr1_+_166237784_166237874	0.931163	SOX2.p2	AK144915|Nme7|171567|non-metastatic cells 7, protein expressed in (nucleoside-diphosphate kinase)	NM_138314|Nme7|171567|non-metastatic cells 7, protein expressed in (nucleoside-diphosphate kinase)	NM_178071|Nme7|171567|non-metastatic cells 7, protein expressed in (nucleoside-diphosphate kinase)	AK043515|Nme7|171567|non-metastatic cells 7, protein expressed in (nucleoside-diphosphate kinase)	AK085222|Nme7|171567|non-metastatic cells 7, protein expressed in (nucleoside-diphosphate kinase)	AK164652|Nme7|171567|non-metastatic cells 7, protein expressed in (nucleoside-diphosphate kinase)	AK044962|Nme7|171567|non-metastatic cells 7, protein expressed in (nucleoside-diphosphate kinase)	BC038021|Nme7|171567|non-metastatic cells 7, protein expressed in (nucleoside-diphosphate kinase)	BC049225|Nme7|171567|non-metastatic cells 7, protein expressed in (nucleoside-diphosphate kinase)
mm9_v1_chr10_-_116333934_116333934	0.930884	SOX2.p2	AK144383|Gm239|237558|predicted gene 239	AK144411|Gm239|237558|predicted gene 239	NM_001033333|Gm239|237558|predicted gene 239
mm9_v1_chr13_-_41165827_41165833	0.929746	SOX2.p2	X66983|Mak|17152|male germ cell-associated kinase	NM_008547|Mak|17152|male germ cell-associated kinase
mm9_v1_chr6_-_132314127_132314152	0.929463	SOX2.p2	M11897|Gm4736|114600|predicted gene 4736	X63004|Prpmp5|381832|proline-rich protein MP5	BC171936|Gm8882|667929|predicted gene 8882	BC171935|Gm8882|667929|predicted gene 8882	NM_001177588|Gm8882|667929|predicted gene 8882	NM_053251|Gm4736|114600|predicted gene 4736
mm9_v1_chr6_+_50150160_50150179	0.929212	SOX2.p2	AK047380|Mpp6|56524|membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)
mm9_v1_chr17_+_72119030_72119041	0.928929	SOX2.p2	AK029962|Clip4|78785|CAP-GLY domain containing linker protein family, member 4	NM_175378|Clip4|78785|CAP-GLY domain containing linker protein family, member 4	AK018895|Clip4|78785|CAP-GLY domain containing linker protein family, member 4	AK075758|Clip4|78785|CAP-GLY domain containing linker protein family, member 4	AK161301|Clip4|78785|CAP-GLY domain containing linker protein family, member 4
mm9_v1_chr11_-_58615400_58615517	0.928835	SOX2.p2	FJ468008|Fam183b|75429|family with sequence similarity 183, member B	BC094630|Fam183b|75429|family with sequence similarity 183, member B	BC061254|Fam183b|75429|family with sequence similarity 183, member B	BC048748|Fam183b|75429|family with sequence similarity 183, member B	AK157972|Fam183b|75429|family with sequence similarity 183, member B	AK013920|Fam183b|75429|family with sequence similarity 183, member B	NM_001162878|Fam183b|75429|family with sequence similarity 183, member B	NM_029283|Fam183b|75429|family with sequence similarity 183, member B	BC126964|Fam183b|75429|family with sequence similarity 183, member B	BC117741|Fam183b|75429|family with sequence similarity 183, member B
mm9_v1_chr5_-_73033990_73033990	0.927978	SOX2.p2	NM_007723|Cnga1|12788|cyclic nucleotide gated channel alpha 1
mm9_v1_chr4_+_32504409_32504501	0.92725	SOX2.p2	NM_001109661|Bach2|12014|BTB and CNC homology 2	BC131642|Bach2|12014|BTB and CNC homology 2
mm9_v1_chr11_-_20612281_20612323	0.926979	SOX2.p2	AK150458|Aftph|216549|aftiphilin	AK152308|Aftph|216549|aftiphilin	AK152487|Aftph|216549|aftiphilin	AK161532|Aftph|216549|aftiphilin
mm9_v1_chr1_-_55084217_55084256	0.925046	SOX2.p2	BC060125|Sf3b1|81898|splicing factor 3b, subunit 1	BC003419|Sf3b1|81898|splicing factor 3b, subunit 1	BC028959|Sf3b1|81898|splicing factor 3b, subunit 1	BC058563|Sf3b1|81898|splicing factor 3b, subunit 1	AK146989|Sf3b1|81898|splicing factor 3b, subunit 1	AK140982|Sf3b1|81898|splicing factor 3b, subunit 1	AK171454|Sf3b1|81898|splicing factor 3b, subunit 1	BC080754|Sf3b1|81898|splicing factor 3b, subunit 1
mm9_v1_chr1_-_55283618_55283625	0.924938	SOX2.p2	AK012229|Rftn2|74013|raftlin family member 2	AK031158|Rftn2|74013|raftlin family member 2	BC038341|Rftn2|74013|raftlin family member 2	NM_028713|Rftn2|74013|raftlin family member 2
mm9_v1_chr8_+_108939247_108939300	0.924932	SOX2.p2	BC046230|Zfp90|22751|zinc finger protein 90	AK147423|Zfp90|22751|zinc finger protein 90	BC046298|Zfp90|22751|zinc finger protein 90	AK050519|Zfp90|22751|zinc finger protein 90	X79828|Zfp90|22751|zinc finger protein 90
mm9_v1_chr8_-_119098475_119098517	0.923419	SOX2.p2	
mm9_v1_chr5_+_25021884_25021967	0.923182	SOX2.p2	AK133375|Cct8l1|242891|chaperonin containing TCP1, subunit 8 (theta)-like 1	NM_198621|Cct8l1|242891|chaperonin containing TCP1, subunit 8 (theta)-like 1	BC050797|Cct8l1|242891|chaperonin containing TCP1, subunit 8 (theta)-like 1
mm9_v1_chr5_-_23122181_23122418	0.923024	SOX2.p2	AB006036|Srpk2|20817|serine/arginine-rich protein specific kinase 2	BC020178|Srpk2|20817|serine/arginine-rich protein specific kinase 2	AK136861|Srpk2|20817|serine/arginine-rich protein specific kinase 2	AK169580|Srpk2|20817|serine/arginine-rich protein specific kinase 2	NM_009274|Srpk2|20817|serine/arginine-rich protein specific kinase 2
mm9_v1_chr7_-_117509277_117509385	0.921873	SOX2.p2	BC015069|Sbf2|319934|SET binding factor 2
mm9_v1_chr14_-_122138082_122138150	0.921787	SOX2.p2	BC158050|Dock9|105445|dedicator of cytokinesis 9	AK122431|Dock9|105445|dedicator of cytokinesis 9	NM_001128307|Dock9|105445|dedicator of cytokinesis 9	NM_001128308|Dock9|105445|dedicator of cytokinesis 9
mm9_v1_chr4_-_151692589_151692733	0.921006	SOX2.p2	BC023223|Rnf207|433809|ring finger protein 207	BC141256|Rnf207|433809|ring finger protein 207	BC141257|Rnf207|433809|ring finger protein 207	AK042379|Rnf207|433809|ring finger protein 207	BC022631|Rnf207|433809|ring finger protein 207	AK052224|Rnf207|433809|ring finger protein 207	NM_001033489|Rnf207|433809|ring finger protein 207
mm9_v1_chr6_+_120314442_120314515	0.920926	SOX2.p2	BC080691|Kdm5a|214899|lysine (K)-specific demethylase 5A	AK133589|Kdm5a|214899|lysine (K)-specific demethylase 5A	AK154025|Kdm5a|214899|lysine (K)-specific demethylase 5A	BC010717|Kdm5a|214899|lysine (K)-specific demethylase 5A
mm9_v1_chr11_+_58144207_58144291	0.920669	SOX2.p2	AK156171|Sh3bp5l|79566|SH3 binding domain protein 5 like	AK159202|Sh3bp5l|79566|SH3 binding domain protein 5 like	AK172333|Sh3bp5l|79566|SH3 binding domain protein 5 like	NM_001161338|Sh3bp5l|79566|SH3 binding domain protein 5 like	NM_024480|Sh3bp5l|79566|SH3 binding domain protein 5 like	BC094418|Sh3bp5l|79566|SH3 binding domain protein 5 like	AK166491|Sh3bp5l|79566|SH3 binding domain protein 5 like	AK144928|Sh3bp5l|79566|SH3 binding domain protein 5 like	AK086088|Sh3bp5l|79566|SH3 binding domain protein 5 like	AK150129|Sh3bp5l|79566|SH3 binding domain protein 5 like	AK167203|Sh3bp5l|79566|SH3 binding domain protein 5 like
mm9_v1_chrX_-_110299092_110299131	0.920255	SOX2.p2	BC047461|Chm|12662|choroidermia	AK035956|Chm|12662|choroidermia	AK141830|Chm|12662|choroidermia	AF218084|Chm|12662|choroidermia	NM_018818|Chm|12662|choroidermia	AK021238|Chm|12662|choroidermia
mm9_v1_chr11_-_97023157_97023169	0.917331	SOX2.p2	BC004096|Kpnb1|16211|karyopherin (importin) beta 1
mm9_v1_chrX_-_24728580_24728580	0.916327	SOX2.p2	BC087929|Gm5169|382277|predicted gene 5169	NM_001040669|Gm5169|382277|predicted gene 5169
mm9_v1_chrX_-_26129763_26129763	0.916325	SOX2.p2	BC048742|Gm14525|100039120|predicted gene 14525	NM_001162364|Gm14525|100039120|predicted gene 14525
mm9_v1_chr15_-_74466690_74466747	0.91569	SOX2.p2	AK006048|1700016M24Rik|69439|RIKEN cDNA 1700016M24 gene	NM_001177437|1700016M24Rik|69439|RIKEN cDNA 1700016M24 gene
mm9_v1_chr17_+_13109289_13109379	0.914268	SOX2.p2	AK151445|Tcp1|21454|t-complex protein 1	AK153430|Tcp1|21454|t-complex protein 1	AK166966|Tcp1|21454|t-complex protein 1	AK150666|Tcp1|21454|t-complex protein 1	AK150744|Tcp1|21454|t-complex protein 1	AK151903|Tcp1|21454|t-complex protein 1	AK152633|Tcp1|21454|t-complex protein 1	AK149611|Tcp1|21454|t-complex protein 1	AK151068|Tcp1|21454|t-complex protein 1	AK165665|Tcp1|21454|t-complex protein 1	NM_013686|Tcp1|21454|t-complex protein 1	AK149755|Tcp1|21454|t-complex protein 1	AK152759|Tcp1|21454|t-complex protein 1	AK153037|Tcp1|21454|t-complex protein 1	AK166828|Tcp1|21454|t-complex protein 1	AK167529|Tcp1|21454|t-complex protein 1	AK152641|Tcp1|21454|t-complex protein 1	BC003809|Tcp1|21454|t-complex protein 1	M12899|Tcp1|21454|t-complex protein 1	D90344|Tcp1|21454|t-complex protein 1
mm9_v1_chr18_+_65047408_65047414	0.912497	SOX2.p2	NM_001114386|Nedd4l|83814|neural precursor cell expressed, developmentally down-regulated gene 4-like
mm9_v1_chr12_+_36652206_36652279	0.912033	SOX2.p2	BC023499|Agr3|403205|anterior gradient homolog 3 (Xenopus laevis)	NM_207531|Agr3|403205|anterior gradient homolog 3 (Xenopus laevis)	AK053177|Agr3|403205|anterior gradient homolog 3 (Xenopus laevis)
mm9_v1_chr16_-_36131169_36131274	0.91065	SOX2.p2	BC139156|Csta|209294|cystatin A	BC139157|Csta|209294|cystatin A	AK137702|Csta|209294|cystatin A	NM_001033239|Csta|209294|cystatin A
mm9_v1_chr7_-_31319977_31320096	0.90973	SOX2.p2	BC065166|Arhgap33|233071|Rho GTPase activating protein 33	BC065086|Arhgap33|233071|Rho GTPase activating protein 33	NM_178252|Arhgap33|233071|Rho GTPase activating protein 33	BC066047|Arhgap33|233071|Rho GTPase activating protein 33	AK142180|Arhgap33|233071|Rho GTPase activating protein 33
mm9_v1_chr14_+_79915429_79915530	0.90816	SOX2.p2	AK132456|Elf1|13709|E74-like factor 1	U19617|Elf1|13709|E74-like factor 1	AK156098|Elf1|13709|E74-like factor 1	BC037743|Elf1|13709|E74-like factor 1	BC027532|Elf1|13709|E74-like factor 1	BC053914|Elf1|13709|E74-like factor 1
mm9_v1_chr15_+_102807462_102807462	0.907274	SOX2.p2	BC050838|Hoxc9|15427|homeobox C9	NM_008272|Hoxc9|15427|homeobox C9
mm9_v1_chr7_-_31524374_31524374	0.907179	SOX2.p2	NM_008085|Gapdhs|14447|glyceraldehyde-3-phosphate dehydrogenase, spermatogenic
mm9_v1_chr7_-_29100168_29100268	0.907013	SOX2.p2	AK192346|Supt5h|20924|suppressor of Ty 5 homolog (S. cerevisiae)	AK214897|Supt5h|20924|suppressor of Ty 5 homolog (S. cerevisiae)
mm9_v1_chr15_-_8660393_8660418	0.904892	SOX2.p2	BC028638|Slc1a3|20512|solute carrier family 1 (glial high affinity glutamate transporter), member 3	BC066154|Slc1a3|20512|solute carrier family 1 (glial high affinity glutamate transporter), member 3	AK045716|Slc1a3|20512|solute carrier family 1 (glial high affinity glutamate transporter), member 3
mm9_v1_chr13_+_94074449_94074449	0.903833	SOX2.p2	AF093257|Homer1|26556|homer homolog 1 (Drosophila)	NM_011982|Homer1|26556|homer homolog 1 (Drosophila)	NM_147176|Homer1|26556|homer homolog 1 (Drosophila)
mm9_v1_chrX_+_8927724_8927724	0.90325	SOX2.p2	NM_001085537|Gm14501|547154|predicted gene 14501
mm9_v1_chr8_+_96334452_96334737	0.901581	SOX2.p2	AK160434|Gnao1|14681|guanine nucleotide binding protein, alpha O	AK035907|Gnao1|14681|guanine nucleotide binding protein, alpha O	NM_001113384|Gnao1|14681|guanine nucleotide binding protein, alpha O	NM_010308|Gnao1|14681|guanine nucleotide binding protein, alpha O
mm9_v1_chr18_+_10325174_10325177	0.901271	SOX2.p2	AK142556|Greb1l|381157|growth regulation by estrogen in breast cancer-like	NM_001083628|Greb1l|381157|growth regulation by estrogen in breast cancer-like
mm9_v1_chrX_-_24077885_24077885	0.899402	SOX2.p2	NM_001100444|Gm5934|546272|predicted gene 5934
mm9_v1_chr17_+_8533225_8533295	0.899006	SOX2.p2	BC060190|Prr18|320111|proline rich region 18	AK045379|Prr18|320111|proline rich region 18
mm9_v1_chr6_+_134870680_134870720	0.897028	SOX2.p2	AK046676|Cdkn1b|12576|cyclin-dependent kinase inhibitor 1B	AK162146|Cdkn1b|12576|cyclin-dependent kinase inhibitor 1B	U10440|Cdkn1b|12576|cyclin-dependent kinase inhibitor 1B
mm9_v1_chr11_-_76391228_76391228	0.895781	SOX2.p2	NM_198894|Abr|109934|active BCR-related gene
mm9_v1_chr13_-_67601323_67601457	0.894595	SOX2.p2	BC139150|Zfp58|238693|zinc finger protein 58	BC139151|Zfp58|238693|zinc finger protein 58	AK041250|Zfp58|238693|zinc finger protein 58	AK162259|Zfp58|238693|zinc finger protein 58	AK167399|Zfp58|238693|zinc finger protein 58	NM_001007575|Zfp58|238693|zinc finger protein 58
mm9_v1_chr3_+_92169108_92169139	0.894281	SOX2.p2	AY158990|Sprr2f|20760|small proline-rich protein 2F	NM_011472|Sprr2f|20760|small proline-rich protein 2F	BC120756|Sprr2f|20760|small proline-rich protein 2F	BC120758|Sprr2f|20760|small proline-rich protein 2F
mm9_v1_chr6_-_38238095_38238171	0.89403	SOX2.p2	AK045178|Zc3hav1l|209032|zinc finger CCCH-type, antiviral 1-like
mm9_v1_chr18_-_53904193_53904270	0.893965	SOX2.p2	AK044952|Cep120|225523|centrosomal protein 120	BC053439|Cep120|225523|centrosomal protein 120	NM_178686|Cep120|225523|centrosomal protein 120	AK089236|Cep120|225523|centrosomal protein 120	AK089242|Cep120|225523|centrosomal protein 120	AK044808|Cep120|225523|centrosomal protein 120	AK079319|Cep120|225523|centrosomal protein 120	AK047594|Cep120|225523|centrosomal protein 120	AK038916|Cep120|225523|centrosomal protein 120
mm9_v1_chr6_+_30491641_30491643	0.893403	SOX2.p2	NM_001024698|Cpa2|232680|carboxypeptidase A2, pancreatic
mm9_v1_chr6_+_30561009_30561009	0.893108	SOX2.p2	AF466283|Cpa5|74649|carboxypeptidase A5	AK015256|Cpa5|74649|carboxypeptidase A5	NM_144537|Cpa5|74649|carboxypeptidase A5
mm9_v1_chr1_+_182837982_182838044	0.892288	SOX2.p2	AK187139|Pycr2|69051|pyrroline-5-carboxylate reductase family, member 2
mm9_v1_chr16_-_17144301_17144301	0.890525	SOX2.p2	BC050881|Ccdc116|76872|coiled-coil domain containing 116	NM_001164606|Ccdc116|76872|coiled-coil domain containing 116
mm9_v1_chr16_-_96304116_96304132	0.889709	SOX2.p2	BC056618|Brwd1|93871|bromodomain and WD repeat domain containing 1
mm9_v1_chr9_+_83728295_83728324	0.888762	SOX2.p2	NM_001110265|Ttk|22137|Ttk protein kinase	NM_009445|Ttk|22137|Ttk protein kinase	AK164093|Ttk|22137|Ttk protein kinase	AK049200|Ttk|22137|Ttk protein kinase	AK041487|Ttk|22137|Ttk protein kinase	BC058851|Ttk|22137|Ttk protein kinase
mm9_v1_chr2_+_177876710_177876721	0.887912	SOX2.p2	BC058621|Phactr3|74189|phosphatase and actin regulator 3
mm9_v1_chr13_-_46788898_46788932	0.887142	SOX2.p2	
mm9_v1_chr2_+_121692687_121692705	0.886175	SOX2.p2	BC064446|Casc4|319996|cancer susceptibility candidate 4	NM_177054|Casc4|319996|cancer susceptibility candidate 4	NM_199038|Casc4|319996|cancer susceptibility candidate 4
mm9_v1_chr15_+_89398756_89398806	0.88583	SOX2.p2	AK006695|Acr|11434|acrosin prepropeptide	NM_013455|Acr|11434|acrosin prepropeptide	BC103577|Acr|11434|acrosin prepropeptide	BC103578|Acr|11434|acrosin prepropeptide	BC103579|Acr|11434|acrosin prepropeptide	BC103580|Acr|11434|acrosin prepropeptide	D00754|Acr|11434|acrosin prepropeptide	AK160427|Acr|11434|acrosin prepropeptide
mm9_v1_chr12_+_33987379_33987464	0.882097	SOX2.p2	NM_001033436|Atxn7l1|380753|ataxin 7-like 1	AK156016|Atxn7l1|380753|ataxin 7-like 1	BC147479|Atxn7l1|380753|ataxin 7-like 1	BC147483|Atxn7l1|380753|ataxin 7-like 1
mm9_v1_chr18_-_15309939_15309954	0.8803	SOX2.p2	AY899808|Kctd1|106931|potassium channel tetramerisation domain containing 1	NM_134112|Kctd1|106931|potassium channel tetramerisation domain containing 1
mm9_v1_chr5_-_101227486_101227632	0.879257	SOX2.p2	BC109169|Helq|191578|helicase, POLQ-like	BC109170|Helq|191578|helicase, POLQ-like	AK052427|Helq|191578|helicase, POLQ-like	BC082601|Helq|191578|helicase, POLQ-like	AK050769|Helq|191578|helicase, POLQ-like	AK040335|Helq|191578|helicase, POLQ-like	NM_001081107|Helq|191578|helicase, POLQ-like
mm9_v1_chr16_+_96457407_96457407	0.87901	SOX2.p2	BC047347|B3galt5|93961|UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	BC051669|B3galt5|93961|UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	NM_001122993|B3galt5|93961|UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5
mm9_v1_chr5_-_77524256_77524291	0.878817	SOX2.p2	AK008297|Hopx|74318|HOP homeobox	AK008439|Hopx|74318|HOP homeobox	BC024546|Hopx|74318|HOP homeobox	AF492704|Hopx|74318|HOP homeobox	AK003784|Hopx|74318|HOP homeobox	NM_001159900|Hopx|74318|HOP homeobox	NM_001159901|Hopx|74318|HOP homeobox
mm9_v1_chr6_-_39370351_39370385	0.878741	SOX2.p2	BC003329|Mkrn1|54484|makorin, ring finger protein, 1	AK077060|Mkrn1|54484|makorin, ring finger protein, 1	NM_018810|Mkrn1|54484|makorin, ring finger protein, 1	AF192785|Mkrn1|54484|makorin, ring finger protein, 1
mm9_v1_chr1_+_134402806_134402867	0.878504	SOX2.p2	AK015245|Tmem81|74626|transmembrane protein 81	NM_029025|Tmem81|74626|transmembrane protein 81	AK045585|Tmem81|74626|transmembrane protein 81
mm9_v1_chr5_+_36235967_36236084	0.878203	SOX2.p2	BC050814|Afap1|70292|actin filament associated protein 1	NM_027373|Afap1|70292|actin filament associated protein 1	AK161385|Afap1|70292|actin filament associated protein 1	AK080756|Afap1|70292|actin filament associated protein 1	AK129483|Afap1|70292|actin filament associated protein 1	AK147706|Afap1|70292|actin filament associated protein 1
mm9_v1_chr1_-_173957316_173957398	0.874459	SOX2.p2	AK033128|Vangl2|93840|vang-like 2 (van gogh, Drosophila)	AY035370|Vangl2|93840|vang-like 2 (van gogh, Drosophila)	AK129311|Vangl2|93840|vang-like 2 (van gogh, Drosophila)	BC052195|Vangl2|93840|vang-like 2 (van gogh, Drosophila)	NM_033509|Vangl2|93840|vang-like 2 (van gogh, Drosophila)
mm9_v1_chr11_+_78312621_78312770	0.872574	SOX2.p2	NM_011707|Vtn|22370|vitronectin	AK011736|Vtn|22370|vitronectin	AK090325|Vtn|22370|vitronectin	AK167494|Vtn|22370|vitronectin
mm9_v1_chr12_-_21396339_21396369	0.871693	SOX2.p2	
mm9_v1_chr16_-_36455460_36455484	0.871323	SOX2.p2	AY169236|Stfa3|20863|stefin A3	M92419|Stfa3|20863|stefin A3	BC107224|Stfa3|20863|stefin A3	BC107225|Stfa3|20863|stefin A3	AK014349|Stfa3|20863|stefin A3	NM_025288|Stfa3|20863|stefin A3
mm9_v1_chr7_-_54856741_54856741	0.868465	SOX2.p2	AY042193|Mrgpra3|233222|MAS-related GPR, member A3	NM_153067|Mrgpra3|233222|MAS-related GPR, member A3
mm9_v1_chr5_-_97885939_97886039	0.867828	SOX2.p2	AK075761|Gk2|14626|glycerol kinase 2	BC061147|Gk2|14626|glycerol kinase 2	AF117734|Gk2|14626|glycerol kinase 2	NM_010294|Gk2|14626|glycerol kinase 2	BC050764|Gk2|14626|glycerol kinase 2
mm9_v1_chr17_+_36054140_36054142	0.867695	SOX2.p2	BC052059|Ppp1r10|52040|protein phosphatase 1, regulatory subunit 10	NM_001163818|Ppp1r10|52040|protein phosphatase 1, regulatory subunit 10	AJ504718|Ppp1r10|52040|protein phosphatase 1, regulatory subunit 10
mm9_v1_chr11_-_54965186_54965209	0.867499	SOX2.p2	AY211261|Slc36a3|215332|solute carrier family 36 (proton/amino acid symporter), member 3	AK132910|Slc36a3|215332|solute carrier family 36 (proton/amino acid symporter), member 3	AF453745|Slc36a3|215332|solute carrier family 36 (proton/amino acid symporter), member 3	NM_172258|Slc36a3|215332|solute carrier family 36 (proton/amino acid symporter), member 3	BC049682|Slc36a3|215332|solute carrier family 36 (proton/amino acid symporter), member 3
mm9_v1_chr11_+_29592946_29593072	0.867055	SOX2.p2	AK220511|Rtn4|68585|reticulon 4	AY102281|Rtn4|68585|reticulon 4	AY102282|Rtn4|68585|reticulon 4	AY102284|Rtn4|68585|reticulon 4	AY114152|Rtn4|68585|reticulon 4	AY114153|Rtn4|68585|reticulon 4	AK034902|Rtn4|68585|reticulon 4	BC056373|Rtn4|68585|reticulon 4
mm9_v1_chr11_-_18918923_18918971	0.866611	SOX2.p2	AK032947|Meis1|17268|Meis homeobox 1	AK049720|Meis1|17268|Meis homeobox 1	BC023689|Meis1|17268|Meis homeobox 1	AK168684|Meis1|17268|Meis homeobox 1	AK134321|Meis1|17268|Meis homeobox 1	AK140748|Meis1|17268|Meis homeobox 1	NM_001193271|Meis1|17268|Meis homeobox 1	NM_010789|Meis1|17268|Meis homeobox 1
mm9_v1_chr4_-_36665923_36665995	0.866459	SOX2.p2	BC090619|Lingo2|242384|leucine rich repeat and Ig domain containing 2	NM_001166000|Lingo2|242384|leucine rich repeat and Ig domain containing 2
mm9_v1_chrX_-_16896428_16896493	0.866399	SOX2.p2	BC120659|Efhc2|74405|EF-hand domain (C-terminal) containing 2	BC125625|Efhc2|74405|EF-hand domain (C-terminal) containing 2	AK016714|Efhc2|74405|EF-hand domain (C-terminal) containing 2	AK029501|Efhc2|74405|EF-hand domain (C-terminal) containing 2	NM_028916|Efhc2|74405|EF-hand domain (C-terminal) containing 2
mm9_v1_chr12_-_71212906_71213013	0.865532	SOX2.p2	BC137789|Nin|18080|ninein	BC144913|Nin|18080|ninein	BC144914|Nin|18080|ninein	AK129394|Nin|18080|ninein	NM_008697|Nin|18080|ninein	U40342|Nin|18080|ninein	AK162150|Nin|18080|ninein	AK167264|Nin|18080|ninein
mm9_v1_chr5_-_105539282_105539310	0.865014	SOX2.p2	BC057170|Gbp9|236573|guanylate-binding protein 9	DQ985742|Gbp9|236573|guanylate-binding protein 9	AK165231|Gbp9|236573|guanylate-binding protein 9	AK088861|Gbp9|236573|guanylate-binding protein 9	NM_172777|Gbp9|236573|guanylate-binding protein 9
mm9_v1_chr1_-_168339909_168339980	0.864623	SOX2.p2	AK031716|Pogk|71592|pogo transposable element with KRAB domain	BC072587|Pogk|71592|pogo transposable element with KRAB domain	AK048067|Pogk|71592|pogo transposable element with KRAB domain	AK048752|Pogk|71592|pogo transposable element with KRAB domain	AK053898|Pogk|71592|pogo transposable element with KRAB domain	NM_001142948|Pogk|71592|pogo transposable element with KRAB domain	NM_175170|Pogk|71592|pogo transposable element with KRAB domain
mm9_v1_chr7_-_106628404_106628486	0.864157	SOX2.p2	AK197233|Rps3|27050|ribosomal protein S3	AK197426|Rps3|27050|ribosomal protein S3	AK201330|Rps3|27050|ribosomal protein S3	AK211385|Rps3|27050|ribosomal protein S3
mm9_v1_chr5_-_137510950_137511054	0.863371	SOX2.p2	AK192071|Ap1s1|11769|adaptor protein complex AP-1, sigma 1
mm9_v1_chr16_+_44370127_44370136	0.862065	SOX2.p2	BC024956|Spice1|212514|spindle and centriole associated protein 1
mm9_v1_chr7_-_26197807_26197904	0.861589	SOX2.p2	AY374329|Cxcl17|232983|chemokine (C-X-C motif) ligand 17	AK143005|Cxcl17|232983|chemokine (C-X-C motif) ligand 17	AY598463|Cxcl17|232983|chemokine (C-X-C motif) ligand 17	BC024561|Cxcl17|232983|chemokine (C-X-C motif) ligand 17	NM_153576|Cxcl17|232983|chemokine (C-X-C motif) ligand 17
mm9_v1_chr4_-_118862555_118862615	0.86069	SOX2.p2	BC063257|Ermap|27028|erythroblast membrane-associated protein	AF153906|Ermap|27028|erythroblast membrane-associated protein	AK036702|Ermap|27028|erythroblast membrane-associated protein	AK158114|Ermap|27028|erythroblast membrane-associated protein	AK137510|Ermap|27028|erythroblast membrane-associated protein	NM_013848|Ermap|27028|erythroblast membrane-associated protein
mm9_v1_chr4_+_88487719_88487764	0.859084	SOX2.p2	BC119349|Ifna4|15967|interferon alpha 4	BC119351|Ifna4|15967|interferon alpha 4	NM_010504|Ifna4|15967|interferon alpha 4	BC116217|Ifna4|15967|interferon alpha 4
mm9_v1_chr8_-_48437701_48437701	0.858946	SOX2.p2	BC100572|Stox2|71069|storkhead box 2	BC100573|Stox2|71069|storkhead box 2	NM_175162|Stox2|71069|storkhead box 2
mm9_v1_chr9_+_123676286_123676425	0.858254	SOX2.p2	AK162996|Ccr9|12769|chemokine (C-C motif) receptor 9	AK050615|Ccr9|12769|chemokine (C-C motif) receptor 9	AK153975|Ccr9|12769|chemokine (C-C motif) receptor 9	NM_001166625|Ccr9|12769|chemokine (C-C motif) receptor 9	NM_009913|Ccr9|12769|chemokine (C-C motif) receptor 9	AK040129|Ccr9|12769|chemokine (C-C motif) receptor 9	AJ132336|Ccr9|12769|chemokine (C-C motif) receptor 9	AJ131357|Ccr9|12769|chemokine (C-C motif) receptor 9	AK038272|Ccr9|12769|chemokine (C-C motif) receptor 9
mm9_v1_chr2_+_104430617_104430708	0.858126	SOX2.p2	AK158169|Cstf3|228410|cleavage stimulation factor, 3' pre-RNA, subunit 3	NM_001037326|Cstf3|228410|cleavage stimulation factor, 3' pre-RNA, subunit 3	NM_145529|Cstf3|228410|cleavage stimulation factor, 3' pre-RNA, subunit 3	NM_177253|Cstf3|228410|cleavage stimulation factor, 3' pre-RNA, subunit 3	BC003241|Cstf3|228410|cleavage stimulation factor, 3' pre-RNA, subunit 3	BC058605|Cstf3|228410|cleavage stimulation factor, 3' pre-RNA, subunit 3	AK028899|Cstf3|228410|cleavage stimulation factor, 3' pre-RNA, subunit 3
mm9_v1_chr1_-_55283189_55283376	0.85701	SOX2.p2	BC026871|Rftn2|74013|raftlin family member 2	AK014318|Rftn2|74013|raftlin family member 2
mm9_v1_chr19_-_12840121_12840121	0.856749	SOX2.p2	BC027539|Cntf|12803|ciliary neurotrophic factor	NM_170786|Cntf|12803|ciliary neurotrophic factor
mm9_v1_chr9_+_83728331_83728347	0.855665	SOX2.p2	AX775731|Ttk|22137|Ttk protein kinase	M86377|Ttk|22137|Ttk protein kinase
mm9_v1_chr5_-_134713923_134714158	0.852713	SOX2.p2	
mm9_v1_chr4_+_49072327_49072465	0.852468	SOX2.p2	AK053451|E130309F12Rik|272031|RIKEN cDNA E130309F12 gene	AK087514|E130309F12Rik|272031|RIKEN cDNA E130309F12 gene	AY345342|E130309F12Rik|272031|RIKEN cDNA E130309F12 gene	NM_178756|E130309F12Rik|272031|RIKEN cDNA E130309F12 gene	BC096762|E130309F12Rik|272031|RIKEN cDNA E130309F12 gene	AK047614|E130309F12Rik|272031|RIKEN cDNA E130309F12 gene	AK043762|E130309F12Rik|272031|RIKEN cDNA E130309F12 gene
mm9_v1_chr11_-_102308966_102308985	0.851802	SOX2.p2	NM_199200|Fam171a2|217219|family with sequence similarity 171, member A2
mm9_v1_chrX_-_26362794_26362794	0.850891	SOX2.p2	NM_001104946|Gm2012|100039030|predicted gene 2012	NM_001114754|Gm6121|619991|predicted gene 6121
mm9_v1_chr14_-_44749035_44749035	0.845571	SOX2.p2	AK015686|4930503E14Rik|74954|RIKEN cDNA 4930503E14 gene	NM_029131|4930503E14Rik|74954|RIKEN cDNA 4930503E14 gene
mm9_v1_chr6_+_24698345_24698366	0.845154	SOX2.p2	AK014599|Hyal4|77042|hyaluronoglucosaminidase 4	BC125402|Hyal4|77042|hyaluronoglucosaminidase 4	BC132096|Hyal4|77042|hyaluronoglucosaminidase 4	NM_029848|Hyal4|77042|hyaluronoglucosaminidase 4
mm9_v1_chr19_+_7492081_7492131	0.844939	SOX2.p2	NM_175381|2700081O15Rik|108899|RIKEN cDNA 2700081O15 gene
mm9_v1_chr9_+_44295329_44295421	0.844276	SOX2.p2	AK155681|Bcl9l|80288|B-cell CLL/lymphoma 9-like
mm9_v1_chr5_-_135391395_135391399	0.841667	SOX2.p2	AF516681|Cldn13|57255|claudin 13	AK010869|Cldn13|57255|claudin 13	NM_020504|Cldn13|57255|claudin 13
mm9_v1_chr11_-_99902845_99902867	0.839653	SOX2.p2	BC125420|Krt34|16672|keratin 34	BC125446|Krt34|16672|keratin 34	AK014631|Krt34|16672|keratin 34	NM_027563|Krt34|16672|keratin 34
mm9_v1_chr7_-_53435334_53435402	0.839022	SOX2.p2	BC141411|Abcc8|20927|ATP-binding cassette, sub-family C (CFTR/MRP), member 8	AK086472|Abcc8|20927|ATP-binding cassette, sub-family C (CFTR/MRP), member 8	NM_011510|Abcc8|20927|ATP-binding cassette, sub-family C (CFTR/MRP), member 8
mm9_v1_chr17_-_65989095_65989095	0.838113	SOX2.p2	AF196282|Txndc2|213272|thioredoxin domain containing 2 (spermatozoa)	NM_153519|Txndc2|213272|thioredoxin domain containing 2 (spermatozoa)
mm9_v1_chr11_+_45869473_45869501	0.834362	SOX2.p2	NM_009616|Adam19|11492|a disintegrin and metallopeptidase domain 19 (meltrin beta)	BC093480|Adam19|11492|a disintegrin and metallopeptidase domain 19 (meltrin beta)
mm9_v1_chr11_-_23419100_23419194	0.833002	SOX2.p2	AK007052|1700093K21Rik|67358|RIKEN cDNA 1700093K21 gene	BC049567|1700093K21Rik|67358|RIKEN cDNA 1700093K21 gene	NM_026105|1700093K21Rik|67358|RIKEN cDNA 1700093K21 gene
mm9_v1_chr8_+_91220921_91220958	0.83141	SOX2.p2	NM_001128170|Cyld|74256|cylindromatosis (turban tumor syndrome)	NM_001128171|Cyld|74256|cylindromatosis (turban tumor syndrome)	NM_173369|Cyld|74256|cylindromatosis (turban tumor syndrome)	NM_001128169|Cyld|74256|cylindromatosis (turban tumor syndrome)	AK122389|Cyld|74256|cylindromatosis (turban tumor syndrome)	AK147204|Cyld|74256|cylindromatosis (turban tumor syndrome)
mm9_v1_chr7_+_31536489_31536560	0.830967	SOX2.p2	BC051531|Sbsn|282619|suprabasin	NM_001083903|Sbsn|282619|suprabasin	NM_172205|Sbsn|282619|suprabasin	AY115494|Sbsn|282619|suprabasin	AY444556|Sbsn|282619|suprabasin	BC139385|Sbsn|282619|suprabasin	AK081760|Sbsn|282619|suprabasin	BC092350|Sbsn|282619|suprabasin
mm9_v1_chr13_+_22036962_22036998	0.830628	SOX2.p2	BC053084|Zfp184|193452|zinc finger protein 184 (Kruppel-like)	NM_183014|Zfp184|193452|zinc finger protein 184 (Kruppel-like)	AK036164|Zfp184|193452|zinc finger protein 184 (Kruppel-like)
mm9_v1_chr6_+_120314116_120314182	0.829447	SOX2.p2	AK041568|Kdm5a|214899|lysine (K)-specific demethylase 5A	NM_145997|Kdm5a|214899|lysine (K)-specific demethylase 5A	AK166055|Kdm5a|214899|lysine (K)-specific demethylase 5A	AK159079|Kdm5a|214899|lysine (K)-specific demethylase 5A	AK144877|Kdm5a|214899|lysine (K)-specific demethylase 5A	AK139619|Kdm5a|214899|lysine (K)-specific demethylase 5A	AK046187|Kdm5a|214899|lysine (K)-specific demethylase 5A	BC011506|Kdm5a|214899|lysine (K)-specific demethylase 5A
mm9_v1_chrX_+_157205944_157206093	0.828524	SOX2.p2	BC046422|Rs1|20147|retinoschisis (X-linked, juvenile) 1 (human)	NM_011302|Rs1|20147|retinoschisis (X-linked, juvenile) 1 (human)	AF084561|Rs1|20147|retinoschisis (X-linked, juvenile) 1 (human)	AF073780|Rs1|20147|retinoschisis (X-linked, juvenile) 1 (human)	AJ011381|Rs1|20147|retinoschisis (X-linked, juvenile) 1 (human)
mm9_v1_chr12_+_80309899_80309933	0.825526	SOX2.p2	AK164157|Rdh12|77974|retinol dehydrogenase 12	AK039233|Rdh12|77974|retinol dehydrogenase 12	NM_030017|Rdh12|77974|retinol dehydrogenase 12	AK020927|Rdh12|77974|retinol dehydrogenase 12	BC016204|Rdh12|77974|retinol dehydrogenase 12	BC067213|Rdh12|77974|retinol dehydrogenase 12
mm9_v1_chr17_+_17967938_17968143	0.822883	SOX2.p2	NM_001162909|Ncrna00085|75202|non-protein coding RNA 85	AK016052|Ncrna00085|75202|non-protein coding RNA 85	AK020993|Ncrna00085|75202|non-protein coding RNA 85	BC171977|Ncrna00085|75202|non-protein coding RNA 85	BC171982|Ncrna00085|75202|non-protein coding RNA 85	BC171984|Ncrna00085|75202|non-protein coding RNA 85
mm9_v1_chr11_+_59355080_59355087	0.822134	SOX2.p2	AF486632|Nlrp3|216799|NLR family, pyrin domain containing 3
mm9_v1_chr5_-_122907002_122907003	0.821633	SOX2.p2	AK134659|Atp2a2|11938|ATPase, Ca++ transporting, cardiac muscle, slow twitch 2
mm9_v1_chr9_+_44048756_44048763	0.821073	SOX2.p2	NM_001081369|Ccdc153|270150|coiled-coil domain containing 153
mm9_v1_chr11_-_115940157_115940300	0.820683	SOX2.p2	
mm9_v1_chr19_+_53218486_53218486	0.820335	SOX2.p2	BC037116|Add3|27360|adducin 3 (gamma)	NM_013758|Add3|27360|adducin 3 (gamma)
mm9_v1_chr11_-_60988419_60988468	0.82022	SOX2.p2	BC080737|Usp22|216825|ubiquitin specific peptidase 22	AK160992|Usp22|216825|ubiquitin specific peptidase 22
mm9_v1_chr19_-_4801605_4801652	0.818232	SOX2.p2	
mm9_v1_chrX_+_160528118_160528196	0.817675	SOX2.p2	AF178085|Tmem27|57394|transmembrane protein 27	NM_020626|Tmem27|57394|transmembrane protein 27	AK148534|Tmem27|57394|transmembrane protein 27	AK002337|Tmem27|57394|transmembrane protein 27	BC049912|Tmem27|57394|transmembrane protein 27
mm9_v1_chr17_+_8627287_8627315	0.816789	SOX2.p2	NM_009309|T|20997|brachyury	X51683|T|20997|brachyury	BC120807|T|20997|brachyury
mm9_v1_chr9_+_109719138_109719140	0.816784	SOX2.p2	BC048588|Spink8|78709|serine peptidase inhibitor, Kazal type 8	NM_183136|Spink8|78709|serine peptidase inhibitor, Kazal type 8
mm9_v1_chr11_+_51781124_51781401	0.815803	SOX2.p2	NM_029976|Cdkn2aipnl|52626|CDKN2A interacting protein N-terminal like	AK020751|Cdkn2aipnl|52626|CDKN2A interacting protein N-terminal like	AB041653|Cdkn2aipnl|52626|CDKN2A interacting protein N-terminal like	BC116362|Cdkn2aipnl|52626|CDKN2A interacting protein N-terminal like	BC116363|Cdkn2aipnl|52626|CDKN2A interacting protein N-terminal like	AK150573|Cdkn2aipnl|52626|CDKN2A interacting protein N-terminal like	AK171740|Cdkn2aipnl|52626|CDKN2A interacting protein N-terminal like	AK077515|Cdkn2aipnl|52626|CDKN2A interacting protein N-terminal like	BC099516|Cdkn2aipnl|52626|CDKN2A interacting protein N-terminal like
mm9_v1_chr5_+_107860567_107860567	0.81124	SOX2.p2	AK014940|Lpcat2b|70902|lysophosphatidylcholine acyltransferase 2B	AK029548|Lpcat2b|70902|lysophosphatidylcholine acyltransferase 2B	NM_027599|Lpcat2b|70902|lysophosphatidylcholine acyltransferase 2B
mm9_v1_chr4_-_24778203_24778245	0.809923	SOX2.p2	AK134944|Klhl32|212390|kelch-like 32 (Drosophila)	NM_001033531|Klhl32|212390|kelch-like 32 (Drosophila)	NM_001163020|Klhl32|212390|kelch-like 32 (Drosophila)
mm9_v1_chr9_+_44048807_44048916	0.80965	SOX2.p2	BC038167|Ccdc153|270150|coiled-coil domain containing 153
mm9_v1_chr10_+_82329370_82329405	0.809473	SOX2.p2	AK161275|Eid3|66341|EP300 interacting inhibitor of differentiation 3	AK161307|Eid3|66341|EP300 interacting inhibitor of differentiation 3	NM_025499|Eid3|66341|EP300 interacting inhibitor of differentiation 3	AK007194|Eid3|66341|EP300 interacting inhibitor of differentiation 3	AK006438|Eid3|66341|EP300 interacting inhibitor of differentiation 3	BC099545|Eid3|66341|EP300 interacting inhibitor of differentiation 3	AK132745|Eid3|66341|EP300 interacting inhibitor of differentiation 3
mm9_v1_chr8_-_55606109_55606134	0.808669	SOX2.p2	AK051731|Spcs3|76687|signal peptidase complex subunit 3 homolog (S. cerevisiae)
mm9_v1_chr4_-_147662005_147662073	0.80777	SOX2.p2	BC070441|Ptchd2|242748|patched domain containing 2	BC072569|Ptchd2|242748|patched domain containing 2	AK090326|Ptchd2|242748|patched domain containing 2	NM_001083342|Ptchd2|242748|patched domain containing 2
mm9_v1_chr9_-_117161564_117161606	0.807524	SOX2.p2	BC108402|Rbms3|207181|RNA binding motif, single stranded interacting protein	AK052196|Rbms3|207181|RNA binding motif, single stranded interacting protein	AK032938|Rbms3|207181|RNA binding motif, single stranded interacting protein	AK081921|Rbms3|207181|RNA binding motif, single stranded interacting protein	AK051776|Rbms3|207181|RNA binding motif, single stranded interacting protein	AK041098|Rbms3|207181|RNA binding motif, single stranded interacting protein	NM_001172122|Rbms3|207181|RNA binding motif, single stranded interacting protein	NM_001172123|Rbms3|207181|RNA binding motif, single stranded interacting protein	NM_001172124|Rbms3|207181|RNA binding motif, single stranded interacting protein	NM_001172126|Rbms3|207181|RNA binding motif, single stranded interacting protein	NM_178660|Rbms3|207181|RNA binding motif, single stranded interacting protein
mm9_v1_chr5_+_34185760_34185844	0.802136	SOX2.p2	NM_001081102|Whsc1|107823|Wolf-Hirschhorn syndrome candidate 1 (human)	NM_001177884|Whsc1|107823|Wolf-Hirschhorn syndrome candidate 1 (human)	NM_175231|Whsc1|107823|Wolf-Hirschhorn syndrome candidate 1 (human)	BC079668|Whsc1|107823|Wolf-Hirschhorn syndrome candidate 1 (human)
mm9_v1_chr3_+_121129396_121129492	0.800126	SOX2.p2	AK169098|Cnn3|71994|calponin 3, acidic	AK159555|Cnn3|71994|calponin 3, acidic	AK169021|Cnn3|71994|calponin 3, acidic	AK167201|Cnn3|71994|calponin 3, acidic	AK051628|Cnn3|71994|calponin 3, acidic	AK159871|Cnn3|71994|calponin 3, acidic	AK167613|Cnn3|71994|calponin 3, acidic	AK166578|Cnn3|71994|calponin 3, acidic	BC055711|Cnn3|71994|calponin 3, acidic	AK005460|Cnn3|71994|calponin 3, acidic	NM_028044|Cnn3|71994|calponin 3, acidic	AK051121|Cnn3|71994|calponin 3, acidic	AK169410|Cnn3|71994|calponin 3, acidic
mm9_v1_chr14_-_63796620_63796725	0.799002	SOX2.p2	AK168629|Fdft1|14137|farnesyl diphosphate farnesyl transferase 1	BC054722|Fdft1|14137|farnesyl diphosphate farnesyl transferase 1	NM_010191|Fdft1|14137|farnesyl diphosphate farnesyl transferase 1	D29016|Fdft1|14137|farnesyl diphosphate farnesyl transferase 1	AK162294|Fdft1|14137|farnesyl diphosphate farnesyl transferase 1	BC138301|Fdft1|14137|farnesyl diphosphate farnesyl transferase 1	AK158633|Fdft1|14137|farnesyl diphosphate farnesyl transferase 1	BC138302|Fdft1|14137|farnesyl diphosphate farnesyl transferase 1	AK076062|Fdft1|14137|farnesyl diphosphate farnesyl transferase 1	AK146766|Fdft1|14137|farnesyl diphosphate farnesyl transferase 1	AK169317|Fdft1|14137|farnesyl diphosphate farnesyl transferase 1
mm9_v1_chr19_-_10557362_10557417	0.797643	SOX2.p2	BC118523|4930579J09Rik|67752|RIKEN cDNA 4930579J09 gene	AY032666|4930579J09Rik|67752|RIKEN cDNA 4930579J09 gene	NM_133689|4930579J09Rik|67752|RIKEN cDNA 4930579J09 gene	AK005821|4930579J09Rik|67752|RIKEN cDNA 4930579J09 gene	AK016325|4930579J09Rik|67752|RIKEN cDNA 4930579J09 gene
mm9_v1_chr6_-_129593305_129593354	0.7972	SOX2.p2	AF195779|Klrc3|58179|killer cell lectin-like receptor subfamily C, member 3	BC130234|Klrc3|58179|killer cell lectin-like receptor subfamily C, member 3	NM_021378|Klrc3|58179|killer cell lectin-like receptor subfamily C, member 3	BC144931|Klrc3|58179|killer cell lectin-like receptor subfamily C, member 3
mm9_v1_chr5_-_141124884_141125029	0.792776	SOX2.p2	AK052340|Ttyh3|78339|tweety homolog 3 (Drosophila)	BC059083|Ttyh3|78339|tweety homolog 3 (Drosophila)	BC062917|Ttyh3|78339|tweety homolog 3 (Drosophila)	NM_175274|Ttyh3|78339|tweety homolog 3 (Drosophila)
mm9_v1_chr5_-_115263896_115263992	0.792422	SOX2.p2	AK165632|1500011B03Rik|66236|RIKEN cDNA 1500011B03 gene	AK087533|1500011B03Rik|66236|RIKEN cDNA 1500011B03 gene	AK018264|1500011B03Rik|66236|RIKEN cDNA 1500011B03 gene	AK005199|1500011B03Rik|66236|RIKEN cDNA 1500011B03 gene	BC061238|1500011B03Rik|66236|RIKEN cDNA 1500011B03 gene	AK161363|1500011B03Rik|66236|RIKEN cDNA 1500011B03 gene
mm9_v1_chr5_-_52541869_52541943	0.790209	SOX2.p2	AK208682|Dhx15|13204|DEAH (Asp-Glu-Ala-His) box polypeptide 15
mm9_v1_chr3_+_88769733_88769733	0.790015	SOX2.p2	NM_138679|Ash1l|192195|ash1 (absent, small, or homeotic)-like (Drosophila)
mm9_v1_chr17_+_78907402_78907511	0.789734	SOX2.p2	AK158117|Vit|74199|vitrin	NM_001197028|Vit|74199|vitrin	NM_028813|Vit|74199|vitrin	BC034120|Vit|74199|vitrin	AF454755|Vit|74199|vitrin	AK013193|Vit|74199|vitrin	AK051606|Vit|74199|vitrin
mm9_v1_chr6_-_113841356_113841375	0.789208	SOX2.p2	DQ406822|Atp2b2|11941|ATPase, Ca++ transporting, plasma membrane 2	AK051287|Atp2b2|11941|ATPase, Ca++ transporting, plasma membrane 2	BC075643|Atp2b2|11941|ATPase, Ca++ transporting, plasma membrane 2	NM_001036684|Atp2b2|11941|ATPase, Ca++ transporting, plasma membrane 2
mm9_v1_chr11_+_85124739_85124974	0.789188	SOX2.p2	BC051966|Ppm1d|53892|protein phosphatase 1D magnesium-dependent, delta isoform	NM_016910|Ppm1d|53892|protein phosphatase 1D magnesium-dependent, delta isoform	AK157818|Ppm1d|53892|protein phosphatase 1D magnesium-dependent, delta isoform	AK166632|Ppm1d|53892|protein phosphatase 1D magnesium-dependent, delta isoform	AK171714|Ppm1d|53892|protein phosphatase 1D magnesium-dependent, delta isoform	AK051509|Ppm1d|53892|protein phosphatase 1D magnesium-dependent, delta isoform	AK050831|Ppm1d|53892|protein phosphatase 1D magnesium-dependent, delta isoform	BC023492|Ppm1d|53892|protein phosphatase 1D magnesium-dependent, delta isoform	AK053727|Ppm1d|53892|protein phosphatase 1D magnesium-dependent, delta isoform	AF200464|Ppm1d|53892|protein phosphatase 1D magnesium-dependent, delta isoform
mm9_v1_chr9_-_71743854_71743929	0.788678	SOX2.p2	AK135376|Tcf12|21406|transcription factor 12	AK132002|Tcf12|21406|transcription factor 12	AK133958|Tcf12|21406|transcription factor 12	AK078415|Tcf12|21406|transcription factor 12
mm9_v1_chr10_-_25798768_25798857	0.78816	SOX2.p2	AK048673|Tmem200a|77220|transmembrane protein 200A	AK173299|Tmem200a|77220|transmembrane protein 200A	NM_029881|Tmem200a|77220|transmembrane protein 200A
mm9_v1_chr9_+_70390523_70390626	0.787502	SOX2.p2	AK077578|Sltm|66660|SAFB-like, transcription modulator	NM_026337|Sltm|66660|SAFB-like, transcription modulator	AK078251|Sltm|66660|SAFB-like, transcription modulator	AK011815|Sltm|66660|SAFB-like, transcription modulator
mm9_v1_chr2_+_143858837_143858837	0.787345	SOX2.p2	AK076863|Banf2|403171|barrier to autointegration factor 2	BC049628|Banf2|403171|barrier to autointegration factor 2	NM_001044750|Banf2|403171|barrier to autointegration factor 2	NM_207275|Banf2|403171|barrier to autointegration factor 2
mm9_v1_chr7_+_17460662_17460665	0.784592	SOX2.p2	DQ832319|Dact3|629378|dapper homolog 3, antagonist of beta-catenin (xenopus)	NM_001081655|Dact3|629378|dapper homolog 3, antagonist of beta-catenin (xenopus)
mm9_v1_chr19_-_4785312_4785318	0.784344	SOX2.p2	
mm9_v1_chr9_+_82723591_82723695	0.78342	SOX2.p2	AK076594|Irak1bp1|65099|interleukin-1 receptor-associated kinase 1 binding protein 1	AK013036|Irak1bp1|65099|interleukin-1 receptor-associated kinase 1 binding protein 1	AK045436|Irak1bp1|65099|interleukin-1 receptor-associated kinase 1 binding protein 1	BC046301|Irak1bp1|65099|interleukin-1 receptor-associated kinase 1 binding protein 1	BC061099|Irak1bp1|65099|interleukin-1 receptor-associated kinase 1 binding protein 1	AF093135|Irak1bp1|65099|interleukin-1 receptor-associated kinase 1 binding protein 1	AK014712|Irak1bp1|65099|interleukin-1 receptor-associated kinase 1 binding protein 1	AK020448|Irak1bp1|65099|interleukin-1 receptor-associated kinase 1 binding protein 1
mm9_v1_chr7_-_135090238_135090238	0.7821	SOX2.p2	NM_001081374|Prss36|77613|protease, serine, 36
mm9_v1_chr3_-_89206571_89206714	0.781041	SOX2.p2	NM_020517|Lenep|57275|lens epithelial protein	AK053703|Lenep|57275|lens epithelial protein	BC006806|Lenep|57275|lens epithelial protein
mm9_v1_chr6_-_53770406_53770488	0.780768	SOX2.p2	AK122338|Tril|66873|TLR4 interactor with leucine-rich repeats	AK033401|Tril|66873|TLR4 interactor with leucine-rich repeats	AK004681|Tril|66873|TLR4 interactor with leucine-rich repeats
mm9_v1_chr14_-_34260308_34260313	0.778711	SOX2.p2	BC053027|Mapk8|26419|mitogen-activated protein kinase 8
mm9_v1_chr4_+_143689782_143689782	0.776644	SOX2.p2	AK145585|Pramel4|347710|preferentially expressed antigen in melanoma like 4	BC132592|Gm13102|100041077|predicted gene 13102	BC132620|Gm13102|100041077|predicted gene 13102	NM_001085419|Gm13102|100041077|predicted gene 13102
mm9_v1_chr7_+_135409196_135409210	0.776394	SOX2.p2	AK128900|Slc5a2|246787|solute carrier family 5 (sodium/glucose cotransporter), member 2	AY033886|Slc5a2|246787|solute carrier family 5 (sodium/glucose cotransporter), member 2	BC022226|Slc5a2|246787|solute carrier family 5 (sodium/glucose cotransporter), member 2	NM_133254|Slc5a2|246787|solute carrier family 5 (sodium/glucose cotransporter), member 2
mm9_v1_chr1_+_100317700_100317730	0.774934	SOX2.p2	AK014872|Slco6d1|70866|solute carrier organic anion transporter family, member 6d1	NM_001164233|Slco6d1|70866|solute carrier organic anion transporter family, member 6d1	NM_027584|Slco6d1|70866|solute carrier organic anion transporter family, member 6d1	AK133206|Slco6d1|70866|solute carrier organic anion transporter family, member 6d1	BC112423|Slco6d1|70866|solute carrier organic anion transporter family, member 6d1	BC113131|Slco6d1|70866|solute carrier organic anion transporter family, member 6d1
mm9_v1_chr1_-_127808790_127808807	0.774871	SOX2.p2	AB041649|Lypd1|72585|Ly6/Plaur domain containing 1	AK045592|Lypd1|72585|Ly6/Plaur domain containing 1	NM_145100|Lypd1|72585|Ly6/Plaur domain containing 1
mm9_v1_chr2_+_163843294_163843512	0.773866	SOX2.p2	AK206846|Ywhab|54401|tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide	AK207996|Ywhab|54401|tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide	AK212148|Ywhab|54401|tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide	AK214843|Ywhab|54401|tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide	AK215126|Ywhab|54401|tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide	AK219468|Ywhab|54401|tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide
mm9_v1_chr7_+_149135837_149135911	0.773682	SOX2.p2	AK158574|Brsk2|75770|BR serine/threonine kinase 2
mm9_v1_chr12_+_112951212_112951331	0.773251	SOX2.p2	AK006963|2810002N01Rik|68020|RIKEN cDNA 2810002N01 gene
mm9_v1_chr18_+_77365613_77365672	0.771331	SOX2.p2	AK078097|Pias2|17344|protein inhibitor of activated STAT 2
mm9_v1_chr17_-_35840931_35841083	0.768074	SOX2.p2	L57509|Ddr1|12305|discoidin domain receptor family, member 1	AK143088|Ddr1|12305|discoidin domain receptor family, member 1	AK031442|Ddr1|12305|discoidin domain receptor family, member 1	NM_007584|Ddr1|12305|discoidin domain receptor family, member 1	NM_172962|Ddr1|12305|discoidin domain receptor family, member 1
mm9_v1_chr2_-_25078049_25078090	0.767743	SOX2.p2	AK194925|Tubb2c|227613|tubulin, beta 2C	AK214079|Tubb2c|227613|tubulin, beta 2C
mm9_v1_chr10_-_116675657_116675663	0.765906	SOX2.p2	BC120771|9530003J23Rik|77397|RIKEN cDNA 9530003J23 gene	BC120797|9530003J23Rik|77397|RIKEN cDNA 9530003J23 gene	AK020538|9530003J23Rik|77397|RIKEN cDNA 9530003J23 gene	AK035427|9530003J23Rik|77397|RIKEN cDNA 9530003J23 gene
mm9_v1_chr11_+_104092749_104092776	0.765075	SOX2.p2	M18775|Mapt|17762|microtubule-associated protein tau	M18776|Mapt|17762|microtubule-associated protein tau	NM_001038609|Mapt|17762|microtubule-associated protein tau	NM_010838|Mapt|17762|microtubule-associated protein tau	AK078167|Mapt|17762|microtubule-associated protein tau
mm9_v1_chr7_+_140829357_140829384	0.764654	SOX2.p2	NM_178115|2700050L05Rik|214764|RIKEN cDNA 2700050L05 gene	AK052387|2700050L05Rik|214764|RIKEN cDNA 2700050L05 gene
mm9_v1_chr11_-_79343891_79344047	0.762844	SOX2.p2	AK171332|Evi2a|14017|ecotropic viral integration site 2a	AK044098|Evi2a|14017|ecotropic viral integration site 2a	AK162958|Evi2a|14017|ecotropic viral integration site 2a	AK171594|Evi2a|14017|ecotropic viral integration site 2a	AK160302|Evi2a|14017|ecotropic viral integration site 2a	M34896|Evi2a|14017|ecotropic viral integration site 2a
mm9_v1_chr6_+_8900018_8900018	0.761616	SOX2.p2	BC145953|Nxph1|18231|neurexophilin 1	BC145955|Nxph1|18231|neurexophilin 1	NM_008751|Nxph1|18231|neurexophilin 1
mm9_v1_chr6_-_37249957_37249977	0.760055	SOX2.p2	AK081360|Dgki|320127|diacylglycerol kinase, iota	NM_001081206|Dgki|320127|diacylglycerol kinase, iota
mm9_v1_chr2_-_155984800_155984951	0.758747	SOX2.p2	AK134091|Rbm39|170791|RNA binding motif protein 39
mm9_v1_chr10_-_41905549_41905563	0.758087	SOX2.p2	AK041595|Foxo3|56484|forkhead box O3	AK159465|Foxo3|56484|forkhead box O3
mm9_v1_chr7_+_51443605_51443632	0.757456	SOX2.p2	BC146015|Klk1b24|16617|kallikrein 1-related peptidase b24	BC146019|Klk1b24|16617|kallikrein 1-related peptidase b24	AB039277|Klk1b24|16617|kallikrein 1-related peptidase b24	NM_010643|Klk1b24|16617|kallikrein 1-related peptidase b24
mm9_v1_chr1_-_127808723_127808763	0.757423	SOX2.p2	BC058599|Lypd1|72585|Ly6/Plaur domain containing 1
mm9_v1_chr4_+_154335029_154335081	0.757267	SOX2.p2	AK139390|Hes5|15208|hairy and enhancer of split 5 (Drosophila)	AK078170|Hes5|15208|hairy and enhancer of split 5 (Drosophila)	AK087508|Hes5|15208|hairy and enhancer of split 5 (Drosophila)	AK156545|Hes5|15208|hairy and enhancer of split 5 (Drosophila)	NM_010419|Hes5|15208|hairy and enhancer of split 5 (Drosophila)	BC099863|Hes5|15208|hairy and enhancer of split 5 (Drosophila)	BC099864|Hes5|15208|hairy and enhancer of split 5 (Drosophila)	BC099865|Hes5|15208|hairy and enhancer of split 5 (Drosophila)	BC103539|Hes5|15208|hairy and enhancer of split 5 (Drosophila)
mm9_v1_chr4_-_88204148_88204148	0.756961	SOX2.p2	BC116216|Gm12597|242517|predicted gene 12597	NM_206870|Gm12597|242517|predicted gene 12597
mm9_v1_chr16_-_17144515_17144515	0.756541	SOX2.p2	AK015290|Ccdc116|76872|coiled-coil domain containing 116	NM_029779|Ccdc116|76872|coiled-coil domain containing 116
mm9_v1_chr6_-_124414668_124414803	0.755352	SOX2.p2	AJ278486|Clstn3|232370|calsyntenin 3	BC055054|Clstn3|232370|calsyntenin 3	AK032336|Clstn3|232370|calsyntenin 3	NM_153508|Clstn3|232370|calsyntenin 3
mm9_v1_chr9_+_109719158_109719169	0.755294	SOX2.p2	AK021276|Spink8|78709|serine peptidase inhibitor, Kazal type 8	DQ437329|Spink8|78709|serine peptidase inhibitor, Kazal type 8
mm9_v1_chr9_+_108698323_108698461	0.754872	SOX2.p2	BC039922|Ip6k2|76500|inositol hexaphosphate kinase 2	NM_029634|Ip6k2|76500|inositol hexaphosphate kinase 2	BC060059|Ip6k2|76500|inositol hexaphosphate kinase 2
mm9_v1_chr2_+_29934214_29934285	0.753142	SOX2.p2	AK142988|Pkn3|263803|protein kinase N3	AK142182|Pkn3|263803|protein kinase N3	BC034126|Pkn3|263803|protein kinase N3	NM_153805|Pkn3|263803|protein kinase N3
mm9_v1_chrX_-_100678555_100678592	0.750695	SOX2.p2	L04961|Xist|213742|inactive X specific transcripts	AK002727|Xist|213742|inactive X specific transcripts
mm9_v1_chr3_+_89862664_89862687	0.750287	SOX2.p2	BC022598|4933434E20Rik|99650|RIKEN cDNA 4933434E20 gene
mm9_v1_chr3_+_33707638_33707720	0.749532	SOX2.p2	AK016428|Ttc14|67120|tetratricopeptide repeat domain 14	BC103802|Ttc14|67120|tetratricopeptide repeat domain 14
mm9_v1_chr14_+_37881214_37881259	0.748035	SOX2.p2	BC037728|Lrit2|239038|leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	AK044611|Lrit2|239038|leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	AK044383|Lrit2|239038|leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	NM_173418|Lrit2|239038|leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	BC057628|Lrit2|239038|leucine-rich repeat, immunoglobulin-like and transmembrane domains 2
mm9_v1_chr11_+_60513191_60513346	0.747672	SOX2.p2	NM_001159404|Llgl1|16897|lethal giant larvae homolog 1 (Drosophila)	NM_001159405|Llgl1|16897|lethal giant larvae homolog 1 (Drosophila)	NM_008502|Llgl1|16897|lethal giant larvae homolog 1 (Drosophila)	BC055399|Llgl1|16897|lethal giant larvae homolog 1 (Drosophila)	AK159412|Llgl1|16897|lethal giant larvae homolog 1 (Drosophila)	D16141|Llgl1|16897|lethal giant larvae homolog 1 (Drosophila)	BC050913|Llgl1|16897|lethal giant larvae homolog 1 (Drosophila)
mm9_v1_chr11_-_119948111_119948163	0.74717	SOX2.p2	D43921|Azi1|12009|5-azacytidine induced gene 1	AK133245|Azi1|12009|5-azacytidine induced gene 1	NM_009734|Azi1|12009|5-azacytidine induced gene 1
mm9_v1_chr7_-_94641859_94642021	0.746827	SOX2.p2	M26729|Tyr|22173|tyrosinase	AK148341|Tyr|22173|tyrosinase	BC079678|Tyr|22173|tyrosinase	AK148432|Tyr|22173|tyrosinase	D00440|Tyr|22173|tyrosinase	M24560|Tyr|22173|tyrosinase	NM_011661|Tyr|22173|tyrosinase	D00131|Tyr|22173|tyrosinase	AK148172|Tyr|22173|tyrosinase	AK148357|Tyr|22173|tyrosinase	AK014619|Tyr|22173|tyrosinase	AY526904|Tyr|22173|tyrosinase	X12782|Tyr|22173|tyrosinase	M20234|Tyr|22173|tyrosinase
mm9_v1_chr7_-_52124950_52125085	0.745904	SOX2.p2	BC008543|Ptov1|84113|prostate tumor over expressed gene 1
mm9_v1_chrX_+_29130521_29130581	0.745873	SOX2.p2	BC061169|Gm4836|22526|predicted gene 4836	NM_001102678|Gm10096|100039377|predicted gene 10096	NM_001109970|Gm10486|100039550|predicted gene 10486	X72697|Gm10486|100039550|predicted gene 10486	BC087930|Gm10486|100039550|predicted gene 10486	NM_001099347|Gm10230|100042175|predicted gene 10230	NM_001100610|Gm14632|100042144|predicted gene 14632	NM_001110250|Gm14819|100039585|predicted gene 14819	BC099541|Gm10488|100042109|predicted gene 10488	NM_001099325|Gm10488|100042109|predicted gene 10488	NM_001109969|Gm10058|100039240|predicted gene 10058	BC099540|Gm10486|100039550|predicted gene 10486	NM_001099919|Gm10147|100039324|predicted gene 10147
mm9_v1_chr10_-_12581443_12581532	0.74571	SOX2.p2	Y12229|Utrn|22288|utrophin	NM_011682|Utrn|22288|utrophin
mm9_v1_chr1_-_91911151_91911240	0.744637	SOX2.p2	AY057054|Asb18|208372|ankyrin repeat and SOCS box-containing 18	BC107370|Asb18|208372|ankyrin repeat and SOCS box-containing 18	BC107371|Asb18|208372|ankyrin repeat and SOCS box-containing 18	BC127152|Asb18|208372|ankyrin repeat and SOCS box-containing 18	NM_139152|Asb18|208372|ankyrin repeat and SOCS box-containing 18	BC141295|Asb18|208372|ankyrin repeat and SOCS box-containing 18	BC145621|Asb18|208372|ankyrin repeat and SOCS box-containing 18
mm9_v1_chr17_-_29052264_29052268	0.739947	SOX2.p2	BC117930|4930539E08Rik|207819|RIKEN cDNA 4930539E08 gene	AK033585|4930539E08Rik|207819|RIKEN cDNA 4930539E08 gene	NM_172450|4930539E08Rik|207819|RIKEN cDNA 4930539E08 gene
mm9_v1_chr15_+_92427539_92427556	0.736406	SOX2.p2	NM_001164594|Pdzrn4|239618|PDZ domain containing RING finger 4	AK135524|Pdzrn4|239618|PDZ domain containing RING finger 4
mm9_v1_chrX_-_24498453_24498513	0.732738	SOX2.p2	BC099540|Gm10486|100039550|predicted gene 10486	NM_001099919|Gm10147|100039324|predicted gene 10147	BC099541|Gm10488|100042109|predicted gene 10488	NM_001109969|Gm10058|100039240|predicted gene 10058	BC087930|Gm10486|100039550|predicted gene 10486	NM_001099347|Gm10230|100042175|predicted gene 10230	NM_001100610|Gm14632|100042144|predicted gene 14632	NM_001110250|Gm14819|100039585|predicted gene 14819	X72697|Gm10486|100039550|predicted gene 10486	BC061169|Gm4836|22526|predicted gene 4836	NM_001102678|Gm10096|100039377|predicted gene 10096	NM_001109970|Gm10486|100039550|predicted gene 10486
mm9_v1_chrX_-_26904190_26904250	0.732738	SOX2.p2	BC099540|Gm10486|100039550|predicted gene 10486	NM_001099919|Gm10147|100039324|predicted gene 10147	BC099541|Gm10488|100042109|predicted gene 10488	NM_001109969|Gm10058|100039240|predicted gene 10058	BC087930|Gm10486|100039550|predicted gene 10486	NM_001099347|Gm10230|100042175|predicted gene 10230	NM_001100610|Gm14632|100042144|predicted gene 14632	NM_001110250|Gm14819|100039585|predicted gene 14819	X72697|Gm10486|100039550|predicted gene 10486	BC061169|Gm4836|22526|predicted gene 4836	NM_001102678|Gm10096|100039377|predicted gene 10096	NM_001109970|Gm10486|100039550|predicted gene 10486
mm9_v1_chr14_+_76815627_76815627	0.732082	SOX2.p2	BC058660|Tsc22d1|21807|TSC22 domain family, member 1	NM_207652|Tsc22d1|21807|TSC22 domain family, member 1
mm9_v1_chr17_-_20761835_20761840	0.729679	SOX2.p2	BC134352|Fpr-rs3|14290|formyl peptide receptor, related sequence 3	NM_008040|Fpr-rs3|14290|formyl peptide receptor, related sequence 3
mm9_v1_chr10_-_26095736_26095813	0.728915	SOX2.p2	BC082309|L3mbtl3|237339|l(3)mbt-like 3 (Drosophila)	AK031398|L3mbtl3|237339|l(3)mbt-like 3 (Drosophila)
mm9_v1_chr4_-_144028600_144028674	0.728726	SOX2.p2	BC116372|1700012P22Rik|69364|RIKEN cDNA 1700012P22 gene	BC126971|1700012P22Rik|69364|RIKEN cDNA 1700012P22 gene	AK005933|1700012P22Rik|69364|RIKEN cDNA 1700012P22 gene	BC099569|1700012P22Rik|69364|RIKEN cDNA 1700012P22 gene	NM_027056|1700012P22Rik|69364|RIKEN cDNA 1700012P22 gene
mm9_v1_chr12_-_112951127_112951165	0.727963	SOX2.p2	AK160246|Bag5|70369|BCL2-associated athanogene 5
mm9_v1_chr3_+_102862151_102862295	0.727856	SOX2.p2	X13664|Nras|18176|neuroblastoma ras oncogene	NM_010937|Nras|18176|neuroblastoma ras oncogene	AK011704|Nras|18176|neuroblastoma ras oncogene	AK165960|Nras|18176|neuroblastoma ras oncogene	AK150357|Nras|18176|neuroblastoma ras oncogene	BC058755|Nras|18176|neuroblastoma ras oncogene	BC014704|Nras|18176|neuroblastoma ras oncogene	BC051443|Nras|18176|neuroblastoma ras oncogene
mm9_v1_chrX_+_104284572_104284678	0.727817	SOX2.p2	AK038124|P2ry10|78826|purinergic receptor P2Y, G-protein coupled 10	AK041351|P2ry10|78826|purinergic receptor P2Y, G-protein coupled 10	AK088234|P2ry10|78826|purinergic receptor P2Y, G-protein coupled 10	NM_172435|P2ry10|78826|purinergic receptor P2Y, G-protein coupled 10	BC053707|P2ry10|78826|purinergic receptor P2Y, G-protein coupled 10
mm9_v1_chr3_-_68808386_68808491	0.725363	SOX2.p2	BC034101|Ift80|68259|intraflagellar transport 80 homolog (Chlamydomonas)	AK042231|Ift80|68259|intraflagellar transport 80 homolog (Chlamydomonas)	AK129339|Ift80|68259|intraflagellar transport 80 homolog (Chlamydomonas)	AK147305|Ift80|68259|intraflagellar transport 80 homolog (Chlamydomonas)	NM_026641|Ift80|68259|intraflagellar transport 80 homolog (Chlamydomonas)
mm9_v1_chr14_+_65271350_65271386	0.724575	SOX2.p2	AK019919|Kif13b|16554|kinesin family member 13B	NM_001081177|Kif13b|16554|kinesin family member 13B	AK031482|Kif13b|16554|kinesin family member 13B
mm9_v1_chrX_+_32607378_32607438	0.724129	SOX2.p2	BC061169|Gm4836|22526|predicted gene 4836	NM_001100609|Gm10487|100039467|predicted gene 10487	NM_001102678|Gm10096|100039377|predicted gene 10096	NM_001109970|Gm10486|100039550|predicted gene 10486	NM_009529|Gm4836|22526|predicted gene 4836	X72697|Gm10486|100039550|predicted gene 10486	BC087930|Gm10486|100039550|predicted gene 10486	NM_001099347|Gm10230|100042175|predicted gene 10230	NM_001100610|Gm14632|100042144|predicted gene 14632	NM_001110250|Gm14819|100039585|predicted gene 14819	BC099541|Gm10488|100042109|predicted gene 10488	NM_001099325|Gm10488|100042109|predicted gene 10488	NM_001109969|Gm10058|100039240|predicted gene 10058	BC099540|Gm10486|100039550|predicted gene 10486	NM_001099919|Gm10147|100039324|predicted gene 10147
mm9_v1_chrX_+_32944181_32944241	0.724129	SOX2.p2	BC061169|Gm4836|22526|predicted gene 4836	NM_001100609|Gm10487|100039467|predicted gene 10487	NM_001102678|Gm10096|100039377|predicted gene 10096	NM_001109970|Gm10486|100039550|predicted gene 10486	NM_009529|Gm4836|22526|predicted gene 4836	X72697|Gm10486|100039550|predicted gene 10486	BC087930|Gm10486|100039550|predicted gene 10486	NM_001099347|Gm10230|100042175|predicted gene 10230	NM_001100610|Gm14632|100042144|predicted gene 14632	NM_001110250|Gm14819|100039585|predicted gene 14819	BC099541|Gm10488|100042109|predicted gene 10488	NM_001099325|Gm10488|100042109|predicted gene 10488	NM_001109969|Gm10058|100039240|predicted gene 10058	BC099540|Gm10486|100039550|predicted gene 10486	NM_001099919|Gm10147|100039324|predicted gene 10147
mm9_v1_chrX_+_29483950_29484010	0.723786	SOX2.p2	BC061169|Gm4836|22526|predicted gene 4836	NM_001100609|Gm10487|100039467|predicted gene 10487	NM_001102678|Gm10096|100039377|predicted gene 10096	NM_001109970|Gm10486|100039550|predicted gene 10486	NM_009529|Gm4836|22526|predicted gene 4836	X72697|Gm10486|100039550|predicted gene 10486	BC087930|Gm10486|100039550|predicted gene 10486	NM_001099347|Gm10230|100042175|predicted gene 10230	NM_001100610|Gm14632|100042144|predicted gene 14632	NM_001110250|Gm14819|100039585|predicted gene 14819	BC099541|Gm10488|100042109|predicted gene 10488	NM_001099325|Gm10488|100042109|predicted gene 10488	NM_001109969|Gm10058|100039240|predicted gene 10058	BC099540|Gm10486|100039550|predicted gene 10486	NM_001099919|Gm10147|100039324|predicted gene 10147
mm9_v1_chr7_+_63305622_63305758	0.72152	SOX2.p2	AF071173|Herc2|15204|hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 2	AF061529|Herc2|15204|hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 2
mm9_v1_chr1_-_55084269_55084299	0.720935	SOX2.p2	AK012632|Sf3b1|81898|splicing factor 3b, subunit 1	BC037098|Sf3b1|81898|splicing factor 3b, subunit 1
mm9_v1_chr14_-_64147067_64147107	0.72092	SOX2.p2	AF073881|Mtmr9|210376|myotubularin related protein 9
mm9_v1_chr5_+_34974750_34974884	0.719654	SOX2.p2	
mm9_v1_chr15_+_39491073_39491119	0.719419	SOX2.p2	AK054553|Rims2|116838|regulating synaptic membrane exocytosis 2	AK032619|Rims2|116838|regulating synaptic membrane exocytosis 2
mm9_v1_chr12_+_88075318_88075318	0.719322	SOX2.p2	NM_001195767|Gm6772|627607|predicted gene 6772
mm9_v1_chrX_-_28258880_28258940	0.719056	SOX2.p2	BC099540|Gm10486|100039550|predicted gene 10486	NM_001099919|Gm10147|100039324|predicted gene 10147	BC099541|Gm10488|100042109|predicted gene 10488	NM_001099325|Gm10488|100042109|predicted gene 10488	NM_001109969|Gm10058|100039240|predicted gene 10058	BC087930|Gm10486|100039550|predicted gene 10486	NM_001099347|Gm10230|100042175|predicted gene 10230	NM_001100610|Gm14632|100042144|predicted gene 14632	NM_001110250|Gm14819|100039585|predicted gene 14819	X72697|Gm10486|100039550|predicted gene 10486	BC061169|Gm4836|22526|predicted gene 4836	NM_001100609|Gm10487|100039467|predicted gene 10487	NM_001102678|Gm10096|100039377|predicted gene 10096	NM_001109970|Gm10486|100039550|predicted gene 10486	NM_009529|Gm4836|22526|predicted gene 4836
mm9_v1_chrX_-_27251094_27251154	0.719056	SOX2.p2	BC099540|Gm10486|100039550|predicted gene 10486	NM_001099919|Gm10147|100039324|predicted gene 10147	BC099541|Gm10488|100042109|predicted gene 10488	NM_001099325|Gm10488|100042109|predicted gene 10488	NM_001109969|Gm10058|100039240|predicted gene 10058	BC087930|Gm10486|100039550|predicted gene 10486	NM_001099347|Gm10230|100042175|predicted gene 10230	NM_001100610|Gm14632|100042144|predicted gene 14632	NM_001110250|Gm14819|100039585|predicted gene 14819	X72697|Gm10486|100039550|predicted gene 10486	BC061169|Gm4836|22526|predicted gene 4836	NM_001100609|Gm10487|100039467|predicted gene 10487	NM_001102678|Gm10096|100039377|predicted gene 10096	NM_001109970|Gm10486|100039550|predicted gene 10486	NM_009529|Gm4836|22526|predicted gene 4836
mm9_v1_chr14_-_55482884_55482994	0.71858	SOX2.p2	AK129361|Homez|239099|homeodomain leucine zipper-encoding gene	AY258064|Homez|239099|homeodomain leucine zipper-encoding gene	NM_001177705|Homez|239099|homeodomain leucine zipper-encoding gene
mm9_v1_chrX_-_26822007_26822067	0.718318	SOX2.p2	BC099540|Gm10486|100039550|predicted gene 10486	NM_001099919|Gm10147|100039324|predicted gene 10147	BC099541|Gm10488|100042109|predicted gene 10488	NM_001099325|Gm10488|100042109|predicted gene 10488	NM_001109969|Gm10058|100039240|predicted gene 10058	BC087930|Gm10486|100039550|predicted gene 10486	NM_001099347|Gm10230|100042175|predicted gene 10230	NM_001100610|Gm14632|100042144|predicted gene 14632	NM_001110250|Gm14819|100039585|predicted gene 14819	X72697|Gm10486|100039550|predicted gene 10486	BC061169|Gm4836|22526|predicted gene 4836	NM_001100609|Gm10487|100039467|predicted gene 10487	NM_001102678|Gm10096|100039377|predicted gene 10096	NM_001109970|Gm10486|100039550|predicted gene 10486	NM_009529|Gm4836|22526|predicted gene 4836
mm9_v1_chrX_-_27912080_27912140	0.718318	SOX2.p2	BC099540|Gm10486|100039550|predicted gene 10486	NM_001099919|Gm10147|100039324|predicted gene 10147	BC099541|Gm10488|100042109|predicted gene 10488	NM_001099325|Gm10488|100042109|predicted gene 10488	NM_001109969|Gm10058|100039240|predicted gene 10058	BC087930|Gm10486|100039550|predicted gene 10486	NM_001099347|Gm10230|100042175|predicted gene 10230	NM_001100610|Gm14632|100042144|predicted gene 14632	NM_001110250|Gm14819|100039585|predicted gene 14819	X72697|Gm10486|100039550|predicted gene 10486	BC061169|Gm4836|22526|predicted gene 4836	NM_001100609|Gm10487|100039467|predicted gene 10487	NM_001102678|Gm10096|100039377|predicted gene 10096	NM_001109970|Gm10486|100039550|predicted gene 10486	NM_009529|Gm4836|22526|predicted gene 4836
mm9_v1_chr1_+_134088010_134088033	0.717422	SOX2.p2	AK144269|Lemd1|213409|LEM domain containing 1	NM_001033250|Lemd1|213409|LEM domain containing 1	BC115462|Lemd1|213409|LEM domain containing 1	BC115463|Lemd1|213409|LEM domain containing 1	BC066109|Lemd1|213409|LEM domain containing 1
mm9_v1_chr9_+_70390659_70390695	0.716963	SOX2.p2	AK017715|Sltm|66660|SAFB-like, transcription modulator	AF462146|Sltm|66660|SAFB-like, transcription modulator	NM_025690|Sltm|66660|SAFB-like, transcription modulator	BC139202|Sltm|66660|SAFB-like, transcription modulator	BC145577|Sltm|66660|SAFB-like, transcription modulator
mm9_v1_chrX_+_20259602_20259729	0.716036	SOX2.p2	AK189333|Uba1|22201|ubiquitin-like modifier activating enzyme 1	AK219712|Uba1|22201|ubiquitin-like modifier activating enzyme 1
mm9_v1_chr4_-_154041819_154041975	0.715946	SOX2.p2	AK006772|Actrt2|73353|actin-related protein T2	BC052344|Actrt2|73353|actin-related protein T2	AK077010|Actrt2|73353|actin-related protein T2	NM_028513|Actrt2|73353|actin-related protein T2
mm9_v1_chr10_+_59569206_59569342	0.71481	SOX2.p2	AK122233|Spock2|94214|sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2
mm9_v1_chr9_+_7502336_7502360	0.712624	SOX2.p2	AK020292|Mmp10|17384|matrix metallopeptidase 10	NM_019471|Mmp10|17384|matrix metallopeptidase 10	BC130027|Mmp10|17384|matrix metallopeptidase 10	Y13185|Mmp10|17384|matrix metallopeptidase 10
mm9_v1_chrX_-_27597810_27597870	0.711681	SOX2.p2	BC099540|Gm10486|100039550|predicted gene 10486	NM_001099919|Gm10147|100039324|predicted gene 10147	BC099541|Gm10488|100042109|predicted gene 10488	NM_001109969|Gm10058|100039240|predicted gene 10058	BC087930|Gm10486|100039550|predicted gene 10486	NM_001099347|Gm10230|100042175|predicted gene 10230	NM_001100610|Gm14632|100042144|predicted gene 14632	NM_001110250|Gm14819|100039585|predicted gene 14819	X72697|Gm10486|100039550|predicted gene 10486	BC061169|Gm4836|22526|predicted gene 4836	NM_001100609|Gm10487|100039467|predicted gene 10487	NM_001102678|Gm10096|100039377|predicted gene 10096	NM_001109970|Gm10486|100039550|predicted gene 10486	NM_009529|Gm4836|22526|predicted gene 4836
mm9_v1_chrX_-_29947647_29947707	0.711681	SOX2.p2	BC099540|Gm10486|100039550|predicted gene 10486	NM_001099919|Gm10147|100039324|predicted gene 10147	BC099541|Gm10488|100042109|predicted gene 10488	NM_001109969|Gm10058|100039240|predicted gene 10058	BC087930|Gm10486|100039550|predicted gene 10486	NM_001099347|Gm10230|100042175|predicted gene 10230	NM_001100610|Gm14632|100042144|predicted gene 14632	NM_001110250|Gm14819|100039585|predicted gene 14819	X72697|Gm10486|100039550|predicted gene 10486	BC061169|Gm4836|22526|predicted gene 4836	NM_001100609|Gm10487|100039467|predicted gene 10487	NM_001102678|Gm10096|100039377|predicted gene 10096	NM_001109970|Gm10486|100039550|predicted gene 10486	NM_009529|Gm4836|22526|predicted gene 4836
mm9_v1_chr8_+_63703064_63703069	0.711052	SOX2.p2	AF030131|Sh3rf1|59009|SH3 domain containing ring finger 1
mm9_v1_chr16_-_45724720_45724763	0.708518	SOX2.p2	AK012333|Tagln3|56370|transgelin 3
mm9_v1_chrX_+_62300818_62300824	0.708261	SOX2.p2	AK006526|Ctag2|70062|cancer/testis antigen 2	NM_027302|Ctag2|70062|cancer/testis antigen 2	BC049681|Ctag2|70062|cancer/testis antigen 2
mm9_v1_chr11_-_106993235_106993235	0.708184	SOX2.p2	NM_176850|Bptf|207165|bromodomain PHD finger transcription factor
mm9_v1_chr11_-_119409041_119409133	0.707551	SOX2.p2	BC139018|Nptx1|18164|neuronal pentraxin 1	BC139020|Nptx1|18164|neuronal pentraxin 1	BC093479|Nptx1|18164|neuronal pentraxin 1	NM_008730|Nptx1|18164|neuronal pentraxin 1
mm9_v1_chr11_+_110829346_110829387	0.707528	SOX2.p2	AK078905|Kcnj16|16517|potassium inwardly-rectifying channel, subfamily J, member 16	AK128942|Kcnj16|16517|potassium inwardly-rectifying channel, subfamily J, member 16	NM_010604|Kcnj16|16517|potassium inwardly-rectifying channel, subfamily J, member 16	BC033442|Kcnj16|16517|potassium inwardly-rectifying channel, subfamily J, member 16
mm9_v1_chr17_+_18718690_18718690	0.707192	SOX2.p2	NM_001104547|Vmn2r96|433070|vomeronasal 2, receptor 96
mm9_v1_chr2_+_167802175_167802258	0.707071	SOX2.p2	AK179877|Ptpn1|19246|protein tyrosine phosphatase, non-receptor type 1
mm9_v1_chr12_+_118997623_118997625	0.705921	SOX2.p2	AK134824|Rapgef5|217944|Rap guanine nucleotide exchange factor (GEF) 5
mm9_v1_chr11_-_101646571_101646623	0.705288	SOX2.p2	AK166136|Etv4|18612|ets variant gene 4 (E1A enhancer binding protein, E1AF)	AK144590|Etv4|18612|ets variant gene 4 (E1A enhancer binding protein, E1AF)	AK144538|Etv4|18612|ets variant gene 4 (E1A enhancer binding protein, E1AF)	NM_008815|Etv4|18612|ets variant gene 4 (E1A enhancer binding protein, E1AF)
mm9_v1_chr1_-_162133574_162133640	0.704543	SOX2.p2	AK164472|Cacybp|12301|calcyclin binding protein
mm9_v1_chr15_-_98438063_98438063	0.702536	SOX2.p2	AK147516|Adcy6|11512|adenylate cyclase 6	NM_007405|Adcy6|11512|adenylate cyclase 6
mm9_v1_chr7_+_146434402_146434460	0.702321	SOX2.p2	AK160932|Pwwp2b|101631|PWWP domain containing 2B
mm9_v1_chr5_-_92512486_92512611	0.702243	SOX2.p2	AK153893|G3bp2|23881|GTPase activating protein (SH3 domain) binding protein 2	AK153221|G3bp2|23881|GTPase activating protein (SH3 domain) binding protein 2	AK151732|G3bp2|23881|GTPase activating protein (SH3 domain) binding protein 2	NM_001080794|G3bp2|23881|GTPase activating protein (SH3 domain) binding protein 2	NM_001080796|G3bp2|23881|GTPase activating protein (SH3 domain) binding protein 2	BC119806|G3bp2|23881|GTPase activating protein (SH3 domain) binding protein 2	BC122883|G3bp2|23881|GTPase activating protein (SH3 domain) binding protein 2
mm9_v1_chr13_+_76105186_76105207	0.700851	SOX2.p2	AK006554|Spata9|75571|spermatogenesis associated 9	NM_029343|Spata9|75571|spermatogenesis associated 9	AK016416|Spata9|75571|spermatogenesis associated 9	BC048558|Spata9|75571|spermatogenesis associated 9
mm9_v1_chr9_-_110782576_110782616	0.700825	SOX2.p2	AK031966|Tmie|20776|transmembrane inner ear	AF481143|Tmie|20776|transmembrane inner ear	NM_146260|Tmie|20776|transmembrane inner ear	AK030341|Tmie|20776|transmembrane inner ear
mm9_v1_chr5_-_135422795_135422804	0.696541	SOX2.p2	AK162721|Cldn4|12740|claudin 4	AK145152|Cldn4|12740|claudin 4	NM_009903|Cldn4|12740|claudin 4
mm9_v1_chr2_-_25070107_25070150	0.696232	SOX2.p2	AK029738|4933433C11Rik|74472|RIKEN cDNA 4933433C11 gene	BC132286|4933433C11Rik|74472|RIKEN cDNA 4933433C11 gene	BC138006|4933433C11Rik|74472|RIKEN cDNA 4933433C11 gene	NM_028961|4933433C11Rik|74472|RIKEN cDNA 4933433C11 gene	AK017033|4933433C11Rik|74472|RIKEN cDNA 4933433C11 gene
mm9_v1_chr5_+_88431549_88431605	0.695449	SOX2.p2	NM_011422|Smr3a|20599|submaxillary gland androgen regulated protein 3A	X71629|Smr3a|20599|submaxillary gland androgen regulated protein 3A	X71631|Smr3a|20599|submaxillary gland androgen regulated protein 3A	BC035428|Smr3a|20599|submaxillary gland androgen regulated protein 3A	BC034553|Smr3a|20599|submaxillary gland androgen regulated protein 3A	BC055857|Smr3a|20599|submaxillary gland androgen regulated protein 3A	BC031806|Smr3a|20599|submaxillary gland androgen regulated protein 3A	BC141243|Smr3a|20599|submaxillary gland androgen regulated protein 3A	BC145569|Smr3a|20599|submaxillary gland androgen regulated protein 3A	BC031921|Smr3a|20599|submaxillary gland androgen regulated protein 3A
mm9_v1_chr14_-_48188088_48188108	0.694228	SOX2.p2	AK029330|Atg14|100504663|VATG14 autophagy related 14 homolog (S. cerevisiae)	AK029967|Atg14|100504663|VATG14 autophagy related 14 homolog (S. cerevisiae)	BC090995|Atg14|100504663|VATG14 autophagy related 14 homolog (S. cerevisiae)	AK054196|Atg14|100504663|VATG14 autophagy related 14 homolog (S. cerevisiae)	NM_172599|Atg14|100504663|VATG14 autophagy related 14 homolog (S. cerevisiae)
mm9_v1_chr4_-_82666973_82667005	0.693575	SOX2.p2	BC138427|Frem1|329872|Fras1 related extracellular matrix protein 1	BC145274|Frem1|329872|Fras1 related extracellular matrix protein 1	AJ616838|Frem1|329872|Fras1 related extracellular matrix protein 1	NM_177863|Frem1|329872|Fras1 related extracellular matrix protein 1
mm9_v1_chr7_+_51206036_51206051	0.693076	SOX2.p2	BC031798|Klk1b8|16624|kallikrein 1-related peptidase b8	NM_008457|Klk1b8|16624|kallikrein 1-related peptidase b8	X03994|Klk1b8|16624|kallikrein 1-related peptidase b8
mm9_v1_chr10_-_25798407_25798455	0.692986	SOX2.p2	AK032569|Tmem200a|77220|transmembrane protein 200A	AK163932|Tmem200a|77220|transmembrane protein 200A
mm9_v1_chr11_+_72904084_72904096	0.692437	SOX2.p2	U12236|Itgae|16407|integrin alpha E, epithelial-associated	AK040983|Itgae|16407|integrin alpha E, epithelial-associated	AK154021|Itgae|16407|integrin alpha E, epithelial-associated	BC150690|Itgae|16407|integrin alpha E, epithelial-associated	DQ386608|Itgae|16407|integrin alpha E, epithelial-associated	NM_008399|Itgae|16407|integrin alpha E, epithelial-associated	NM_172944|Itgae|16407|integrin alpha E, epithelial-associated
mm9_v1_chr4_+_46485096_46485220	0.691593	SOX2.p2	
mm9_v1_chr7_+_29477867_29477867	0.690583	SOX2.p2	AK053292|Fbxo27|233040|F-box protein 27	NM_207238|Fbxo27|233040|F-box protein 27
mm9_v1_chr2_-_26092876_26092939	0.69029	SOX2.p2	AK157992|Qsox2|227638|quiescin Q6 sulfhydryl oxidase 2	AK140324|Qsox2|227638|quiescin Q6 sulfhydryl oxidase 2	AK165642|Qsox2|227638|quiescin Q6 sulfhydryl oxidase 2	BC030934|Qsox2|227638|quiescin Q6 sulfhydryl oxidase 2	NM_153559|Qsox2|227638|quiescin Q6 sulfhydryl oxidase 2
mm9_v1_chr5_-_135422730_135422775	0.690062	SOX2.p2	BC132376|Cldn4|12740|claudin 4	BC132378|Cldn4|12740|claudin 4	AB000713|Cldn4|12740|claudin 4
mm9_v1_chr2_-_39046224_39046253	0.689611	SOX2.p2	BC132485|Scai|320271|suppressor of cancer cell invasion	BC144986|Scai|320271|suppressor of cancer cell invasion	BC144987|Scai|320271|suppressor of cancer cell invasion	BC144989|Scai|320271|suppressor of cancer cell invasion	AK044772|Scai|320271|suppressor of cancer cell invasion	AK082408|Scai|320271|suppressor of cancer cell invasion	AK083280|Scai|320271|suppressor of cancer cell invasion	NM_178778|Scai|320271|suppressor of cancer cell invasion	AK163712|Scai|320271|suppressor of cancer cell invasion
mm9_v1_chr8_+_87493507_87493627	0.689401	SOX2.p2	AK005225|Prdx2|21672|peroxiredoxin 2	AK088280|Prdx2|21672|peroxiredoxin 2	AK008433|Prdx2|21672|peroxiredoxin 2	NM_011563|Prdx2|21672|peroxiredoxin 2	BC002034|Prdx2|21672|peroxiredoxin 2	AK010653|Prdx2|21672|peroxiredoxin 2	X82067|Prdx2|21672|peroxiredoxin 2	AK011963|Prdx2|21672|peroxiredoxin 2	U20611|Prdx2|21672|peroxiredoxin 2	U51679|Prdx2|21672|peroxiredoxin 2	BC081454|Prdx2|21672|peroxiredoxin 2
mm9_v1_chr7_+_63305516_63305584	0.68785	SOX2.p2	NM_010418|Herc2|15204|hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 2
mm9_v1_chr2_+_60047917_60048030	0.687336	SOX2.p2	AK034109|March7|57438|membrane-associated ring finger (C3HC4) 7	AK143177|March7|57438|membrane-associated ring finger (C3HC4) 7	AK166666|March7|57438|membrane-associated ring finger (C3HC4) 7	AK168555|March7|57438|membrane-associated ring finger (C3HC4) 7	AF155739|March7|57438|membrane-associated ring finger (C3HC4) 7	NM_020575|March7|57438|membrane-associated ring finger (C3HC4) 7	AK167246|March7|57438|membrane-associated ring finger (C3HC4) 7
mm9_v1_chr2_+_127429570_127429640	0.686769	SOX2.p2	AK047438|Mrps5|77721|mitochondrial ribosomal protein S5
mm9_v1_chr11_+_3883638_3883715	0.686757	SOX2.p2	AK007645|Gal3st1|53897|galactose-3-O-sulfotransferase 1	NM_001177703|Gal3st1|53897|galactose-3-O-sulfotransferase 1	NM_016922|Gal3st1|53897|galactose-3-O-sulfotransferase 1	BC026806|Gal3st1|53897|galactose-3-O-sulfotransferase 1
mm9_v1_chr16_+_18877129_18877328	0.686069	SOX2.p2	BC052856|Hira|15260|histone cell cycle regulation defective homolog A (S. cerevisiae)	BC060181|Hira|15260|histone cell cycle regulation defective homolog A (S. cerevisiae)
mm9_v1_chrY_-_1426317_1426356	0.685881	SOX2.p2	M24401|Zfy2|22768|zinc finger protein 2, Y linked	AK133222|Zfy2|22768|zinc finger protein 2, Y linked	NM_009571|Zfy2|22768|zinc finger protein 2, Y linked
mm9_v1_chr13_-_111070392_111070417	0.685489	SOX2.p2	AK014050|Rab3c|67295|RAB3C, member RAS oncogene family	NM_023852|Rab3c|67295|RAB3C, member RAS oncogene family
mm9_v1_chr2_-_160934743_160934810	0.684477	SOX2.p2	BC145629|Chd6|71389|chromodomain helicase DNA binding protein 6	BC150806|Chd6|71389|chromodomain helicase DNA binding protein 6	AK018129|Chd6|71389|chromodomain helicase DNA binding protein 6	AK040495|Chd6|71389|chromodomain helicase DNA binding protein 6	AK142177|Chd6|71389|chromodomain helicase DNA binding protein 6	AK086807|Chd6|71389|chromodomain helicase DNA binding protein 6	AK162083|Chd6|71389|chromodomain helicase DNA binding protein 6	NM_173368|Chd6|71389|chromodomain helicase DNA binding protein 6	AK080892|Chd6|71389|chromodomain helicase DNA binding protein 6	AK080927|Chd6|71389|chromodomain helicase DNA binding protein 6
mm9_v1_chr3_-_96729852_96729942	0.68409	SOX2.p2	GU363513|Gja8|14616|gap junction protein, alpha 8	NM_008123|Gja8|14616|gap junction protein, alpha 8	BC120513|Gja8|14616|gap junction protein, alpha 8	BC125569|Gja8|14616|gap junction protein, alpha 8	GU363514|Gja8|14616|gap junction protein, alpha 8
mm9_v1_chr8_-_119502780_119502858	0.682956	SOX2.p2	BC137750|1700030J22Rik|69528|RIKEN cDNA 1700030J22 gene	BC137751|1700030J22Rik|69528|RIKEN cDNA 1700030J22 gene	BC049630|1700030J22Rik|69528|RIKEN cDNA 1700030J22 gene	AK030075|1700030J22Rik|69528|RIKEN cDNA 1700030J22 gene	NM_027103|1700030J22Rik|69528|RIKEN cDNA 1700030J22 gene	AK006553|1700030J22Rik|69528|RIKEN cDNA 1700030J22 gene	BC100501|1700030J22Rik|69528|RIKEN cDNA 1700030J22 gene
mm9_v1_chr2_-_147011990_147012137	0.682568	SOX2.p2	AK043561|Nkx2-2|18088|NK2 transcription factor related, locus 2 (Drosophila)	BC138159|Nkx2-2|18088|NK2 transcription factor related, locus 2 (Drosophila)	BC138160|Nkx2-2|18088|NK2 transcription factor related, locus 2 (Drosophila)	U31566|Nkx2-2|18088|NK2 transcription factor related, locus 2 (Drosophila)	AK141002|Nkx2-2|18088|NK2 transcription factor related, locus 2 (Drosophila)	NM_001077632|Nkx2-2|18088|NK2 transcription factor related, locus 2 (Drosophila)	NM_010919|Nkx2-2|18088|NK2 transcription factor related, locus 2 (Drosophila)
mm9_v1_chr4_+_103292164_103292269	0.68168	SOX2.p2	BC051993|Dab1|13131|disabled homolog 1 (Drosophila)
mm9_v1_chr4_+_54960816_54960816	0.680536	SOX2.p2	NM_172867|Zfp462|242466|zinc finger protein 462
mm9_v1_chr4_+_153516477_153516537	0.680441	SOX2.p2	NM_021499|Wdr8|59002|WD repeat domain 8	AK156969|Wdr8|59002|WD repeat domain 8	AK172690|Wdr8|59002|WD repeat domain 8	AB034911|Wdr8|59002|WD repeat domain 8	AK160331|Wdr8|59002|WD repeat domain 8	AK011773|Wdr8|59002|WD repeat domain 8	BC016120|Wdr8|59002|WD repeat domain 8	AK051688|Wdr8|59002|WD repeat domain 8
mm9_v1_chrX_-_147241307_147241451	0.679077	SOX2.p2	AK179193|Maged2|80884|melanoma antigen, family D, 2
mm9_v1_chr4_+_9196439_9196508	0.678404	SOX2.p2	AK034888|Clvs1|74438|clavesin 1	AK083985|Clvs1|74438|clavesin 1	AK047462|Clvs1|74438|clavesin 1	AK083810|Clvs1|74438|clavesin 1	NM_028940|Clvs1|74438|clavesin 1	AK084350|Clvs1|74438|clavesin 1	AK043072|Clvs1|74438|clavesin 1	AK032549|Clvs1|74438|clavesin 1	BC062923|Clvs1|74438|clavesin 1
mm9_v1_chrX_+_150916544_150916544	0.678118	SOX2.p2	AK016025|4930542N07Rik|75185|RIKEN cDNA 4930542N07 gene	NM_029199|4930542N07Rik|75185|RIKEN cDNA 4930542N07 gene
mm9_v1_chr18_+_80243633_80243827	0.67801	SOX2.p2	NM_053117|Pard6g|93737|par-6 partitioning defective 6 homolog gamma (C. elegans)	BC037678|Pard6g|93737|par-6 partitioning defective 6 homolog gamma (C. elegans)	AK035811|Pard6g|93737|par-6 partitioning defective 6 homolog gamma (C. elegans)
mm9_v1_chr18_+_35989376_35989483	0.67796	SOX2.p2	AK005364|Cxxc5|67393|CXXC finger 5	BC089314|Cxxc5|67393|CXXC finger 5	NM_133687|Cxxc5|67393|CXXC finger 5
mm9_v1_chr4_+_130225132_130225155	0.677804	SOX2.p2	AK154059|Pum1|80912|pumilio 1 (Drosophila)
mm9_v1_chr9_-_88417710_88417730	0.676889	SOX2.p2	BC032970|Snhg5|72655|small nucleolar RNA host gene 5	AK012825|Snhg5|72655|small nucleolar RNA host gene 5
mm9_v1_chr2_-_7002344_7002370	0.676613	SOX2.p2	NM_001110229|Celf2|14007|CUGBP, Elav-like family member 2	NM_001110230|Celf2|14007|CUGBP, Elav-like family member 2	NM_001160292|Celf2|14007|CUGBP, Elav-like family member 2	AK159996|Celf2|14007|CUGBP, Elav-like family member 2
mm9_v1_chr3_+_26536552_26536628	0.676278	SOX2.p2	AK076628|Spata16|70862|spermatogenesis associated 16	NM_027583|Spata16|70862|spermatogenesis associated 16	NM_029150|Spata16|70862|spermatogenesis associated 16	BC100443|Spata16|70862|spermatogenesis associated 16	AK015690|Spata16|70862|spermatogenesis associated 16	AK014869|Spata16|70862|spermatogenesis associated 16	BC132205|Spata16|70862|spermatogenesis associated 16	BC132539|Spata16|70862|spermatogenesis associated 16
mm9_v1_chr1_-_64167818_64167853	0.676123	SOX2.p2	AF327568|Klf7|93691|Kruppel-like factor 7 (ubiquitous)
mm9_v1_chr16_-_78576873_78576891	0.675904	SOX2.p2	AK005829|D16Ertd472e|67102|DNA segment, Chr 16, ERATO Doi 472, expressed	BC019957|D16Ertd472e|67102|DNA segment, Chr 16, ERATO Doi 472, expressed
mm9_v1_chr6_-_57929295_57929295	0.673393	SOX2.p2	NM_053238|Vmn1r25|113865|vomeronasal 1 receptor 25
mm9_v1_chr5_+_117807290_117807469	0.673378	SOX2.p2	AK080976|Wsb2|59043|WD repeat and SOCS box-containing 2	BC055100|Wsb2|59043|WD repeat and SOCS box-containing 2	NM_021539|Wsb2|59043|WD repeat and SOCS box-containing 2	AK157999|Wsb2|59043|WD repeat and SOCS box-containing 2	AF072881|Wsb2|59043|WD repeat and SOCS box-containing 2	AF033188|Wsb2|59043|WD repeat and SOCS box-containing 2
mm9_v1_chr14_-_31304341_31304341	0.671582	SOX2.p2	AJ437292|Cacna1d|12289|calcium channel, voltage-dependent, L type, alpha 1D subunit	NM_028981|Cacna1d|12289|calcium channel, voltage-dependent, L type, alpha 1D subunit
mm9_v1_chr6_-_18059054_18059060	0.670829	SOX2.p2	AF459789|Asz1|74068|ankyrin repeat, SAM and basic leucine zipper domain containing 1	AK016595|Asz1|74068|ankyrin repeat, SAM and basic leucine zipper domain containing 1	BC058859|Asz1|74068|ankyrin repeat, SAM and basic leucine zipper domain containing 1	NM_023729|Asz1|74068|ankyrin repeat, SAM and basic leucine zipper domain containing 1
mm9_v1_chr11_-_106642684_106642809	0.66946	SOX2.p2	AK149022|Ddx5|13207|DEAD (Asp-Glu-Ala-Asp) box polypeptide 5
mm9_v1_chr17_-_32421025_32421067	0.668389	SOX2.p2	BC082782|Brd4|57261|bromodomain containing 4	AK147545|Brd4|57261|bromodomain containing 4	BC138835|Brd4|57261|bromodomain containing 4	BC138834|Brd4|57261|bromodomain containing 4	AF461395|Brd4|57261|bromodomain containing 4	AF461396|Brd4|57261|bromodomain containing 4	NM_020508|Brd4|57261|bromodomain containing 4	NM_198094|Brd4|57261|bromodomain containing 4
mm9_v1_chr2_+_31101302_31101442	0.667843	SOX2.p2	BC059825|Ncs1|14299|neuronal calcium sensor 1	NM_019681|Ncs1|14299|neuronal calcium sensor 1
mm9_v1_chr7_+_19425314_19425337	0.667363	SOX2.p2	AB086266|Mill2|243864|MHC I like leukocyte 2	AB086267|Mill2|243864|MHC I like leukocyte 2	NM_153760|Mill2|243864|MHC I like leukocyte 2	NM_153761|Mill2|243864|MHC I like leukocyte 2	BC137748|Mill2|243864|MHC I like leukocyte 2	BC144886|Mill2|243864|MHC I like leukocyte 2	AK137167|Mill2|243864|MHC I like leukocyte 2
mm9_v1_chr16_-_89488129_89488198	0.664879	SOX2.p2	D86423|Krtap8-1|16703|keratin associated protein 8-1	AK133727|Krtap8-1|16703|keratin associated protein 8-1	NM_010675|Krtap8-1|16703|keratin associated protein 8-1
mm9_v1_chr15_-_101524677_101524737	0.66484	SOX2.p2	BC122884|Krt6b|16688|keratin 6B	BC124556|Krt6b|16688|keratin 6B	BC119554|Krt6b|16688|keratin 6B	BC119555|Krt6b|16688|keratin 6B	BC139807|Krt6b|16688|keratin 6B	BC064470|Krt6a|16687|keratin 6A	K02108|Krt6a|16687|keratin 6A	BC080820|Krt6a|16687|keratin 6A	NM_008476|Krt6a|16687|keratin 6A	AK009394|Krt6a|16687|keratin 6A
mm9_v1_chr1_+_34636537_34636571	0.663001	SOX2.p2	NM_213727|Fam123c|211383|family with sequence similarity 123, member C	BC070435|Fam123c|211383|family with sequence similarity 123, member C
mm9_v1_chr1_+_6720153_6720223	0.661977	SOX2.p2	AK133743|St18|240690|suppression of tumorigenicity 18	BC118528|St18|240690|suppression of tumorigenicity 18	AK137440|St18|240690|suppression of tumorigenicity 18	AK141513|St18|240690|suppression of tumorigenicity 18
mm9_v1_chr11_+_29593657_29593773	0.661737	SOX2.p2	AK211699|Rtn4|68585|reticulon 4	AK218123|Rtn4|68585|reticulon 4	AY102280|Rtn4|68585|reticulon 4	NM_194051|Rtn4|68585|reticulon 4
mm9_v1_chr1_+_132697478_132697478	0.660957	SOX2.p2	AB048834|Fcamr|64435|Fc receptor, IgA, IgM, high affinity	BC110549|Fcamr|64435|Fc receptor, IgA, IgM, high affinity	BC110550|Fcamr|64435|Fc receptor, IgA, IgM, high affinity	NM_001170632|Fcamr|64435|Fc receptor, IgA, IgM, high affinity	NM_144960|Fcamr|64435|Fc receptor, IgA, IgM, high affinity
mm9_v1_chr7_+_133903186_133903314	0.66079	SOX2.p2	S58470|Mapk3|26417|mitogen-activated protein kinase 3	BC013754|Mapk3|26417|mitogen-activated protein kinase 3
mm9_v1_chr7_-_111042984_111042984	0.660781	SOX2.p2	NM_013617|Olfr64|18366|olfactory receptor 64
mm9_v1_chr16_-_96349292_96349333	0.660074	SOX2.p2	NM_008251|Hmgn1|15312|high mobility group nucleosomal binding domain 1
mm9_v1_chr12_+_73889998_73890039	0.65947	SOX2.p2	AK009105|Ppm1a|19042|protein phosphatase 1A, magnesium dependent, alpha isoform
mm9_v1_chr4_+_135842023_135842037	0.658834	SOX2.p2	AK148255|Zfp46|22704|zinc finger protein 46
mm9_v1_chr16_+_36156891_36156920	0.656929	SOX2.p2	AK050597|Stfa2l1|268885|stefin A2 like 1	NM_173869|Stfa2l1|268885|stefin A2 like 1	BC117052|Stfa2l1|268885|stefin A2 like 1	BC119354|Stfa2l1|268885|stefin A2 like 1	AY163161|Stfa2l1|268885|stefin A2 like 1
mm9_v1_chr17_+_8533573_8533603	0.65659	SOX2.p2	AK039752|Prr18|320111|proline rich region 18	NM_178774|Prr18|320111|proline rich region 18
mm9_v1_chr14_+_79851641_79851647	0.655948	SOX2.p2	AK159684|Gm5465|432879|predicted gene 5465	NM_001034882|Gm5465|432879|predicted gene 5465	AK163295|Gm5465|432879|predicted gene 5465
mm9_v1_chr9_+_105299234_105299250	0.654117	SOX2.p2	AK003146|Aste1|66595|asteroid homolog 1 (Drosophila)
mm9_v1_chr5_+_22988226_22988243	0.653489	SOX2.p2	
mm9_v1_chr3_-_116126932_116126949	0.652481	SOX2.p2	AK043956|Cdc14a|229776|CDC14 cell division cycle 14 homolog A (S. cerevisiae)	AK052560|Cdc14a|229776|CDC14 cell division cycle 14 homolog A (S. cerevisiae)	AK142294|Cdc14a|229776|CDC14 cell division cycle 14 homolog A (S. cerevisiae)	NM_001080818|Cdc14a|229776|CDC14 cell division cycle 14 homolog A (S. cerevisiae)	NM_001173553|Cdc14a|229776|CDC14 cell division cycle 14 homolog A (S. cerevisiae)
mm9_v1_chr2_+_69485227_69485311	0.65238	SOX2.p2	AK006743|Bbs5|72569|Bardet-Biedl syndrome 5 (human)	BC061031|Bbs5|72569|Bardet-Biedl syndrome 5 (human)	AK012283|Bbs5|72569|Bardet-Biedl syndrome 5 (human)	NM_028284|Bbs5|72569|Bardet-Biedl syndrome 5 (human)
mm9_v1_chr3_-_119486136_119486235	0.65183	SOX2.p2	AK207246|Ptbp2|56195|polypyrimidine tract binding protein 2	AF095718|Ptbp2|56195|polypyrimidine tract binding protein 2	BC010255|Ptbp2|56195|polypyrimidine tract binding protein 2	AK137348|Ptbp2|56195|polypyrimidine tract binding protein 2	AK050624|Ptbp2|56195|polypyrimidine tract binding protein 2	AK050650|Ptbp2|56195|polypyrimidine tract binding protein 2	AK041655|Ptbp2|56195|polypyrimidine tract binding protein 2	AK015056|Ptbp2|56195|polypyrimidine tract binding protein 2
mm9_v1_chr15_+_32107043_32107046	0.651306	SOX2.p2	BC111811|Tas2r119|57254|taste receptor, type 2, member 119	BC128079|Tas2r119|57254|taste receptor, type 2, member 119	BC152359|Tas2r119|57254|taste receptor, type 2, member 119	NM_020503|Tas2r119|57254|taste receptor, type 2, member 119	BC128078|Tas2r119|57254|taste receptor, type 2, member 119
mm9_v1_chr6_+_41488583_41488591	0.650587	SOX2.p2	
mm9_v1_chr1_-_192802869_192802928	0.650529	SOX2.p2	AK140989|Vash2|226841|vasohibin 2	NM_144879|Vash2|226841|vasohibin 2
mm9_v1_chr8_-_106816961_106817080	0.650261	SOX2.p2	AY162281|Cmtm2a|73381|CKLF-like MARVEL transmembrane domain containing 2A	AY172740|Cmtm2a|73381|CKLF-like MARVEL transmembrane domain containing 2A	AK005603|Cmtm2a|73381|CKLF-like MARVEL transmembrane domain containing 2A	AK161303|Cmtm2a|73381|CKLF-like MARVEL transmembrane domain containing 2A	BC049747|Cmtm2a|73381|CKLF-like MARVEL transmembrane domain containing 2A	AY241871|Cmtm2a|73381|CKLF-like MARVEL transmembrane domain containing 2A	AK006874|Cmtm2a|73381|CKLF-like MARVEL transmembrane domain containing 2A	NM_027022|Cmtm2a|73381|CKLF-like MARVEL transmembrane domain containing 2A
mm9_v1_chrX_+_148237785_148237953	0.650219	SOX2.p2	AK163416|Huwe1|59026|HECT, UBA and WWE domain containing 1	NM_021523|Huwe1|59026|HECT, UBA and WWE domain containing 1	AK049460|Huwe1|59026|HECT, UBA and WWE domain containing 1	DQ097265|Huwe1|59026|HECT, UBA and WWE domain containing 1	AK045183|Huwe1|59026|HECT, UBA and WWE domain containing 1	AY772010|Huwe1|59026|HECT, UBA and WWE domain containing 1	AK165140|Huwe1|59026|HECT, UBA and WWE domain containing 1	AK165648|Huwe1|59026|HECT, UBA and WWE domain containing 1	AK031374|Huwe1|59026|HECT, UBA and WWE domain containing 1
mm9_v1_chr1_+_59970358_59970454	0.646966	SOX2.p2	BC080299|Fam117b|72750|family with sequence similarity 117, member B
mm9_v1_chr5_-_31504258_31504301	0.64599	SOX2.p2	AK052459|Zfp513|101023|zinc finger protein 513
mm9_v1_chr11_-_51414445_51414449	0.645044	SOX2.p2	
mm9_v1_chr3_-_30799013_30799120	0.644734	SOX2.p2	AK050678|Phc3|241915|polyhomeotic-like 3 (Drosophila)
mm9_v1_chr12_-_77347671_77347732	0.644395	SOX2.p2	AK016434|Tex21|80384|testis expressed gene 21	AK016471|Tex21|80384|testis expressed gene 21	AB000682|Tex21|80384|testis expressed gene 21	AK016448|Tex21|80384|testis expressed gene 21	BC100432|Tex21|80384|testis expressed gene 21	NM_001159532|Tex21|80384|testis expressed gene 21	NM_019784|Tex21|80384|testis expressed gene 21
mm9_v1_chr11_-_86621074_86621127	0.641841	SOX2.p2	BC058276|Dhx40|67487|DEAH (Asp-Glu-Ala-His) box polypeptide 40	AK135592|Dhx40|67487|DEAH (Asp-Glu-Ala-His) box polypeptide 40	AK031000|Dhx40|67487|DEAH (Asp-Glu-Ala-His) box polypeptide 40	AK004610|Dhx40|67487|DEAH (Asp-Glu-Ala-His) box polypeptide 40
mm9_v1_chr9_+_109954534_109954609	0.641608	SOX2.p2	AK138416|Mtap4|17758|microtubule-associated protein 4	AK146790|Mtap4|17758|microtubule-associated protein 4	BC042645|Mtap4|17758|microtubule-associated protein 4	AK134996|Mtap4|17758|microtubule-associated protein 4
mm9_v1_chr14_-_70132309_70132386	0.641528	SOX2.p2	BC024115|Chmp7|105513|CHMP family, member 7	BC033365|Chmp7|105513|CHMP family, member 7	NM_134078|Chmp7|105513|CHMP family, member 7
mm9_v1_chrX_+_63906333_63906333	0.640588	SOX2.p2	BC111888|Slitrk2|245450|SLIT and NTRK-like family, member 2	BC112406|Slitrk2|245450|SLIT and NTRK-like family, member 2	NM_198863|Slitrk2|245450|SLIT and NTRK-like family, member 2
mm9_v1_chr2_+_112219335_112219462	0.638878	SOX2.p2	AK036861|2410042D21Rik|72425|RIKEN cDNA 2410042D21 gene	NM_024254|2410042D21Rik|72425|RIKEN cDNA 2410042D21 gene	AK168639|2410042D21Rik|72425|RIKEN cDNA 2410042D21 gene	AK049599|2410042D21Rik|72425|RIKEN cDNA 2410042D21 gene	AK151464|2410042D21Rik|72425|RIKEN cDNA 2410042D21 gene	AK010654|2410042D21Rik|72425|RIKEN cDNA 2410042D21 gene	AK152570|2410042D21Rik|72425|RIKEN cDNA 2410042D21 gene	BC003216|2410042D21Rik|72425|RIKEN cDNA 2410042D21 gene	BC012402|2410042D21Rik|72425|RIKEN cDNA 2410042D21 gene	BC080661|2410042D21Rik|72425|RIKEN cDNA 2410042D21 gene	AK162183|2410042D21Rik|72425|RIKEN cDNA 2410042D21 gene
mm9_v1_chr1_+_179374783_179374796	0.638498	SOX2.p2	BC089333|Zfp238|30928|zinc finger protein 238	NM_001012330|Zfp238|30928|zinc finger protein 238
mm9_v1_chr5_+_14514906_14514924	0.637725	SOX2.p2	NM_001110796|Pclo|26875|piccolo (presynaptic cytomatrix protein)	NM_011995|Pclo|26875|piccolo (presynaptic cytomatrix protein)	Y19185|Pclo|26875|piccolo (presynaptic cytomatrix protein)	Y19186|Pclo|26875|piccolo (presynaptic cytomatrix protein)
mm9_v1_chr11_-_102308910_102308956	0.637517	SOX2.p2	BC025575|Fam171a2|217219|family with sequence similarity 171, member A2	BC064455|Fam171a2|217219|family with sequence similarity 171, member A2
mm9_v1_chr7_-_55711614_55711711	0.637346	SOX2.p2	AK148052|Mrgprb1|233231|MAS-related GPR, member B1	AK148166|Mrgprb1|233231|MAS-related GPR, member B1	AK148388|Mrgprb1|233231|MAS-related GPR, member B1	AK148046|Mrgprb1|233231|MAS-related GPR, member B1	AK148241|Mrgprb1|233231|MAS-related GPR, member B1	AK148108|Mrgprb1|233231|MAS-related GPR, member B1	AK148322|Mrgprb1|233231|MAS-related GPR, member B1	AK148279|Mrgprb1|233231|MAS-related GPR, member B1	AK148273|Mrgprb1|233231|MAS-related GPR, member B1	AK148044|Mrgprb1|233231|MAS-related GPR, member B1	AK148253|Mrgprb1|233231|MAS-related GPR, member B1	AK148256|Mrgprb1|233231|MAS-related GPR, member B1	AK148074|Mrgprb1|233231|MAS-related GPR, member B1	AK148114|Mrgprb1|233231|MAS-related GPR, member B1	NM_205810|Mrgprb1|233231|MAS-related GPR, member B1
mm9_v1_chr18_-_7626805_7626890	0.635623	SOX2.p2	AK033081|Mpp7|75739|membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	BC049662|Mpp7|75739|membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	AK012883|Mpp7|75739|membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	AK036956|Mpp7|75739|membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	AK035303|Mpp7|75739|membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	AK050710|Mpp7|75739|membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	AK162694|Mpp7|75739|membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	AK078849|Mpp7|75739|membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	NM_001081287|Mpp7|75739|membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	NM_001161620|Mpp7|75739|membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	AK027937|Mpp7|75739|membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)
mm9_v1_chrX_-_160696001_160696124	0.63554	SOX2.p2	BC138104|Bmx|12169|BMX non-receptor tyrosine kinase	BC138105|Bmx|12169|BMX non-receptor tyrosine kinase	U88091|Bmx|12169|BMX non-receptor tyrosine kinase	AK080038|Bmx|12169|BMX non-receptor tyrosine kinase	AK040936|Bmx|12169|BMX non-receptor tyrosine kinase	NM_009759|Bmx|12169|BMX non-receptor tyrosine kinase
mm9_v1_chr19_-_7785715_7785799	0.633104	SOX2.p2	AF529221|Slc22a19|207151|solute carrier family 22 (organic anion transporter), member 19	BC021384|Slc22a19|207151|solute carrier family 22 (organic anion transporter), member 19	AK052752|Slc22a19|207151|solute carrier family 22 (organic anion transporter), member 19	AK052603|Slc22a19|207151|solute carrier family 22 (organic anion transporter), member 19	NM_144785|Slc22a19|207151|solute carrier family 22 (organic anion transporter), member 19
mm9_v1_chr7_+_104728398_104728430	0.632598	SOX2.p2	AK134242|Rsf1|233532|remodeling and spacing factor 1	NM_001081267|Rsf1|233532|remodeling and spacing factor 1	AK138087|Rsf1|233532|remodeling and spacing factor 1	AK146675|Rsf1|233532|remodeling and spacing factor 1	BC085127|Rsf1|233532|remodeling and spacing factor 1	AK146154|Rsf1|233532|remodeling and spacing factor 1	AK032853|Rsf1|233532|remodeling and spacing factor 1
mm9_v1_chr5_+_103274265_103274294	0.630679	SOX2.p2	AK002660|Arhgap24|231532|Rho GTPase activating protein 24
mm9_v1_chr19_+_8738840_8738844	0.630263	SOX2.p2	AK081248|Chrm1|12669|cholinergic receptor, muscarinic 1, CNS
mm9_v1_chr9_-_119099510_119099524	0.62975	SOX2.p2	BC100471|Slc22a14|382113|solute carrier family 22 (organic cation transporter), member 14	NM_001037749|Slc22a14|382113|solute carrier family 22 (organic cation transporter), member 14	AK133291|Slc22a14|382113|solute carrier family 22 (organic cation transporter), member 14
mm9_v1_chr3_-_102586596_102586636	0.62951	SOX2.p2	M35719|Tshb|22094|thyroid stimulating hormone, beta subunit	M35720|Tshb|22094|thyroid stimulating hormone, beta subunit	M35721|Tshb|22094|thyroid stimulating hormone, beta subunit	M35723|Tshb|22094|thyroid stimulating hormone, beta subunit	NM_001165939|Tshb|22094|thyroid stimulating hormone, beta subunit	NM_001165940|Tshb|22094|thyroid stimulating hormone, beta subunit	NM_009432|Tshb|22094|thyroid stimulating hormone, beta subunit
mm9_v1_chr13_+_34831510_34831510	0.629483	SOX2.p2	AK007247|Fam50b|108161|family with sequence similarity 50, member B	NM_138746|Fam50b|108161|family with sequence similarity 50, member B
mm9_v1_chr17_-_37761577_37761577	0.629386	SOX2.p2	NM_146632|Olfr116|258625|olfactory receptor 116
mm9_v1_chr15_+_75447114_75447188	0.629369	SOX2.p2	NM_001044718|Zfp41|22701|zinc finger protein 41	NM_011759|Zfp41|22701|zinc finger protein 41	AK030420|Zfp41|22701|zinc finger protein 41	BC053927|Zfp41|22701|zinc finger protein 41
mm9_v1_chr7_-_29185514_29185554	0.628112	SOX2.p2	AK133691|Samd4b|233033|sterile alpha motif domain containing 4B
mm9_v1_chr10_-_59682007_59682007	0.628086	SOX2.p2	NM_016803|Chst3|53374|carbohydrate (chondroitin 6/keratan) sulfotransferase 3
mm9_v1_chr12_+_78576551_78576710	0.626109	SOX2.p2	AK188352|Fut8|53618|fucosyltransferase 8	AK210295|Fut8|53618|fucosyltransferase 8	AK216622|Fut8|53618|fucosyltransferase 8
mm9_v1_chr3_+_103718042_103718073	0.625838	SOX2.p2	AB101658|Rsbn1|229675|rosbin, round spermatid basic protein 1	NM_172684|Rsbn1|229675|rosbin, round spermatid basic protein 1	BC139213|Rsbn1|229675|rosbin, round spermatid basic protein 1	BC139215|Rsbn1|229675|rosbin, round spermatid basic protein 1
mm9_v1_chr8_+_34842513_34842603	0.624665	SOX2.p2	AK088342|Gtf2e2|68153|general transcription factor II E, polypeptide 2 (beta subunit)	NM_026584|Gtf2e2|68153|general transcription factor II E, polypeptide 2 (beta subunit)	AK146803|Gtf2e2|68153|general transcription factor II E, polypeptide 2 (beta subunit)	BC020016|Gtf2e2|68153|general transcription factor II E, polypeptide 2 (beta subunit)	AK021183|Gtf2e2|68153|general transcription factor II E, polypeptide 2 (beta subunit)
mm9_v1_chr6_-_41586296_41586345	0.624148	SOX2.p2	AB037373|Trpv6|64177|transient receptor potential cation channel, subfamily V, member 6	BC016101|Trpv6|64177|transient receptor potential cation channel, subfamily V, member 6	AK077234|Trpv6|64177|transient receptor potential cation channel, subfamily V, member 6
mm9_v1_chr19_+_34996847_34996902	0.623721	SOX2.p2	AK135856|Kif20b|240641|kinesin family member 20B	NM_183046|Kif20b|240641|kinesin family member 20B	AK045067|Kif20b|240641|kinesin family member 20B	AK049225|Kif20b|240641|kinesin family member 20B	BC151061|Kif20b|240641|kinesin family member 20B	BC172148|Kif20b|240641|kinesin family member 20B	AK143629|Kif20b|240641|kinesin family member 20B
mm9_v1_chr5_-_115750940_115750978	0.622979	SOX2.p2	AK002522|Dynll1|56455|dynein light chain LC8-type 1	AK010614|Dynll1|56455|dynein light chain LC8-type 1	AK010685|Dynll1|56455|dynein light chain LC8-type 1	AK013721|Dynll1|56455|dynein light chain LC8-type 1	AK013725|Dynll1|56455|dynein light chain LC8-type 1	AK082923|Dynll1|56455|dynein light chain LC8-type 1	AK147977|Dynll1|56455|dynein light chain LC8-type 1
mm9_v1_chr6_-_137519312_137519326	0.622347	SOX2.p2	AK149683|Eps8|13860|epidermal growth factor receptor pathway substrate 8
mm9_v1_chr12_+_120084801_120084801	0.622221	SOX2.p2	AK053093|Sp8|320145|trans-acting transcription factor 8	NM_177082|Sp8|320145|trans-acting transcription factor 8
mm9_v1_chr11_-_11790403_11790410	0.622027	SOX2.p2	AK011834|Ddc|13195|dopa decarboxylase	AK149141|Ddc|13195|dopa decarboxylase	AK160769|Ddc|13195|dopa decarboxylase	NM_016672|Ddc|13195|dopa decarboxylase
mm9_v1_chr6_-_41586378_41586413	0.618924	SOX2.p2	AK085123|Trpv6|64177|transient receptor potential cation channel, subfamily V, member 6	AK168760|Trpv6|64177|transient receptor potential cation channel, subfamily V, member 6	NM_022413|Trpv6|64177|transient receptor potential cation channel, subfamily V, member 6
mm9_v1_chr6_+_103460834_103460869	0.618364	SOX2.p2	AK040765|Chl1|12661|cell adhesion molecule with homology to L1CAM	NM_007697|Chl1|12661|cell adhesion molecule with homology to L1CAM
mm9_v1_chr7_+_113957642_113957692	0.617857	SOX2.p2	AK015248|Olfr701|66786|olfactory receptor 701	AK016560|Olfr701|66786|olfactory receptor 701	NM_028910|Olfr701|66786|olfactory receptor 701	AK017036|Olfr701|66786|olfactory receptor 701
mm9_v1_chr13_+_27288527_27288540	0.616672	SOX2.p2	AF150740|Prl3c1|27372|prolactin family 3, subfamily c, member 1	AF234637|Prl3c1|27372|prolactin family 3, subfamily c, member 1	NM_013766|Prl3c1|27372|prolactin family 3, subfamily c, member 1	AB019118|Prl3c1|27372|prolactin family 3, subfamily c, member 1	BC120576|Prl3c1|27372|prolactin family 3, subfamily c, member 1	BC120578|Prl3c1|27372|prolactin family 3, subfamily c, member 1
mm9_v1_chr15_-_96529121_96529237	0.616357	SOX2.p2	AK164568|Slc38a2|67760|solute carrier family 38, member 2	AK018767|Slc38a2|67760|solute carrier family 38, member 2
mm9_v1_chr1_-_180259089_180259120	0.615131	SOX2.p2	AK049600|Hnrnpu|51810|heterogeneous nuclear ribonucleoprotein U
mm9_v1_chr15_-_99079369_99079394	0.614946	SOX2.p2	AK158611|Mcrs1|51812|microspherule protein 1
mm9_v1_chr11_-_50729643_50729683	0.614636	SOX2.p2	BC057171|Zfp2|22678|zinc finger protein 2	AK042734|Zfp2|22678|zinc finger protein 2	AK141471|Zfp2|22678|zinc finger protein 2	BC089506|Zfp2|22678|zinc finger protein 2	AK131978|Zfp2|22678|zinc finger protein 2	NM_001044697|Zfp2|22678|zinc finger protein 2	NM_001044698|Zfp2|22678|zinc finger protein 2	NM_001044699|Zfp2|22678|zinc finger protein 2	NM_001044700|Zfp2|22678|zinc finger protein 2	AK036776|Zfp2|22678|zinc finger protein 2
mm9_v1_chr11_-_103224633_103224824	0.614616	SOX2.p2	AK017636|Sh3d20|70559|SH3 domain containing 20	NM_183288|Sh3d20|70559|SH3 domain containing 20
mm9_v1_chr8_-_3625251_3625286	0.613846	SOX2.p2	M21532|Pcp2|18545|Purkinje cell protein 2 (L7)	NM_008790|Pcp2|18545|Purkinje cell protein 2 (L7)
mm9_v1_chr2_+_153171730_153171874	0.613846	SOX2.p2	AK122413|Asxl1|228790|additional sex combs like 1 (Drosophila)	NM_001039939|Asxl1|228790|additional sex combs like 1 (Drosophila)
mm9_v1_chr14_-_69273768_69273898	0.611612	SOX2.p2	BC058782|Adam28|13522|a disintegrin and metallopeptidase domain 28	AF153350|Adam28|13522|a disintegrin and metallopeptidase domain 28	AK052479|Adam28|13522|a disintegrin and metallopeptidase domain 28	AK036800|Adam28|13522|a disintegrin and metallopeptidase domain 28	AK081736|Adam28|13522|a disintegrin and metallopeptidase domain 28	AF163293|Adam28|13522|a disintegrin and metallopeptidase domain 28	AF163290|Adam28|13522|a disintegrin and metallopeptidase domain 28	AF163291|Adam28|13522|a disintegrin and metallopeptidase domain 28	AF163292|Adam28|13522|a disintegrin and metallopeptidase domain 28	NM_001048175|Adam28|13522|a disintegrin and metallopeptidase domain 28	NM_010082|Adam28|13522|a disintegrin and metallopeptidase domain 28	NM_183366|Adam28|13522|a disintegrin and metallopeptidase domain 28
mm9_v1_chr11_+_29592897_29592944	0.609698	SOX2.p2	NM_194052|Rtn4|68585|reticulon 4	NM_194053|Rtn4|68585|reticulon 4	NM_194054|Rtn4|68585|reticulon 4
mm9_v1_chr4_+_21858472_21858503	0.60937	SOX2.p2	AK144924|6230409E13Rik|76132|RIKEN cDNA 6230409E13 gene	NM_175234|6230409E13Rik|76132|RIKEN cDNA 6230409E13 gene	AK081616|6230409E13Rik|76132|RIKEN cDNA 6230409E13 gene	AK082464|6230409E13Rik|76132|RIKEN cDNA 6230409E13 gene	AK018081|6230409E13Rik|76132|RIKEN cDNA 6230409E13 gene
mm9_v1_chr1_+_136079079_136079104	0.608539	SOX2.p2	CT010283|Chi3l1|12654|chitinase 3-like 1	EU313768|Chi3l1|12654|chitinase 3-like 1
mm9_v1_chr10_-_75395207_75395224	0.608306	SOX2.p2	NM_008606|Mmp11|17385|matrix metallopeptidase 11	Z12604|Mmp11|17385|matrix metallopeptidase 11	BC052854|Mmp11|17385|matrix metallopeptidase 11	AK142169|Mmp11|17385|matrix metallopeptidase 11	AK165778|Mmp11|17385|matrix metallopeptidase 11
mm9_v1_chr15_+_91503654_91503682	0.606159	SOX2.p2	AK052591|Lrrk2|66725|leucine-rich repeat kinase 2	NM_025730|Lrrk2|66725|leucine-rich repeat kinase 2
mm9_v1_chr15_-_98762108_98762276	0.604738	SOX2.p2	AK203041|Tuba1b|22143|tubulin, alpha 1B	AK199828|Tuba1b|22143|tubulin, alpha 1B	AK194222|Tuba1b|22143|tubulin, alpha 1B	AK194839|Tuba1b|22143|tubulin, alpha 1B	AK194180|Tuba1b|22143|tubulin, alpha 1B	AK200029|Tuba1b|22143|tubulin, alpha 1B	AK197610|Tuba1b|22143|tubulin, alpha 1B	AK200084|Tuba1b|22143|tubulin, alpha 1B
mm9_v1_chr16_-_28929698_28929810	0.603861	SOX2.p2	BC085092|1600021P15Rik|239796|RIKEN cDNA 1600021P15 gene	BC068245|1600021P15Rik|239796|RIKEN cDNA 1600021P15 gene	NM_177718|1600021P15Rik|239796|RIKEN cDNA 1600021P15 gene
mm9_v1_chrX_-_70388714_70388762	0.60299	SOX2.p2	BC094343|Gm14685|574404|predicted gene 14685	NM_001025383|Gm14685|574404|predicted gene 14685
mm9_v1_chr13_+_109444370_109444370	0.602593	SOX2.p2	AF536978|Pde4d|238871|phosphodiesterase 4D, cAMP specific	NM_011056|Pde4d|238871|phosphodiesterase 4D, cAMP specific
mm9_v1_chr6_-_25639904_25639979	0.601803	SOX2.p2	NM_010338|Gpr37|14763|G protein-coupled receptor 37
mm9_v1_chr17_+_35213886_35214099	0.599866	SOX2.p2	NM_027366|Ly6g6e|70274|lymphocyte antigen 6 complex, locus G6E	AK009303|Ly6g6e|70274|lymphocyte antigen 6 complex, locus G6E	BC132420|Ly6g6e|70274|lymphocyte antigen 6 complex, locus G6E	BC138777|Ly6g6e|70274|lymphocyte antigen 6 complex, locus G6E	AJ315550|Ly6g6e|70274|lymphocyte antigen 6 complex, locus G6E	AJ315551|Ly6g6e|70274|lymphocyte antigen 6 complex, locus G6E
mm9_v1_chr17_+_3115197_3115372	0.599502	SOX2.p2	AK171078|Scaf8|106583|SR-related CTD-associated factor 8	AK050652|Scaf8|106583|SR-related CTD-associated factor 8	BC038363|Scaf8|106583|SR-related CTD-associated factor 8	AK207242|Scaf8|106583|SR-related CTD-associated factor 8	AK211575|Scaf8|106583|SR-related CTD-associated factor 8	AK213588|Scaf8|106583|SR-related CTD-associated factor 8	AK213688|Scaf8|106583|SR-related CTD-associated factor 8	AK218304|Scaf8|106583|SR-related CTD-associated factor 8	AK215751|Scaf8|106583|SR-related CTD-associated factor 8
mm9_v1_chr11_+_76015590_76015598	0.599039	SOX2.p2	AK160183|Fam57a|116972|family with sequence similarity 57, member A	AK077374|Fam57a|116972|family with sequence similarity 57, member A
mm9_v1_chr2_-_35973217_35973333	0.598784	SOX2.p2	
mm9_v1_chr7_+_114240980_114240980	0.59864	SOX2.p2	BC139721|Olfr17|18314|olfactory receptor 17	BC140168|Olfr17|18314|olfactory receptor 17	BC143142|Olfr17|18314|olfactory receptor 17	BC143195|Olfr17|18314|olfactory receptor 17	NM_020598|Olfr17|18314|olfactory receptor 17
mm9_v1_chr2_+_120802698_120802797	0.598597	SOX2.p2	AK161890|Tmem62|96957|transmembrane protein 62	BC070410|Tmem62|96957|transmembrane protein 62	NM_175285|Tmem62|96957|transmembrane protein 62
mm9_v1_chr12_-_112951379_112951467	0.598098	SOX2.p2	BC055762|Bag5|70369|BCL2-associated athanogene 5	BC023099|Bag5|70369|BCL2-associated athanogene 5	NM_027404|Bag5|70369|BCL2-associated athanogene 5	BC037642|Bag5|70369|BCL2-associated athanogene 5
mm9_v1_chr9_-_39935623_39935623	0.597757	SOX2.p2	BC138430|Olfr985|258854|olfactory receptor 985	BC138431|Olfr985|258854|olfactory receptor 985	NM_146855|Olfr985|258854|olfactory receptor 985
mm9_v1_chr18_+_11997728_11997798	0.596641	SOX2.p2	AK156273|Cables1|63955|CDK5 and Abl enzyme substrate 1	AF133208|Cables1|63955|CDK5 and Abl enzyme substrate 1	NM_001146287|Cables1|63955|CDK5 and Abl enzyme substrate 1	NM_022021|Cables1|63955|CDK5 and Abl enzyme substrate 1	BC145142|Cables1|63955|CDK5 and Abl enzyme substrate 1	BC150714|Cables1|63955|CDK5 and Abl enzyme substrate 1
mm9_v1_chr18_+_34784277_34784277	0.595766	SOX2.p2	NM_001166407|Kif20a|19348|kinesin family member 20A
mm9_v1_chr10_+_111520409_111520427	0.595585	SOX2.p2	AK014846|Glipr1l2|67537|GLI pathogenesis-related 1 like 2	AK161292|Glipr1l2|67537|GLI pathogenesis-related 1 like 2	BC118017|Glipr1l2|67537|GLI pathogenesis-related 1 like 2	NM_026223|Glipr1l2|67537|GLI pathogenesis-related 1 like 2	AK015834|Glipr1l2|67537|GLI pathogenesis-related 1 like 2
mm9_v1_chr1_+_19198994_19199078	0.595478	SOX2.p2	AK017373|Tcfap2b|21419|transcription factor AP-2 beta	NM_009334|Tcfap2b|21419|transcription factor AP-2 beta	AK005128|Tcfap2b|21419|transcription factor AP-2 beta	AK028906|Tcfap2b|21419|transcription factor AP-2 beta	X78197|Tcfap2b|21419|transcription factor AP-2 beta
mm9_v1_chr6_-_124861656_124861722	0.594842	SOX2.p2	BC120591|Lag3|16768|lymphocyte-activation gene 3	NM_008479|Lag3|16768|lymphocyte-activation gene 3	X98113|Lag3|16768|lymphocyte-activation gene 3
mm9_v1_chrX_+_98877684_98877720	0.594837	SOX2.p2	AK041765|Ogt|108155|O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)
mm9_v1_chr1_+_173259513_173259641	0.592563	SOX2.p2	AK134547|Dedd|21945|death effector domain-containing	AK088329|Dedd|21945|death effector domain-containing	AK157342|Dedd|21945|death effector domain-containing	AK009728|Dedd|21945|death effector domain-containing	BC054445|Dedd|21945|death effector domain-containing
mm9_v1_chr18_+_37915375_37915594	0.59247	SOX2.p2	BC064675|Pcdhga11|93723|protocadherin gamma subfamily A, 11	NM_033594|Pcdhga11|93723|protocadherin gamma subfamily A, 11	BC059837|Pcdhga11|93723|protocadherin gamma subfamily A, 11	AY013794|Pcdhga11|93723|protocadherin gamma subfamily A, 11
mm9_v1_chr12_-_81537525_81537603	0.588392	SOX2.p2	BC046813|Dcaf5|320808|DDB1 and CUL4 associated factor 5	AK165096|Dcaf5|320808|DDB1 and CUL4 associated factor 5	AK137579|Dcaf5|320808|DDB1 and CUL4 associated factor 5	NM_177267|Dcaf5|320808|DDB1 and CUL4 associated factor 5
mm9_v1_chr5_-_8367951_8368174	0.588068	SOX2.p2	BC117707|Adam22|11496|a disintegrin and metallopeptidase domain 22	BC117708|Adam22|11496|a disintegrin and metallopeptidase domain 22	HM004095|Adam22|11496|a disintegrin and metallopeptidase domain 22	AB009674|Adam22|11496|a disintegrin and metallopeptidase domain 22	AK082335|Adam22|11496|a disintegrin and metallopeptidase domain 22	NM_001007220|Adam22|11496|a disintegrin and metallopeptidase domain 22	NM_001007221|Adam22|11496|a disintegrin and metallopeptidase domain 22	NM_001098225|Adam22|11496|a disintegrin and metallopeptidase domain 22	AK042962|Adam22|11496|a disintegrin and metallopeptidase domain 22
mm9_v1_chr5_+_54200903_54200980	0.58181	SOX2.p2	BC020138|Tbc1d19|67249|TBC1 domain family, member 19	AK012836|Tbc1d19|67249|TBC1 domain family, member 19	AK076128|Tbc1d19|67249|TBC1 domain family, member 19	AK177065|Tbc1d19|67249|TBC1 domain family, member 19
mm9_v1_chr6_-_124729735_124729744	0.581307	SOX2.p2	NM_013588|Lrrc23|16977|leucine rich repeat containing 23	AK015011|Lrrc23|16977|leucine rich repeat containing 23	BC049601|Lrrc23|16977|leucine rich repeat containing 23
mm9_v1_chr7_-_23014502_23014502	0.581223	SOX2.p2	NM_001166742|Vmn1r118|667259|vomeronasal 1 receptor 118	NM_001167150|Gm8453|667094|predicted gene 8453	NM_001167151|Gm4498|100043523|predicted gene 4498
mm9_v1_chr11_+_98724908_98724950	0.57999	SOX2.p2	NM_197940|Wipf2|68524|WAS/WASL interacting protein family, member 2
mm9_v1_chr2_+_74560034_74560034	0.579668	SOX2.p2	NM_010469|Hoxd4|15436|homeobox D4
mm9_v1_chrX_+_80194208_80194241	0.579529	SOX2.p2	AK052856|Dmd|13405|dystrophin, muscular dystrophy	NM_007868|Dmd|13405|dystrophin, muscular dystrophy	M68859|Dmd|13405|dystrophin, muscular dystrophy
mm9_v1_chr9_-_44817429_44817729	0.57939	SOX2.p2	EF474454|Cd3e|12501|CD3 antigen, epsilon polypeptide	GU456631|Cd3e|12501|CD3 antigen, epsilon polypeptide	BC098236|Cd3e|12501|CD3 antigen, epsilon polypeptide	BC028636|Cd3e|12501|CD3 antigen, epsilon polypeptide	BC145926|Cd3e|12501|CD3 antigen, epsilon polypeptide	BC145954|Cd3e|12501|CD3 antigen, epsilon polypeptide	J02990|Cd3e|12501|CD3 antigen, epsilon polypeptide	NM_007648|Cd3e|12501|CD3 antigen, epsilon polypeptide	AK041607|Cd3e|12501|CD3 antigen, epsilon polypeptide
mm9_v1_chr10_-_81090257_81090352	0.576822	SOX2.p2	AK013316|Sirt6|50721|sirtuin 6 (silent mating type information regulation 2, homolog) 6 (S. cerevisiae)	BC052763|Sirt6|50721|sirtuin 6 (silent mating type information regulation 2, homolog) 6 (S. cerevisiae)	NM_181586|Sirt6|50721|sirtuin 6 (silent mating type information regulation 2, homolog) 6 (S. cerevisiae)
mm9_v1_chr14_+_122874598_122874609	0.576531	SOX2.p2	AK051032|Zic2|22772|zinc finger protein of the cerebellum 2	NM_009574|Zic2|22772|zinc finger protein of the cerebellum 2
mm9_v1_chr9_+_50924105_50924222	0.574033	SOX2.p2	AB050983|Btg4|56057|B-cell translocation gene 4	AK136149|Btg4|56057|B-cell translocation gene 4	AK136185|Btg4|56057|B-cell translocation gene 4	NM_019493|Btg4|56057|B-cell translocation gene 4	AK136041|Btg4|56057|B-cell translocation gene 4	AK136124|Btg4|56057|B-cell translocation gene 4	AK162122|Btg4|56057|B-cell translocation gene 4	AK163407|Btg4|56057|B-cell translocation gene 4	BC066811|Btg4|56057|B-cell translocation gene 4	AJ005120|Btg4|56057|B-cell translocation gene 4
mm9_v1_chr9_-_48772926_48773094	0.573085	SOX2.p2	AF155045|Htr3b|57014|5-hydroxytryptamine (serotonin) receptor 3B	BC046990|Htr3b|57014|5-hydroxytryptamine (serotonin) receptor 3B	AK085213|Htr3b|57014|5-hydroxytryptamine (serotonin) receptor 3B	NM_020274|Htr3b|57014|5-hydroxytryptamine (serotonin) receptor 3B
mm9_v1_chr4_+_45903174_45903208	0.572782	SOX2.p2	NM_198660|E230008N13Rik|381522|RIKEN cDNA E230008N13 gene
mm9_v1_chr13_+_43497279_43497424	0.571667	SOX2.p2	AK140839|Nol7|70078|nucleolar protein 7
mm9_v1_chr5_+_33361571_33361768	0.571626	SOX2.p2	AK077596|Ywhah|22629|tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide	AK168520|Ywhah|22629|tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide	AK169035|Ywhah|22629|tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide	AK166922|Ywhah|22629|tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide	AK169189|Ywhah|22629|tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide	BC008187|Ywhah|22629|tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide	U57311|Ywhah|22629|tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide	AK187348|Ywhah|22629|tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide	AK187410|Ywhah|22629|tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide
mm9_v1_chr5_-_122804200_122804240	0.571425	SOX2.p2	AY297460|Rad9b|231724|RAD9 homolog B (S. cerevisiae)	BC021784|Rad9b|231724|RAD9 homolog B (S. cerevisiae)	NM_144912|Rad9b|231724|RAD9 homolog B (S. cerevisiae)	AK081488|Rad9b|231724|RAD9 homolog B (S. cerevisiae)	AK157179|Rad9b|231724|RAD9 homolog B (S. cerevisiae)	AK042331|Rad9b|231724|RAD9 homolog B (S. cerevisiae)	AK136504|Rad9b|231724|RAD9 homolog B (S. cerevisiae)
mm9_v1_chr18_+_14864659_14864697	0.571228	SOX2.p2	AK010717|Psma8|73677|proteasome (prosome, macropain) subunit, alpha type, 8	NM_001163609|Psma8|73677|proteasome (prosome, macropain) subunit, alpha type, 8	BC116990|Psma8|73677|proteasome (prosome, macropain) subunit, alpha type, 8	BC116992|Psma8|73677|proteasome (prosome, macropain) subunit, alpha type, 8	BC144771|Psma8|73677|proteasome (prosome, macropain) subunit, alpha type, 8	BC144772|Psma8|73677|proteasome (prosome, macropain) subunit, alpha type, 8
mm9_v1_chr19_-_19075535_19075606	0.569826	SOX2.p2	DQ779924|Rorb|225998|RAR-related orphan receptor beta	BC024768|Rorb|225998|RAR-related orphan receptor beta	AK044421|Rorb|225998|RAR-related orphan receptor beta	BC024842|Rorb|225998|RAR-related orphan receptor beta	NM_146095|Rorb|225998|RAR-related orphan receptor beta
mm9_v1_chr6_+_89843170_89843267	0.569471	SOX2.p2	BC151088|Vmn1r44|113854|vomeronasal 1 receptor 44	BC107184|Vmn1r44|113854|vomeronasal 1 receptor 44	BC107185|Vmn1r44|113854|vomeronasal 1 receptor 44	NM_053227|Vmn1r44|113854|vomeronasal 1 receptor 44
mm9_v1_chr6_+_41797547_41797583	0.568767	SOX2.p2	AK138795|Pip|18716|prolactin induced protein	NM_008843|Pip|18716|prolactin induced protein	S73282|Pip|18716|prolactin induced protein	X02510|Pip|18716|prolactin induced protein	BC028889|Pip|18716|prolactin induced protein	AB017907|Pip|18716|prolactin induced protein	BC018264|Pip|18716|prolactin induced protein
mm9_v1_chr11_-_115560620_115560673	0.568111	SOX2.p2	D85748|Grb2|14784|growth factor receptor bound protein 2	U07617|Grb2|14784|growth factor receptor bound protein 2	AK170845|Grb2|14784|growth factor receptor bound protein 2
mm9_v1_chr17_-_40379205_40379215	0.567522	SOX2.p2	BC132536|Crisp3|11572|cysteine-rich secretory protein 3	BC132538|Crisp3|11572|cysteine-rich secretory protein 3	L05560|Crisp3|11572|cysteine-rich secretory protein 3	NM_009639|Crisp3|11572|cysteine-rich secretory protein 3	BC114345|Crisp3|11572|cysteine-rich secretory protein 3	M92850|Crisp3|11572|cysteine-rich secretory protein 3	BC022573|Crisp3|11572|cysteine-rich secretory protein 3
mm9_v1_chr4_+_45696460_45696460	0.565535	SOX2.p2	AK147771|Gm829|329839|predicted gene 829	NM_001033412|Gm829|329839|predicted gene 829
mm9_v1_chr3_+_3508029_3508207	0.565207	SOX2.p2	AK143816|Hnf4g|30942|hepatocyte nuclear factor 4, gamma	NM_013920|Hnf4g|30942|hepatocyte nuclear factor 4, gamma	AJ242626|Hnf4g|30942|hepatocyte nuclear factor 4, gamma	BC125519|Hnf4g|30942|hepatocyte nuclear factor 4, gamma
mm9_v1_chr2_+_153743965_153743965	0.562047	SOX2.p2	BC048084|Rya3|378700|antimicrobial peptide RYA3	NM_194357|Rya3|378700|antimicrobial peptide RYA3
mm9_v1_chr17_-_24278482_24278583	0.561245	SOX2.p2	AK165564|Pdpk1|18607|3-phosphoinositide dependent protein kinase 1	AF126294|Pdpk1|18607|3-phosphoinositide dependent protein kinase 1	AK149162|Pdpk1|18607|3-phosphoinositide dependent protein kinase 1	BC146001|Pdpk1|18607|3-phosphoinositide dependent protein kinase 1	BC146003|Pdpk1|18607|3-phosphoinositide dependent protein kinase 1	AF079535|Pdpk1|18607|3-phosphoinositide dependent protein kinase 1	AK149289|Pdpk1|18607|3-phosphoinositide dependent protein kinase 1	AF086625|Pdpk1|18607|3-phosphoinositide dependent protein kinase 1	AK162677|Pdpk1|18607|3-phosphoinositide dependent protein kinase 1	AK143283|Pdpk1|18607|3-phosphoinositide dependent protein kinase 1	AK147835|Pdpk1|18607|3-phosphoinositide dependent protein kinase 1	AK147149|Pdpk1|18607|3-phosphoinositide dependent protein kinase 1	NM_001080773|Pdpk1|18607|3-phosphoinositide dependent protein kinase 1	NM_011062|Pdpk1|18607|3-phosphoinositide dependent protein kinase 1
mm9_v1_chrX_-_47150892_47150921	0.560758	SOX2.p2	AK030452|Igsf1|209268|immunoglobulin superfamily, member 1	BC089474|Igsf1|209268|immunoglobulin superfamily, member 1	AY227771|Igsf1|209268|immunoglobulin superfamily, member 1	AY227772|Igsf1|209268|immunoglobulin superfamily, member 1	BC100420|Igsf1|209268|immunoglobulin superfamily, member 1	NM_177591|Igsf1|209268|immunoglobulin superfamily, member 1	NM_177915|Igsf1|209268|immunoglobulin superfamily, member 1
mm9_v1_chrX_+_70368406_70368454	0.559935	SOX2.p2	NM_001025383|Gm14685|574404|predicted gene 14685	BC094343|Gm14685|574404|predicted gene 14685
mm9_v1_chr14_-_13178341_13178378	0.558173	SOX2.p2	AK019996|Fezf2|54713|Fez family zinc finger 2	BC055718|Fezf2|54713|Fez family zinc finger 2	NM_080433|Fezf2|54713|Fez family zinc finger 2
mm9_v1_chr14_-_65881225_65881304	0.557697	SOX2.p2	BC066186|Fzd3|14365|frizzled homolog 3 (Drosophila)	BC103714|Fzd3|14365|frizzled homolog 3 (Drosophila)	AK134261|Fzd3|14365|frizzled homolog 3 (Drosophila)	AK160554|Fzd3|14365|frizzled homolog 3 (Drosophila)	BC050965|Fzd3|14365|frizzled homolog 3 (Drosophila)	NM_021458|Fzd3|14365|frizzled homolog 3 (Drosophila)
mm9_v1_chr11_+_80196766_80196898	0.557446	SOX2.p2	AK087885|Zfp207|22680|zinc finger protein 207	NM_001130169|Zfp207|22680|zinc finger protein 207	NM_001130170|Zfp207|22680|zinc finger protein 207	NM_001130171|Zfp207|22680|zinc finger protein 207	NM_011751|Zfp207|22680|zinc finger protein 207	AK140139|Zfp207|22680|zinc finger protein 207	AK146787|Zfp207|22680|zinc finger protein 207	AK159683|Zfp207|22680|zinc finger protein 207	AK033497|Zfp207|22680|zinc finger protein 207	BC003715|Zfp207|22680|zinc finger protein 207	AB013357|Zfp207|22680|zinc finger protein 207	AB032196|Zfp207|22680|zinc finger protein 207
mm9_v1_chrX_+_83289537_83289537	0.556145	SOX2.p2	AK006935|1700072E05Rik|73495|RIKEN cDNA 1700072E05 gene	NM_028554|1700072E05Rik|73495|RIKEN cDNA 1700072E05 gene
mm9_v1_chr17_-_24211852_24211965	0.555918	SOX2.p2	AK079579|Pdpk1|18607|3-phosphoinositide dependent protein kinase 1
mm9_v1_chr4_-_132383213_132383408	0.55585	SOX2.p2	AK198369|Ppp1r8|100336|protein phosphatase 1, regulatory (inhibitor) subunit 8
mm9_v1_chr5_-_93612121_93612133	0.555475	SOX2.p2	AK177612|Ccni|12453|cyclin I	AK198604|Ccni|12453|cyclin I
mm9_v1_chr9_-_57468501_57468580	0.555346	SOX2.p2	AB211986|Lman1l|235416|lectin, mannose-binding 1 like	BC020188|Lman1l|235416|lectin, mannose-binding 1 like	NM_199222|Lman1l|235416|lectin, mannose-binding 1 like
mm9_v1_chr11_+_54683756_54683778	0.555149	SOX2.p2	
mm9_v1_chr7_+_51392136_51392136	0.554513	SOX2.p2	J03877|Klk1b16|16615|kallikrein 1-related peptidase b16	NM_008454|Klk1b16|16615|kallikrein 1-related peptidase b16
mm9_v1_chr7_-_14840218_14840218	0.55435	SOX2.p2	BC147210|Sult2a6|629219|sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 6	BC172008|Sult2a6|629219|sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 6	NM_001081325|Sult2a6|629219|sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 6
mm9_v1_chr15_-_83341285_83341349	0.553557	SOX2.p2	BC010510|Ttll1|319953|tubulin tyrosine ligase-like 1	AK084005|Ttll1|319953|tubulin tyrosine ligase-like 1	AK140472|Ttll1|319953|tubulin tyrosine ligase-like 1	AK031917|Ttll1|319953|tubulin tyrosine ligase-like 1	AK168786|Ttll1|319953|tubulin tyrosine ligase-like 1	AK047046|Ttll1|319953|tubulin tyrosine ligase-like 1	AK169150|Ttll1|319953|tubulin tyrosine ligase-like 1	NM_178869|Ttll1|319953|tubulin tyrosine ligase-like 1
mm9_v1_chr7_-_74367343_74367421	0.552817	SOX2.p2	AK038598|1700112J16Rik|76628|RIKEN cDNA 1700112J16 gene
mm9_v1_chr12_+_57796625_57796715	0.551738	SOX2.p2	AK132404|Pax9|18511|paired box gene 9	NM_011041|Pax9|18511|paired box gene 9	AK034985|Pax9|18511|paired box gene 9	X84000|Pax9|18511|paired box gene 9	BC005794|Pax9|18511|paired box gene 9	BC006930|Pax9|18511|paired box gene 9
mm9_v1_chr14_-_45838944_45839057	0.551724	SOX2.p2	BC052488|Txndc16|70561|thioredoxin domain containing 16	AK017582|Txndc16|70561|thioredoxin domain containing 16	AK034025|Txndc16|70561|thioredoxin domain containing 16
mm9_v1_chr4_-_107356766_107356766	0.550836	SOX2.p2	AF542048|Dmrtb1|56296|DMRT-like family B with proline-rich C-terminal, 1	NM_019872|Dmrtb1|56296|DMRT-like family B with proline-rich C-terminal, 1
mm9_v1_chr9_-_36446186_36446186	0.550108	SOX2.p2	AK144443|A630095E13Rik|235973|RIKEN cDNA A630095E13 gene	NM_001033325|A630095E13Rik|235973|RIKEN cDNA A630095E13 gene
mm9_v1_chr16_-_36367622_36367655	0.549692	SOX2.p2	AY169235|BC117090|100038854|cDNA sequence BC1179090	BC117064|BC117090|100038854|cDNA sequence BC1179090	BC117090|BC117090|100038854|cDNA sequence BC1179090	NM_001082546|BC100530|100034684|cDNA sequence BC100530
mm9_v1_chr6_-_136870688_136870700	0.549626	SOX2.p2	BC104406|Erp27|69187|endoplasmic reticulum protein 27	BC104407|Erp27|69187|endoplasmic reticulum protein 27	AK007684|Erp27|69187|endoplasmic reticulum protein 27	AK007800|Erp27|69187|endoplasmic reticulum protein 27	AK131830|Erp27|69187|endoplasmic reticulum protein 27	NM_026983|Erp27|69187|endoplasmic reticulum protein 27
mm9_v1_chr2_-_121239527_121239527	0.548381	SOX2.p2	NM_153075|Catsper2|212670|cation channel, sperm associated 2
mm9_v1_chr12_+_73187085_73187131	0.548118	SOX2.p2	AK009884|Jkamp|104771|JNK1/MAPK8-associated membrane protein	BC002238|Jkamp|104771|JNK1/MAPK8-associated membrane protein	NM_024205|Jkamp|104771|JNK1/MAPK8-associated membrane protein
mm9_v1_chrX_+_73509642_73509644	0.547728	SOX2.p2	BC048515|Gm4937|238829|predicted gene 4937	NM_001013760|Gm4937|238829|predicted gene 4937
mm9_v1_chr10_+_122701051_122701245	0.547051	SOX2.p2	AK139403|Fam19a2|268354|family with sequence similarity 19, member A2	NM_182807|Fam19a2|268354|family with sequence similarity 19, member A2	AK140763|Fam19a2|268354|family with sequence similarity 19, member A2	BC027082|Fam19a2|268354|family with sequence similarity 19, member A2
mm9_v1_chr3_-_153573930_153573930	0.546979	SOX2.p2	NM_001163479|Rabggtb|19352|RAB geranylgeranyl transferase, b subunit
mm9_v1_chr2_+_164158497_164158520	0.54689	SOX2.p2	AK007282|Svs5|20944|seminal vesicle secretory protein 5	BC114349|Svs5|20944|seminal vesicle secretory protein 5	NM_009301|Svs5|20944|seminal vesicle secretory protein 5	X63161|Svs5|20944|seminal vesicle secretory protein 5
mm9_v1_chr7_+_23840558_23840558	0.546838	SOX2.p2	NM_001166747|Vmn1r135|667404|vomeronasal 1 receptor 135	NM_001166755|Vmn1r163|667586|vomeronasal 1 receptor 163
mm9_v1_chr2_-_6642489_6642726	0.546478	SOX2.p2	AK137555|Celf2|14007|CUGBP, Elav-like family member 2	AK151818|Celf2|14007|CUGBP, Elav-like family member 2	AK152628|Celf2|14007|CUGBP, Elav-like family member 2	AK153267|Celf2|14007|CUGBP, Elav-like family member 2	AK162651|Celf2|14007|CUGBP, Elav-like family member 2	AK172648|Celf2|14007|CUGBP, Elav-like family member 2	AK169542|Celf2|14007|CUGBP, Elav-like family member 2
mm9_v1_chr15_-_36724008_36724060	0.545935	SOX2.p2	AK083368|Ywhaz|22631|tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide
mm9_v1_chr2_-_113839354_113839354	0.545773	SOX2.p2	BC058595|Gjd2|14617|gap junction protein, delta 2	NM_010290|Gjd2|14617|gap junction protein, delta 2
mm9_v1_chr4_+_94281210_94281261	0.544364	SOX2.p2	NM_026319|Ift74|67694|intraflagellar transport 74 homolog (Chlamydomonas)	BC005798|Ift74|67694|intraflagellar transport 74 homolog (Chlamydomonas)	AK014770|Ift74|67694|intraflagellar transport 74 homolog (Chlamydomonas)	AK011690|Ift74|67694|intraflagellar transport 74 homolog (Chlamydomonas)	AK053369|Ift74|67694|intraflagellar transport 74 homolog (Chlamydomonas)	BC023760|Ift74|67694|intraflagellar transport 74 homolog (Chlamydomonas)	BC049156|Ift74|67694|intraflagellar transport 74 homolog (Chlamydomonas)
mm9_v1_chr18_+_69843730_69844096	0.543373	SOX2.p2	AK021032|Tcf4|21413|transcription factor 4	AK047926|Tcf4|21413|transcription factor 4	AK045400|Tcf4|21413|transcription factor 4	AK083152|Tcf4|21413|transcription factor 4	AK039181|Tcf4|21413|transcription factor 4	AK040346|Tcf4|21413|transcription factor 4	AK032345|Tcf4|21413|transcription factor 4
mm9_v1_chr3_-_108013851_108013851	0.54055	SOX2.p2	AK046849|Atxn7l2|72522|ataxin 7-like 2	NM_175183|Atxn7l2|72522|ataxin 7-like 2
mm9_v1_chrX_+_136916509_136916509	0.539918	SOX2.p2	AK047241|Frmpd3|245643|FERM and PDZ domain containing 3	NM_177750|Frmpd3|245643|FERM and PDZ domain containing 3
mm9_v1_chr4_+_126698578_126698591	0.539526	SOX2.p2	BC080848|Sfpq|71514|splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)	BC089305|Sfpq|71514|splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
mm9_v1_chr15_-_77473707_77473715	0.537844	SOX2.p2	AY662646|Apol11b|328563|apolipoprotein L 11b	AK039744|Apol11b|328563|apolipoprotein L 11b	NM_001143686|Apol11b|328563|apolipoprotein L 11b
mm9_v1_chr11_+_4886860_4887033	0.537501	SOX2.p2	AK155892|Ap1b1|11764|adaptor protein complex AP-1, beta 1 subunit	NM_007454|Ap1b1|11764|adaptor protein complex AP-1, beta 1 subunit	AK165747|Ap1b1|11764|adaptor protein complex AP-1, beta 1 subunit	AK170376|Ap1b1|11764|adaptor protein complex AP-1, beta 1 subunit	AK159273|Ap1b1|11764|adaptor protein complex AP-1, beta 1 subunit	AK160042|Ap1b1|11764|adaptor protein complex AP-1, beta 1 subunit	Y07919|Ap1b1|11764|adaptor protein complex AP-1, beta 1 subunit	BC008513|Ap1b1|11764|adaptor protein complex AP-1, beta 1 subunit	AK180383|Ap1b1|11764|adaptor protein complex AP-1, beta 1 subunit
mm9_v1_chr14_-_56880985_56881096	0.537178	SOX2.p2	CT010272|Gzmb|14939|granzyme B	M12302|Gzmb|14939|granzyme B	AK167770|Gzmb|14939|granzyme B	AK157856|Gzmb|14939|granzyme B	BC002085|Gzmb|14939|granzyme B	NM_013542|Gzmb|14939|granzyme B	X04072|Gzmb|14939|granzyme B
mm9_v1_chr16_-_90284552_90284747	0.536893	SOX2.p2	BC053096|Scaf4|224432|SR-related CTD-associated factor 4	AK045266|Scaf4|224432|SR-related CTD-associated factor 4	BC057592|Scaf4|224432|SR-related CTD-associated factor 4	NM_178923|Scaf4|224432|SR-related CTD-associated factor 4	AK048239|Scaf4|224432|SR-related CTD-associated factor 4	AK173120|Scaf4|224432|SR-related CTD-associated factor 4
mm9_v1_chrX_+_108305756_108305756	0.536706	SOX2.p2	AK015303|Cylc1|67407|cylicin, basic protein of sperm head cytoskeleton 1	NM_026134|Cylc1|67407|cylicin, basic protein of sperm head cytoskeleton 1
mm9_v1_chr17_+_34168703_34168796	0.536561	SOX2.p2	AK159671|Rxrb|20182|retinoid X receptor beta	AK013718|Rxrb|20182|retinoid X receptor beta	BC049773|Rxrb|20182|retinoid X receptor beta	NM_011306|Rxrb|20182|retinoid X receptor beta
mm9_v1_chr7_+_73254341_73254400	0.534229	SOX2.p2	AK129255|Chsy1|269941|chondroitin sulfate synthase 1	BC128567|Chsy1|269941|chondroitin sulfate synthase 1	BC153826|Chsy1|269941|chondroitin sulfate synthase 1	BC153827|Chsy1|269941|chondroitin sulfate synthase 1	NM_001081163|Chsy1|269941|chondroitin sulfate synthase 1
mm9_v1_chr12_+_39510297_39510297	0.533692	SOX2.p2	AK032224|Etv1|14009|ets variant gene 1	NM_001163154|Etv1|14009|ets variant gene 1
mm9_v1_chr16_-_96349235_96349291	0.533426	SOX2.p2	X53476|Hmgn1|15312|high mobility group nucleosomal binding domain 1	BC088834|Hmgn1|15312|high mobility group nucleosomal binding domain 1	BC083138|Hmgn1|15312|high mobility group nucleosomal binding domain 1
mm9_v1_chr12_-_77896534_77896540	0.532616	SOX2.p2	NM_030677|Gpx2|14776|glutathione peroxidase 2
mm9_v1_chr7_-_91558407_91558432	0.531588	SOX2.p2	D63644|Arnt2|11864|aryl hydrocarbon receptor nuclear translocator 2
mm9_v1_chr4_+_102243132_102243254	0.531517	SOX2.p2	AK171700|Pde4b|18578|phosphodiesterase 4B, cAMP specific	AK150868|Pde4b|18578|phosphodiesterase 4B, cAMP specific
mm9_v1_chrX_+_51028002_51028007	0.531218	SOX2.p2	AK015678|4930502E18Rik|75013|RIKEN cDNA 4930502E18 gene	BC115663|4930502E18Rik|75013|RIKEN cDNA 4930502E18 gene	BC115664|4930502E18Rik|75013|RIKEN cDNA 4930502E18 gene	NM_029142|4930502E18Rik|75013|RIKEN cDNA 4930502E18 gene
mm9_v1_chr11_-_106992869_106992950	0.531123	SOX2.p2	BC037661|Bptf|207165|bromodomain PHD finger transcription factor	BC046973|Bptf|207165|bromodomain PHD finger transcription factor
mm9_v1_chr4_+_62280692_62280740	0.530646	SOX2.p2	AF319519|Rgs3|50780|regulator of G-protein signaling 3	NM_001081650|Rgs3|50780|regulator of G-protein signaling 3	NM_134257|Rgs3|50780|regulator of G-protein signaling 3	AK028445|Rgs3|50780|regulator of G-protein signaling 3	AF350047|Rgs3|50780|regulator of G-protein signaling 3
mm9_v1_chr2_-_121206675_121206675	0.52921	SOX2.p2	AF375593|Strc|140476|stereocilin	NM_080459|Strc|140476|stereocilin
mm9_v1_chr11_-_74491006_74491182	0.529031	SOX2.p2	AK152284|Pafah1b1|18472|platelet-activating factor acetylhydrolase, isoform 1b, subunit 1	AK164276|Pafah1b1|18472|platelet-activating factor acetylhydrolase, isoform 1b, subunit 1
mm9_v1_chr1_-_30861874_30861889	0.52897	SOX2.p2	AK086788|Phf3|213109|PHD finger protein 3
mm9_v1_chr18_+_45719464_45719553	0.528867	SOX2.p2	AK087908|Kcnn2|140492|potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	AK050390|Kcnn2|140492|potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2
mm9_v1_chr9_-_108481069_108481081	0.527868	SOX2.p2	AB041854|Wdr6|83669|WD repeat domain 6
mm9_v1_chr5_+_123093892_123094082	0.527437	SOX2.p2	AK144585|P2rx7|18439|purinergic receptor P2X, ligand-gated ion channel, 7	NM_001038839|P2rx7|18439|purinergic receptor P2X, ligand-gated ion channel, 7	NM_001038845|P2rx7|18439|purinergic receptor P2X, ligand-gated ion channel, 7	NM_001038887|P2rx7|18439|purinergic receptor P2X, ligand-gated ion channel, 7	NM_011027|P2rx7|18439|purinergic receptor P2X, ligand-gated ion channel, 7	AK171132|P2rx7|18439|purinergic receptor P2X, ligand-gated ion channel, 7	BC062808|P2rx7|18439|purinergic receptor P2X, ligand-gated ion channel, 7	BC141120|P2rx7|18439|purinergic receptor P2X, ligand-gated ion channel, 7	AK145211|P2rx7|18439|purinergic receptor P2X, ligand-gated ion channel, 7	AK145050|P2rx7|18439|purinergic receptor P2X, ligand-gated ion channel, 7	AJ009823|P2rx7|18439|purinergic receptor P2X, ligand-gated ion channel, 7	AJ489296|P2rx7|18439|purinergic receptor P2X, ligand-gated ion channel, 7	AJ489297|P2rx7|18439|purinergic receptor P2X, ligand-gated ion channel, 7	BC128303|P2rx7|18439|purinergic receptor P2X, ligand-gated ion channel, 7	BC128304|P2rx7|18439|purinergic receptor P2X, ligand-gated ion channel, 7
mm9_v1_chr3_+_75361454_75361503	0.526991	SOX2.p2	NM_009250|Serpini1|20713|serine (or cysteine) peptidase inhibitor, clade I, member 1	AK032152|Serpini1|20713|serine (or cysteine) peptidase inhibitor, clade I, member 1	AK133770|Serpini1|20713|serine (or cysteine) peptidase inhibitor, clade I, member 1	BC006776|Serpini1|20713|serine (or cysteine) peptidase inhibitor, clade I, member 1	AJ001700|Serpini1|20713|serine (or cysteine) peptidase inhibitor, clade I, member 1
mm9_v1_chr12_+_72149332_72149349	0.526684	SOX2.p2	AK149171|Arid4a|238247|AT rich interactive domain 4A (RBP1-like)
mm9_v1_chr3_+_108542575_108542575	0.52592	SOX2.p2	AK164420|Aknad1|329738|AKNA domain containing 1	NM_177859|Aknad1|329738|AKNA domain containing 1
mm9_v1_chr2_-_79296732_79296799	0.525622	SOX2.p2	BC094611|Neurod1|18012|neurogenic differentiation 1	BC018241|Neurod1|18012|neurogenic differentiation 1	AK018781|Neurod1|18012|neurogenic differentiation 1	AK005073|Neurod1|18012|neurogenic differentiation 1	NM_010894|Neurod1|18012|neurogenic differentiation 1	AK028055|Neurod1|18012|neurogenic differentiation 1
mm9_v1_chr11_+_6460185_6460185	0.525095	SOX2.p2	AK169727|Ccm2|216527|cerebral cavernous malformation 2 homolog (human)	NM_001190344|Ccm2|216527|cerebral cavernous malformation 2 homolog (human)
mm9_v1_chr10_-_44786842_44786883	0.524776	SOX2.p2	AK010182|2310075K07Rik|100125933|RIKEN cDNA 2310075K07 gene
mm9_v1_chr9_+_48910832_48910883	0.524484	SOX2.p2	AB016229|Tmprss5|80893|transmembrane protease, serine 5 (spinesin)	AB016230|Tmprss5|80893|transmembrane protease, serine 5 (spinesin)	AB041037|Tmprss5|80893|transmembrane protease, serine 5 (spinesin)	NM_030709|Tmprss5|80893|transmembrane protease, serine 5 (spinesin)
mm9_v1_chr16_+_93712194_93712253	0.524463	SOX2.p2	AK002808|Dopey2|70028|dopey family member 2
mm9_v1_chr5_+_88805132_88805132	0.524312	SOX2.p2	AK017352|Amtn|71421|amelotin	NM_027793|Amtn|71421|amelotin
mm9_v1_chr3_-_98314394_98314489	0.523959	SOX2.p2	NM_001111336|Hsd3b4|15495|hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	BC132402|Hsd3b4|15495|hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	BC013449|Hsd3b4|15495|hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	L16919|Hsd3b4|15495|hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	AK146749|Hsd3b4|15495|hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	NM_008294|Hsd3b4|15495|hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4
mm9_v1_chr10_+_82161751_82161806	0.523527	SOX2.p2	NM_001081218|Hcfc2|67933|host cell factor C2
mm9_v1_chr8_+_72426082_72426113	0.523372	SOX2.p2	BC049542|Tssk6|83984|testis-specific serine kinase 6	AF329484|Tssk6|83984|testis-specific serine kinase 6	NM_032004|Tssk6|83984|testis-specific serine kinase 6
mm9_v1_chr8_-_90483124_90483239	0.522418	SOX2.p2	BC079586|Zfp423|94187|zinc finger protein 423	BC139028|Zfp423|94187|zinc finger protein 423	BC139030|Zfp423|94187|zinc finger protein 423
mm9_v1_chr15_+_75824198_75824279	0.520752	SOX2.p2	BC048082|Mapk15|332110|mitogen-activated protein kinase 15	NM_177922|Mapk15|332110|mitogen-activated protein kinase 15
mm9_v1_chr2_-_101489613_101489698	0.52008	SOX2.p2	BC138342|Rag1|19373|recombination activating gene 1	M29475|Rag1|19373|recombination activating gene 1	AK088725|Rag1|19373|recombination activating gene 1	AK162974|Rag1|19373|recombination activating gene 1	DQ112091|B230118H07Rik|68170|RIKEN cDNA B230118H07 gene	DQ112092|B230118H07Rik|68170|RIKEN cDNA B230118H07 gene	NM_009019|Rag1|19373|recombination activating gene 1
mm9_v1_chr9_-_108480927_108481054	0.519334	SOX2.p2	BC054367|Wdr6|83669|WD repeat domain 6	AK163752|Wdr6|83669|WD repeat domain 6	AK052235|Wdr6|83669|WD repeat domain 6	AK146617|Wdr6|83669|WD repeat domain 6	AK165935|Wdr6|83669|WD repeat domain 6	AK046119|Wdr6|83669|WD repeat domain 6	AK037181|Wdr6|83669|WD repeat domain 6	AK166265|Wdr6|83669|WD repeat domain 6	AF348591|Wdr6|83669|WD repeat domain 6	BC050894|Wdr6|83669|WD repeat domain 6	NM_031392|Wdr6|83669|WD repeat domain 6	AK169357|Wdr6|83669|WD repeat domain 6
mm9_v1_chrX_+_150158113_150158178	0.519244	SOX2.p2	AK008724|2210013O21Rik|70123|RIKEN cDNA 2210013O21 gene
mm9_v1_chr3_-_146432922_146432972	0.518531	SOX2.p2	AK139419|Prkacb|18749|protein kinase, cAMP dependent, catalytic, beta
mm9_v1_chrX_-_18038399_18038522	0.517695	SOX2.p2	AK085770|4930578C19Rik|75905|RIKEN cDNA 4930578C19 gene	BC118515|4930578C19Rik|75905|RIKEN cDNA 4930578C19 gene	NM_175228|4930578C19Rik|75905|RIKEN cDNA 4930578C19 gene	AK016298|4930578C19Rik|75905|RIKEN cDNA 4930578C19 gene	AK163928|4930578C19Rik|75905|RIKEN cDNA 4930578C19 gene
mm9_v1_chr15_-_98313113_98313113	0.516585	SOX2.p2	BC006922|Lalba|16770|lactalbumin, alpha	BC069916|Lalba|16770|lactalbumin, alpha	M80909|Lalba|16770|lactalbumin, alpha	NM_010679|Lalba|16770|lactalbumin, alpha
mm9_v1_chrX_-_104598651_104598723	0.516403	SOX2.p2	AK135229|Itm2a|16431|integral membrane protein 2A	BC031420|Itm2a|16431|integral membrane protein 2A	AK051956|Itm2a|16431|integral membrane protein 2A	AK167351|Itm2a|16431|integral membrane protein 2A	L38971|Itm2a|16431|integral membrane protein 2A	NM_008409|Itm2a|16431|integral membrane protein 2A
mm9_v1_chr6_-_49213980_49214011	0.515626	SOX2.p2	AK171788|Tra2a|101214|transformer 2 alpha homolog (Drosophila)	AK172413|Tra2a|101214|transformer 2 alpha homolog (Drosophila)	BC057448|Tra2a|101214|transformer 2 alpha homolog (Drosophila)	BC058764|Tra2a|101214|transformer 2 alpha homolog (Drosophila)	AK076606|Tra2a|101214|transformer 2 alpha homolog (Drosophila)
mm9_v1_chr7_+_16487010_16487010	0.515121	SOX2.p2	AB472694|Egam-1c|100047130|Egam-1C	NM_001145190|Egam-1c|100047130|Egam-1C
mm9_v1_chr4_+_140644259_140644259	0.514432	SOX2.p2	AK077155|Spata21|329972|spermatogenesis associated 21	NM_177867|Spata21|329972|spermatogenesis associated 21
mm9_v1_chr6_-_53770687_53770818	0.513975	SOX2.p2	BC043099|Tril|66873|TLR4 interactor with leucine-rich repeats	BC059224|Tril|66873|TLR4 interactor with leucine-rich repeats	NM_025817|Tril|66873|TLR4 interactor with leucine-rich repeats
mm9_v1_chr19_+_8963366_8963411	0.51384	SOX2.p2	AK012061|1810009A15Rik|66276|RIKEN cDNA 1810009A15 gene	AK007390|1810009A15Rik|66276|RIKEN cDNA 1810009A15 gene	NM_025463|1810009A15Rik|66276|RIKEN cDNA 1810009A15 gene	BC047099|1810009A15Rik|66276|RIKEN cDNA 1810009A15 gene	BC058702|1810009A15Rik|66276|RIKEN cDNA 1810009A15 gene
mm9_v1_chr8_+_85689250_85689250	0.513771	SOX2.p2	AK049049|Tbc1d9|71310|TBC1 domain family, member 9	NM_001111304|Tbc1d9|71310|TBC1 domain family, member 9	NM_027758|Tbc1d9|71310|TBC1 domain family, member 9
mm9_v1_chr12_-_77278242_77278245	0.512378	SOX2.p2	AK054290|Esr2|13983|estrogen receptor 2 (beta)	AK054301|Esr2|13983|estrogen receptor 2 (beta)	AK054413|Esr2|13983|estrogen receptor 2 (beta)	NM_010157|Esr2|13983|estrogen receptor 2 (beta)	NM_207707|Esr2|13983|estrogen receptor 2 (beta)
mm9_v1_chr13_-_107812106_107812216	0.512073	SOX2.p2	AK037037|Kif2a|16563|kinesin family member 2A	BC006803|Kif2a|16563|kinesin family member 2A	D12644|Kif2a|16563|kinesin family member 2A	NM_001145779|Kif2a|16563|kinesin family member 2A	NM_008442|Kif2a|16563|kinesin family member 2A
mm9_v1_chr8_+_77972592_77972689	0.511872	SOX2.p2	AK005693|1700007B14Rik|71831|RIKEN cDNA 1700007B14 gene	NM_001164235|1700007B14Rik|71831|RIKEN cDNA 1700007B14 gene	NM_027944|1700007B14Rik|71831|RIKEN cDNA 1700007B14 gene	BC117767|1700007B14Rik|71831|RIKEN cDNA 1700007B14 gene	BC117768|1700007B14Rik|71831|RIKEN cDNA 1700007B14 gene
mm9_v1_chr2_-_56976258_56976330	0.511492	SOX2.p2	AB014889|Nr4a2|18227|nuclear receptor subfamily 4, group A, member 2
mm9_v1_chr3_+_17954689_17954736	0.511012	SOX2.p2	AF218865|Bhlhe22|59058|basic helix-loop-helix family, member e22
mm9_v1_chr8_+_81552335_81552485	0.510916	SOX2.p2	BC094552|Zfp827|622675|zinc finger protein 827	NM_178267|Zfp827|622675|zinc finger protein 827	BC151183|Zfp827|622675|zinc finger protein 827	AK154905|Zfp827|622675|zinc finger protein 827
mm9_v1_chr3_-_157686385_157686385	0.510594	SOX2.p2	NM_026989|Srsf11|69207|serine/arginine-rich splicing factor 11
mm9_v1_chr19_-_6532339_6532383	0.510446	SOX2.p2	AK045662|Gm14964|100008567|predicted gene 14964
mm9_v1_chr1_-_38954933_38955026	0.510356	SOX2.p2	BC056956|Chst10|98388|carbohydrate sulfotransferase 10	AK047378|Chst10|98388|carbohydrate sulfotransferase 10	NM_145142|Chst10|98388|carbohydrate sulfotransferase 10	AK050676|Chst10|98388|carbohydrate sulfotransferase 10
mm9_v1_chr11_-_120489993_120490076	0.510352	SOX2.p2	AK038934|Mafg|17134|v-maf musculoaponeurotic fibrosarcoma oncogene family, protein G (avian)	AK083165|Mafg|17134|v-maf musculoaponeurotic fibrosarcoma oncogene family, protein G (avian)
mm9_v1_chr18_+_7869164_7869355	0.510131	SOX2.p2	NM_001146298|Wac|225131|WW domain containing adaptor with coiled-coil	NM_153085|Wac|225131|WW domain containing adaptor with coiled-coil	BC080851|Wac|225131|WW domain containing adaptor with coiled-coil
mm9_v1_chr7_+_31350445_31350445	0.506829	SOX2.p2	AK154129|Tmem149|101883|transmembrane protein 149	NM_145580|Tmem149|101883|transmembrane protein 149
mm9_v1_chr11_+_16157685_16157805	0.504484	SOX2.p2	AK033048|Vstm2a|211739|V-set and transmembrane domain containing 2A	NM_145967|Vstm2a|211739|V-set and transmembrane domain containing 2A	AK032473|Vstm2a|211739|V-set and transmembrane domain containing 2A	BC027127|Vstm2a|211739|V-set and transmembrane domain containing 2A	AK079096|Vstm2a|211739|V-set and transmembrane domain containing 2A	AK137363|Vstm2a|211739|V-set and transmembrane domain containing 2A
mm9_v1_chr8_+_109867910_109868036	0.50432	SOX2.p2	
mm9_v1_chr8_-_89269823_89269841	0.504172	SOX2.p2	Z19579|Siah1a|20437|seven in absentia 1A
mm9_v1_chr11_-_72028494_72028582	0.50371	SOX2.p2	AK005655|Med31|67279|mediator of RNA polymerase II transcription, subunit 31 homolog (yeast)	AK013990|Med31|67279|mediator of RNA polymerase II transcription, subunit 31 homolog (yeast)	AK045566|Med31|67279|mediator of RNA polymerase II transcription, subunit 31 homolog (yeast)
mm9_v1_chr9_-_78215938_78216005	0.503632	SOX2.p2	BC092353|Dppa5a|434423|developmental pluripotency associated 5A	BC095979|Dppa5a|434423|developmental pluripotency associated 5A	BC092354|Dppa5a|434423|developmental pluripotency associated 5A	AF490349|Dppa5a|434423|developmental pluripotency associated 5A	AK010519|Dppa5a|434423|developmental pluripotency associated 5A	AK010584|Dppa5a|434423|developmental pluripotency associated 5A	X57708|Dppa5a|434423|developmental pluripotency associated 5A	AK145761|Dppa5a|434423|developmental pluripotency associated 5A	NM_025274|Dppa5a|434423|developmental pluripotency associated 5A
mm9_v1_chr6_+_134932018_134932018	0.503049	SOX2.p2	NM_001109914|Apold1|381823|apolipoprotein L domain containing 1
mm9_v1_chr10_-_93498488_93498564	0.502054	SOX2.p2	AK036017|Vezt|215008|vezatin, adherens junctions transmembrane protein	NM_172538|Vezt|215008|vezatin, adherens junctions transmembrane protein	AK041354|Vezt|215008|vezatin, adherens junctions transmembrane protein	AK031848|Vezt|215008|vezatin, adherens junctions transmembrane protein
mm9_v1_chr1_-_132319534_132319585	0.501678	SOX2.p2	AF143540|Daf2|13137|decay accelerating factor 2	BC115954|Daf2|13137|decay accelerating factor 2	NM_007827|Daf2|13137|decay accelerating factor 2	BC127150|Daf2|13137|decay accelerating factor 2	L41365|Daf2|13137|decay accelerating factor 2
mm9_v1_chr3_-_98367865_98367960	0.501454	SOX2.p2	NM_001111336|Hsd3b4|15495|hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	BC132402|Hsd3b4|15495|hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	BC013449|Hsd3b4|15495|hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	L16919|Hsd3b4|15495|hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	AK146749|Hsd3b4|15495|hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	NM_008294|Hsd3b4|15495|hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4
mm9_v1_chr11_-_53432145_53432166	0.501125	SOX2.p2	AB174765|Il4|16189|interleukin 4	BC027514|Il4|16189|interleukin 4	AF352783|Il4|16189|interleukin 4	M13238|Il4|16189|interleukin 4	NM_021283|Il4|16189|interleukin 4	X03532|Il4|16189|interleukin 4
mm9_v1_chr13_-_23853025_23853117	0.500555	SOX2.p2	NM_178192|Hist1h4a|326619|histone cluster 1, H4a	AK016310|Hist1h4a|326619|histone cluster 1, H4a	BC119241|Hist1h4a|326619|histone cluster 1, H4a	BC119243|Hist1h4a|326619|histone cluster 1, H4a
mm9_v1_chr6_+_57063418_57063418	0.500432	SOX2.p2	NM_053231|Vmn1r10|113858|vomeronasal 1 receptor 10
mm9_v1_chr7_-_4498168_4498168	0.49943	SOX2.p2	BC047148|Syt5|53420|synaptotagmin V	NM_016908|Syt5|53420|synaptotagmin V
mm9_v1_chr5_+_88916999_88917087	0.498985	SOX2.p2	NM_017468|Enam|13801|enamelin	U82698|Enam|13801|enamelin	BC115848|Enam|13801|enamelin
mm9_v1_chr18_+_33098694_33098843	0.497271	SOX2.p2	NM_009793|Camk4|12326|calcium/calmodulin-dependent protein kinase IV	AK030219|Camk4|12326|calcium/calmodulin-dependent protein kinase IV	BC070420|Camk4|12326|calcium/calmodulin-dependent protein kinase IV
mm9_v1_chr5_-_105568547_105568604	0.497084	SOX2.p2	AK220567|Gbp4|17472|guanylate binding protein 4	AK155365|Gbp8|76074|guanylate-binding protein 8	NM_008620|Gbp4|17472|guanylate binding protein 4	EF494423|Gbp4|17472|guanylate binding protein 4	EF494424|Gbp4|17472|guanylate binding protein 4
mm9_v1_chr2_+_74517614_74517665	0.49692	SOX2.p2	AK054090|Hoxd11|15431|homeobox D11
mm9_v1_chr5_-_113006173_113006213	0.496839	SOX2.p2	BC065117|Sez6l|56747|seizure related 6 homolog like	AK083229|Sez6l|56747|seizure related 6 homolog like	AB206790|Sez6l|56747|seizure related 6 homolog like	DQ167195|Sez6l|56747|seizure related 6 homolog like	NM_019982|Sez6l|56747|seizure related 6 homolog like
mm9_v1_chr2_+_22477837_22477846	0.495775	SOX2.p2	D42051|Gad2|14417|glutamic acid decarboxylase 2	NM_008078|Gad2|14417|glutamic acid decarboxylase 2
mm9_v1_chr5_-_123979739_123979846	0.49541	SOX2.p2	AK080345|Vps33a|77573|vacuolar protein sorting 33A (yeast)
mm9_v1_chrX_+_75110096_75110096	0.495199	SOX2.p2	NM_001085544|Gm14744|628923|predicted gene 14744
mm9_v1_chr7_+_29478162_29478199	0.495172	SOX2.p2	AK158463|Fbxo27|233040|F-box protein 27	NM_001163702|Fbxo27|233040|F-box protein 27	AK140275|Fbxo27|233040|F-box protein 27	BC075656|Fbxo27|233040|F-box protein 27
mm9_v1_chr6_+_121133684_121133684	0.494765	SOX2.p2	AK087637|Pex26|74043|peroxisomal biogenesis factor 26	NM_028730|Pex26|74043|peroxisomal biogenesis factor 26
mm9_v1_chr16_+_98218479_98218528	0.494051	SOX2.p2	AK045713|B230307C23Rik|245305|RIKEN cDNA B230307C23 gene	BC056174|B230307C23Rik|245305|RIKEN cDNA B230307C23 gene
mm9_v1_chr11_+_45869506_45869586	0.493024	SOX2.p2	D50410|Adam19|11492|a disintegrin and metallopeptidase domain 19 (meltrin beta)	AK147217|Adam19|11492|a disintegrin and metallopeptidase domain 19 (meltrin beta)	AF019887|Adam19|11492|a disintegrin and metallopeptidase domain 19 (meltrin beta)	BC115767|Adam19|11492|a disintegrin and metallopeptidase domain 19 (meltrin beta)
mm9_v1_chr10_-_93353946_93353946	0.493012	SOX2.p2	AK165301|Metap2|56307|methionine aminopeptidase 2	NM_019648|Metap2|56307|methionine aminopeptidase 2
mm9_v1_chr16_+_11405740_11405785	0.492918	SOX2.p2	AK017102|Snx29|74478|sorting nexin 29	NM_028964|Snx29|74478|sorting nexin 29	AF399755|Snx29|74478|sorting nexin 29
mm9_v1_chr16_-_18629938_18630073	0.492857	SOX2.p2	AK134700|Sept5|18951|septin 5	BC094347|Sept5|18951|septin 5	NM_213614|Sept5|18951|septin 5	BC141073|Sept5|18951|septin 5	BC145331|Sept5|18951|septin 5	BC145332|Sept5|18951|septin 5
mm9_v1_chr1_+_174886898_174886898	0.492285	SOX2.p2	BC119298|Olfr16|18313|olfactory receptor 16	BC119300|Olfr16|18313|olfactory receptor 16	NM_008763|Olfr16|18313|olfactory receptor 16
mm9_v1_chr15_+_35860580_35860704	0.491898	SOX2.p2	AK007749|Vps13b|666173|vacuolar protein sorting 13B (yeast)
mm9_v1_chr14_-_75992922_75992922	0.49173	SOX2.p2	NM_001164139|Spert|67926|spermatid associated	NM_001164140|Spert|67926|spermatid associated
mm9_v1_chr4_-_94223435_94223491	0.491124	SOX2.p2	AK046647|5830433M19Rik|67770|RIKEN cDNA 5830433M19 gene	AK076487|5830433M19Rik|67770|RIKEN cDNA 5830433M19 gene	AK013385|5830433M19Rik|67770|RIKEN cDNA 5830433M19 gene	AK032696|5830433M19Rik|67770|RIKEN cDNA 5830433M19 gene	BC020067|5830433M19Rik|67770|RIKEN cDNA 5830433M19 gene	AK150311|5830433M19Rik|67770|RIKEN cDNA 5830433M19 gene	AK140382|5830433M19Rik|67770|RIKEN cDNA 5830433M19 gene	AK171141|5830433M19Rik|67770|RIKEN cDNA 5830433M19 gene	AK160297|5830433M19Rik|67770|RIKEN cDNA 5830433M19 gene	AK160572|5830433M19Rik|67770|RIKEN cDNA 5830433M19 gene	NM_026368|5830433M19Rik|67770|RIKEN cDNA 5830433M19 gene
mm9_v1_chr5_+_34338625_34338665	0.490625	SOX2.p2	AK147307|Nat8l|269642|N-acetyltransferase 8-like	NM_001001985|Nat8l|269642|N-acetyltransferase 8-like
mm9_v1_chr17_+_7374435_7374635	0.489462	SOX2.p2	BC055331|Rps6ka2|20112|ribosomal protein S6 kinase, polypeptide 2	NM_011299|Rps6ka2|20112|ribosomal protein S6 kinase, polypeptide 2	AK044173|Rps6ka2|20112|ribosomal protein S6 kinase, polypeptide 2	BC043064|Rps6ka2|20112|ribosomal protein S6 kinase, polypeptide 2	BC056946|Rps6ka2|20112|ribosomal protein S6 kinase, polypeptide 2	BC051079|Rps6ka2|20112|ribosomal protein S6 kinase, polypeptide 2	AK019881|Rps6ka2|20112|ribosomal protein S6 kinase, polypeptide 2	AJ131021|Rps6ka2|20112|ribosomal protein S6 kinase, polypeptide 2
mm9_v1_chr19_+_12502394_12502461	0.489205	SOX2.p2	NM_019540|Pfpl|56093|pore forming protein-like	AF250839|Pfpl|56093|pore forming protein-like	BC052215|Pfpl|56093|pore forming protein-like	AK141262|Pfpl|56093|pore forming protein-like
mm9_v1_chr17_+_36131397_36131470	0.488036	SOX2.p2	AK078380|A930015D03Rik|77810|RIKEN cDNA A930015D03 gene	AK020860|A930015D03Rik|77810|RIKEN cDNA A930015D03 gene	AK142942|A930015D03Rik|77810|RIKEN cDNA A930015D03 gene	BC055918|A930015D03Rik|77810|RIKEN cDNA A930015D03 gene
mm9_v1_chr19_+_29038435_29038489	0.48667	SOX2.p2	BC052412|Ppapdc2|74411|phosphatidic acid phosphatase type 2 domain containing 2
mm9_v1_chr4_-_86204177_86204229	0.486645	SOX2.p2	AK015673|Fam154a|75811|family with sequence similarity 154, member A	NM_001081096|Fam154a|75811|family with sequence similarity 154, member A	AK076898|Fam154a|75811|family with sequence similarity 154, member A
mm9_v1_chr7_+_118172447_118172534	0.485851	SOX2.p2	NM_009431|Ctr9|22083|Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	AK040331|Ctr9|22083|Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	BC024749|Ctr9|22083|Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	AK083921|Ctr9|22083|Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	AK045101|Ctr9|22083|Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	AK040205|Ctr9|22083|Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	BC080719|Ctr9|22083|Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	BC060091|Ctr9|22083|Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	AK148536|Ctr9|22083|Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	BC010344|Ctr9|22083|Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	BC053910|Ctr9|22083|Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	L49502|Ctr9|22083|Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)
mm9_v1_chr2_+_76244578_76244594	0.485188	SOX2.p2	AK044411|Osbpl6|99031|oxysterol binding protein-like 6	NM_145525|Osbpl6|99031|oxysterol binding protein-like 6
mm9_v1_chr11_-_4999029_4999066	0.484829	SOX2.p2	AK019460|Ewsr1|14030|Ewing sarcoma breakpoint region 1	AK150345|Ewsr1|14030|Ewing sarcoma breakpoint region 1	AK147909|Ewsr1|14030|Ewing sarcoma breakpoint region 1	AK153276|Ewsr1|14030|Ewing sarcoma breakpoint region 1	AK147103|Ewsr1|14030|Ewing sarcoma breakpoint region 1	BC068226|Ewsr1|14030|Ewing sarcoma breakpoint region 1	AK151625|Ewsr1|14030|Ewing sarcoma breakpoint region 1	AK034755|Ewsr1|14030|Ewing sarcoma breakpoint region 1	AK146791|Ewsr1|14030|Ewing sarcoma breakpoint region 1
mm9_v1_chr18_+_21160434_21160595	0.483264	SOX2.p2	AK136138|Rnf138|56515|ring finger protein 138	AK004238|Rnf138|56515|ring finger protein 138	AK010486|Rnf138|56515|ring finger protein 138	BC003712|Rnf138|56515|ring finger protein 138	AK013419|Rnf138|56515|ring finger protein 138
mm9_v1_chr11_-_42134548_42134554	0.481494	SOX2.p2	AK135145|Gabra6|14399|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 6	AK137331|Gabra6|14399|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 6	NM_001099641|Gabra6|14399|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 6	NM_008068|Gabra6|14399|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 6
mm9_v1_chr11_+_83522505_83522613	0.481002	SOX2.p2	NM_007969|Expi|14038|extracellular proteinase inhibitor	BC010986|Expi|14038|extracellular proteinase inhibitor	X93037|Expi|14038|extracellular proteinase inhibitor	AK145032|Expi|14038|extracellular proteinase inhibitor
mm9_v1_chr5_-_31490075_31490203	0.480768	SOX2.p2	
mm9_v1_chrX_+_109207104_109207128	0.480765	SOX2.p2	BC132332|Tex16|83556|testis expressed gene 16	AF285573|Tex16|83556|testis expressed gene 16	NM_031382|Tex16|83556|testis expressed gene 16
mm9_v1_chr6_+_143115732_143115821	0.480745	SOX2.p2	AK051039|Etnk1|75320|ethanolamine kinase 1	AK044502|Etnk1|75320|ethanolamine kinase 1	NM_029250|Etnk1|75320|ethanolamine kinase 1	AK016135|Etnk1|75320|ethanolamine kinase 1	AK031560|Etnk1|75320|ethanolamine kinase 1	AK033268|Etnk1|75320|ethanolamine kinase 1	AK164928|Etnk1|75320|ethanolamine kinase 1
mm9_v1_chr9_-_123626642_123626742	0.480417	SOX2.p2	AK046515|Lztfl1|93730|leucine zipper transcription factor-like 1	BC037045|Lztfl1|93730|leucine zipper transcription factor-like 1	AJ297352|Lztfl1|93730|leucine zipper transcription factor-like 1	BC098224|Lztfl1|93730|leucine zipper transcription factor-like 1	BC026840|Lztfl1|93730|leucine zipper transcription factor-like 1	NM_033322|Lztfl1|93730|leucine zipper transcription factor-like 1	AK054003|Lztfl1|93730|leucine zipper transcription factor-like 1	AK157770|Lztfl1|93730|leucine zipper transcription factor-like 1	AK145263|Lztfl1|93730|leucine zipper transcription factor-like 1	AK030068|Lztfl1|93730|leucine zipper transcription factor-like 1	AK029671|Lztfl1|93730|leucine zipper transcription factor-like 1	AK041091|Lztfl1|93730|leucine zipper transcription factor-like 1	AK147312|Lztfl1|93730|leucine zipper transcription factor-like 1
mm9_v1_chr3_-_101091814_101091861	0.47934	SOX2.p2	X06143|Cd2|12481|CD2 antigen	BC053731|Cd2|12481|CD2 antigen	M18934|Cd2|12481|CD2 antigen	AK138728|Cd2|12481|CD2 antigen	AF065906|Cd2|12481|CD2 antigen	AF065907|Cd2|12481|CD2 antigen	AF065908|Cd2|12481|CD2 antigen	AF065909|Cd2|12481|CD2 antigen	AF306543|Cd2|12481|CD2 antigen	NM_013486|Cd2|12481|CD2 antigen	Y00023|Cd2|12481|CD2 antigen
mm9_v1_chr10_-_79049826_79049880	0.478007	SOX2.p2	BC061243|Theg|21830|testicular haploid expressed gene	AB033128|Theg|21830|testicular haploid expressed gene	AK017058|Theg|21830|testicular haploid expressed gene	BC050970|Theg|21830|testicular haploid expressed gene	NM_011583|Theg|21830|testicular haploid expressed gene	NM_199226|Theg|21830|testicular haploid expressed gene
mm9_v1_chr3_-_91927868_91927868	0.477821	SOX2.p2	AK079463|Prr9|109314|proline rich 9	NM_175424|Prr9|109314|proline rich 9
mm9_v1_chr7_+_22134391_22134391	0.47772	SOX2.p2	NM_001166739|Vmn1r128|667199|vomeronasal 1 receptor 128
mm9_v1_chr15_-_72929166_72929248	0.476657	SOX2.p2	AK148725|2310051F07Rik|108745|RIKEN cDNA 2310051F07 gene
mm9_v1_chr17_-_35183667_35183733	0.475514	SOX2.p2	NM_001146215|Msh5|17687|mutS homolog 5 (E. coli)	AF107352|Msh5|17687|mutS homolog 5 (E. coli)	AK042083|Msh5|17687|mutS homolog 5 (E. coli)
mm9_v1_chr6_-_145167481_145167570	0.474144	SOX2.p2	BC014700|Kras|16653|v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	BC031623|Kras|16653|v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog
mm9_v1_chr14_+_61351770_61351875	0.472696	SOX2.p2	AK151394|Spata13|219140|spermatogenesis associated 13
mm9_v1_chr11_+_22902903_22902903	0.47258	SOX2.p2	AK194972|Cct4|12464|chaperonin containing Tcp1, subunit 4 (delta)
mm9_v1_chr9_+_86910371_86910467	0.472484	SOX2.p2	AB212223|Ripply2|382089|ripply2 homolog (zebrafish)	NM_001037907|Ripply2|382089|ripply2 homolog (zebrafish)	AK081203|Ripply2|382089|ripply2 homolog (zebrafish)
mm9_v1_chr17_+_24546733_24546845	0.472397	SOX2.p2	BC038271|Abca3|27410|ATP-binding cassette, sub-family A (ABC1), member 3
mm9_v1_chr7_+_29955408_29955425	0.471977	SOX2.p2	AF538033|Ggn|243897|gametogenetin	AF538034|Ggn|243897|gametogenetin	NM_182696|Ggn|243897|gametogenetin	AF538032|Ggn|243897|gametogenetin
mm9_v1_chr4_-_82698070_82698070	0.471298	SOX2.p2	AB160986|Frem1|329872|Fras1 related extracellular matrix protein 1	NM_001198811|Frem1|329872|Fras1 related extracellular matrix protein 1
mm9_v1_chr3_-_127483385_127483450	0.471108	SOX2.p2	AK018401|Alpk1|71481|alpha-kinase 1	AK041315|Alpk1|71481|alpha-kinase 1	AK173191|Alpk1|71481|alpha-kinase 1	NM_027808|Alpk1|71481|alpha-kinase 1
mm9_v1_chr18_+_45428413_45428658	0.471081	SOX2.p2	AK076494|Kcnn2|140492|potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	AK033158|Kcnn2|140492|potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2
mm9_v1_chr9_+_20447321_20447371	0.470705	SOX2.p2	AK154036|Ubl5|66177|ubiquitin-like 5
mm9_v1_chr17_+_18107421_18107421	0.470064	SOX2.p2	NM_008042|Fpr3|14294|formyl peptide receptor 3
mm9_v1_chr7_+_22617369_22617369	0.469605	SOX2.p2	NM_001166747|Vmn1r135|667404|vomeronasal 1 receptor 135	NM_001166755|Vmn1r163|667586|vomeronasal 1 receptor 163
mm9_v1_chr6_-_28084368_28084420	0.469227	SOX2.p2	BC051384|Grm8|14823|glutamate receptor, metabotropic 8	NM_008174|Grm8|14823|glutamate receptor, metabotropic 8	AK038395|Grm8|14823|glutamate receptor, metabotropic 8
mm9_v1_chr6_-_113841295_113841343	0.468695	SOX2.p2	AK147357|Atp2b2|11941|ATPase, Ca++ transporting, plasma membrane 2
mm9_v1_chr2_-_26495749_26495770	0.468376	SOX2.p2	BC046478|Snhg7|72091|small nucleolar RNA host gene (non-protein coding) 7	AK011283|Snhg7|72091|small nucleolar RNA host gene (non-protein coding) 7	AK028166|Snhg7|72091|small nucleolar RNA host gene (non-protein coding) 7
mm9_v1_chr1_+_42752608_42752622	0.468226	SOX2.p2	
mm9_v1_chr7_-_77511242_77511282	0.467665	SOX2.p2	AK012573|Nr2f2|11819|nuclear receptor subfamily 2, group F, member 2	AK012322|Nr2f2|11819|nuclear receptor subfamily 2, group F, member 2
mm9_v1_chr18_+_62112728_62112737	0.467488	SOX2.p2	AK048066|Sh3tc2|225608|SH3 domain and tetratricopeptide repeats 2	AK143600|Sh3tc2|225608|SH3 domain and tetratricopeptide repeats 2	NM_172628|Sh3tc2|225608|SH3 domain and tetratricopeptide repeats 2	AK052534|Sh3tc2|225608|SH3 domain and tetratricopeptide repeats 2
mm9_v1_chr3_+_87973934_87974022	0.467193	SOX2.p2	AK032042|Mef2d|17261|myocyte enhancer factor 2D
mm9_v1_chr9_-_104239997_104240057	0.463621	SOX2.p2	AF210243|Acpp|56318|acid phosphatase, prostate	AK020693|Acpp|56318|acid phosphatase, prostate	AK029273|Acpp|56318|acid phosphatase, prostate	AK163330|Acpp|56318|acid phosphatase, prostate	BC139826|Acpp|56318|acid phosphatase, prostate	NM_019807|Acpp|56318|acid phosphatase, prostate	NM_207668|Acpp|56318|acid phosphatase, prostate	AK076383|Acpp|56318|acid phosphatase, prostate
mm9_v1_chr11_-_70135960_70136019	0.463586	SOX2.p2	U39200|Alox12e|11685|arachidonate lipoxygenase, epidermal	AK138743|Alox12e|11685|arachidonate lipoxygenase, epidermal	BC013751|Alox12e|11685|arachidonate lipoxygenase, epidermal	BC051047|Alox12e|11685|arachidonate lipoxygenase, epidermal	NM_145684|Alox12e|11685|arachidonate lipoxygenase, epidermal	X99252|Alox12e|11685|arachidonate lipoxygenase, epidermal
mm9_v1_chr7_-_135034440_135034483	0.463287	SOX2.p2	AK220244|Prss53|330657|protease, serine, 53	BC147509|Prss53|330657|protease, serine, 53	BC151010|Prss53|330657|protease, serine, 53	BC151017|Prss53|330657|protease, serine, 53	BC172059|Prss53|330657|protease, serine, 53	NM_001081268|Prss53|330657|protease, serine, 53
mm9_v1_chrX_+_66015013_66015108	0.461901	SOX2.p2	BC099411|Fmr1nb|207854|fragile X mental retardation 1 neighbor	NM_001166619|Fmr1nb|207854|fragile X mental retardation 1 neighbor	NM_001166620|Fmr1nb|207854|fragile X mental retardation 1 neighbor	NM_174993|Fmr1nb|207854|fragile X mental retardation 1 neighbor	BC138087|Fmr1nb|207854|fragile X mental retardation 1 neighbor	BC145139|Fmr1nb|207854|fragile X mental retardation 1 neighbor	BC145140|Fmr1nb|207854|fragile X mental retardation 1 neighbor	BC171922|Fmr1nb|207854|fragile X mental retardation 1 neighbor	BC171923|Fmr1nb|207854|fragile X mental retardation 1 neighbor	BC171947|Fmr1nb|207854|fragile X mental retardation 1 neighbor	BC171948|Fmr1nb|207854|fragile X mental retardation 1 neighbor	AK076190|Fmr1nb|207854|fragile X mental retardation 1 neighbor	AY214130|Fmr1nb|207854|fragile X mental retardation 1 neighbor
mm9_v1_chr5_-_105482574_105482592	0.461898	SOX2.p2	BC031475|Gbp8|76074|guanylate-binding protein 8	NM_029509|Gbp8|76074|guanylate-binding protein 8
mm9_v1_chr5_-_75073816_75073896	0.460886	SOX2.p2	AF034746|Lnx1|16924|ligand of numb-protein X 1	BC139771|Lnx1|16924|ligand of numb-protein X 1	AK044127|Lnx1|16924|ligand of numb-protein X 1	BC040367|Lnx1|16924|ligand of numb-protein X 1	AK161194|Lnx1|16924|ligand of numb-protein X 1	AK138326|Lnx1|16924|ligand of numb-protein X 1	NM_001159578|Lnx1|16924|ligand of numb-protein X 1	NM_001159579|Lnx1|16924|ligand of numb-protein X 1	NM_001159580|Lnx1|16924|ligand of numb-protein X 1	NM_010727|Lnx1|16924|ligand of numb-protein X 1
mm9_v1_chr11_-_79056525_79056525	0.460792	SOX2.p2	AK048511|Wsb1|78889|WD repeat and SOCS box-containing 1	NM_001042565|Wsb1|78889|WD repeat and SOCS box-containing 1
mm9_v1_chr16_+_36184297_36184316	0.459623	SOX2.p2	AK089257|Gm5483|433016|predicted gene 5483	NM_001082547|Gm5483|433016|predicted gene 5483	BC147081|Gm5483|433016|predicted gene 5483	BC147082|Gm5483|433016|predicted gene 5483
mm9_v1_chr2_+_3035692_3035956	0.459604	SOX2.p2	BC138175|Fam171a1|269233|family with sequence similarity 171, member A1	BC145171|Fam171a1|269233|family with sequence similarity 171, member A1	AK077831|Fam171a1|269233|family with sequence similarity 171, member A1
mm9_v1_chr6_+_67966702_67966735	0.458898	SOX2.p2	
mm9_v1_chr7_-_21315959_21315959	0.458176	SOX2.p2	AK139578|Gm5156|381936|predicted gene 5156	NM_001037248|Gm5156|381936|predicted gene 5156
mm9_v1_chr7_-_23504728_23504728	0.458176	SOX2.p2	AK139578|Gm5156|381936|predicted gene 5156	NM_001037248|Gm5156|381936|predicted gene 5156
mm9_v1_chr7_-_21515642_21515642	0.458176	SOX2.p2	AK139578|Gm5156|381936|predicted gene 5156	NM_001037248|Gm5156|381936|predicted gene 5156
mm9_v1_chr6_-_142456402_142456478	0.458061	SOX2.p2	X51905|Ldhb|16832|lactate dehydrogenase B	AK002257|Ldhb|16832|lactate dehydrogenase B	BC087888|Ldhb|16832|lactate dehydrogenase B	BC046755|Ldhb|16832|lactate dehydrogenase B	NM_008492|Ldhb|16832|lactate dehydrogenase B	AK131637|Ldhb|16832|lactate dehydrogenase B	AK019391|Ldhb|16832|lactate dehydrogenase B
mm9_v1_chr9_+_110747009_110747009	0.457958	SOX2.p2	AK007173|Prss46|74306|protease, serine, 46	NM_183103|Prss46|74306|protease, serine, 46
mm9_v1_chr2_+_14976877_14977152	0.457286	SOX2.p2	AK042200|Arl5b|75869|ADP-ribosylation factor-like 5B	AK040422|Arl5b|75869|ADP-ribosylation factor-like 5B	BC066810|Arl5b|75869|ADP-ribosylation factor-like 5B	AK041237|Arl5b|75869|ADP-ribosylation factor-like 5B	AK053731|Arl5b|75869|ADP-ribosylation factor-like 5B	NM_029466|Arl5b|75869|ADP-ribosylation factor-like 5B	AK164341|Arl5b|75869|ADP-ribosylation factor-like 5B	AK016359|Arl5b|75869|ADP-ribosylation factor-like 5B
mm9_v1_chr12_-_86447380_86447380	0.457202	SOX2.p2	AK051700|Prox2|73422|prospero homeobox 2	NM_175198|Prox2|73422|prospero homeobox 2
mm9_v1_chr1_+_69998194_69998221	0.457153	SOX2.p2	AK014865|Spag16|66722|sperm associated antigen 16	AK016618|Spag16|66722|sperm associated antigen 16	NM_025728|Spag16|66722|sperm associated antigen 16	AK016352|Spag16|66722|sperm associated antigen 16
mm9_v1_chr8_+_34842810_34842810	0.45628	SOX2.p2	NM_001167922|Gtf2e2|68153|general transcription factor II E, polypeptide 2 (beta subunit)
mm9_v1_chr11_-_95867076_95867257	0.455892	SOX2.p2	AF061569|Igf2bp1|140486|insulin-like growth factor 2 mRNA binding protein 1	AK044850|Igf2bp1|140486|insulin-like growth factor 2 mRNA binding protein 1	AK013940|Igf2bp1|140486|insulin-like growth factor 2 mRNA binding protein 1	BC051679|Igf2bp1|140486|insulin-like growth factor 2 mRNA binding protein 1	NM_009951|Igf2bp1|140486|insulin-like growth factor 2 mRNA binding protein 1
mm9_v1_chrX_-_70282441_70282441	0.455785	SOX2.p2	AK220432|Pnma5|385377|paraneoplastic antigen family 5	NM_001100461|Pnma5|385377|paraneoplastic antigen family 5
mm9_v1_chr7_-_149865451_149865614	0.455272	SOX2.p2	BC145554|Ins2|16334|insulin II	BC132650|Ins2|16334|insulin II	BC132652|Ins2|16334|insulin II	Z47785|Ins2|16334|insulin II	AY899305|Ins2|16334|insulin II	BC066208|Ins2|16334|insulin II	BC099934|Ins2|16334|insulin II	AK007612|Ins2|16334|insulin II	GQ915612|Ins2|16334|insulin II	NM_001185083|Ins2|16334|insulin II	NM_001185084|Ins2|16334|insulin II	NM_008387|Ins2|16334|insulin II
mm9_v1_chr10_+_67000613_67000625	0.454084	SOX2.p2	AK155585|Egr2|13654|early growth response 2	NM_010118|Egr2|13654|early growth response 2	AK153882|Egr2|13654|early growth response 2	X06746|Egr2|13654|early growth response 2
mm9_v1_chr7_+_97177668_97177676	0.453769	SOX2.p2	AK165252|E230029C05Rik|319711|RIKEN cDNA E230029C05 gene	AK157435|E230029C05Rik|319711|RIKEN cDNA E230029C05 gene	AK046045|E230029C05Rik|319711|RIKEN cDNA E230029C05 gene
mm9_v1_chr17_+_18158696_18158700	0.4535	SOX2.p2	BC115535|Fpr-rs4|14291|formyl peptide receptor, related sequence 4	NM_008041|Fpr-rs4|14291|formyl peptide receptor, related sequence 4	BC115534|Fpr-rs4|14291|formyl peptide receptor, related sequence 4
mm9_v1_chr18_+_35966147_35966251	0.453378	SOX2.p2	AK075844|Ube2d2|56550|ubiquitin-conjugating enzyme E2D 2
mm9_v1_chr11_-_106642357_106642481	0.453165	SOX2.p2	AK011169|Ddx5|13207|DEAD (Asp-Glu-Ala-Asp) box polypeptide 5
mm9_v1_chr1_-_38954763_38954854	0.452909	SOX2.p2	AF360543|Chst10|98388|carbohydrate sulfotransferase 10	AK046415|Chst10|98388|carbohydrate sulfotransferase 10	AK171758|Chst10|98388|carbohydrate sulfotransferase 10
mm9_v1_chr14_-_55272452_55272539	0.452428	SOX2.p2	AF124725|Acin1|56215|apoptotic chromatin condensation inducer 1	AF124729|Acin1|56215|apoptotic chromatin condensation inducer 1	BC019127|Acin1|56215|apoptotic chromatin condensation inducer 1	BC094217|Acin1|56215|apoptotic chromatin condensation inducer 1	NM_019567|Acin1|56215|apoptotic chromatin condensation inducer 1	AK012099|Acin1|56215|apoptotic chromatin condensation inducer 1	NM_001085472|Acin1|56215|apoptotic chromatin condensation inducer 1
mm9_v1_chr13_-_93258004_93258035	0.45204	SOX2.p2	AK134948|Zfyve16|218441|zinc finger, FYVE domain containing 16
mm9_v1_chr15_-_81756568_81756667	0.451773	SOX2.p2	AK032967|Polr3h|78929|polymerase (RNA) III (DNA directed) polypeptide H	AK152517|Polr3h|78929|polymerase (RNA) III (DNA directed) polypeptide H	AK019868|Polr3h|78929|polymerase (RNA) III (DNA directed) polypeptide H	NM_030229|Polr3h|78929|polymerase (RNA) III (DNA directed) polypeptide H	BC010793|Polr3h|78929|polymerase (RNA) III (DNA directed) polypeptide H
mm9_v1_chr11_-_119948078_119948092	0.451384	SOX2.p2	BC141108|Azi1|12009|5-azacytidine induced gene 1
mm9_v1_chr7_-_142720274_142720338	0.450606	SOX2.p2	AK085267|Clrn3|212070|clarin 3	AK033715|Clrn3|212070|clarin 3	BC036176|Clrn3|212070|clarin 3	AK146608|Clrn3|212070|clarin 3	NM_178669|Clrn3|212070|clarin 3
mm9_v1_chr11_+_78640103_78640114	0.449326	SOX2.p2	BC130224|1810012P15Rik|66274|RIKEN cDNA 1810012P15 gene	AK009070|1810012P15Rik|66274|RIKEN cDNA 1810012P15 gene
mm9_v1_chr19_-_41876509_41876573	0.449278	SOX2.p2	AK220317|Arhgap19|71085|Rho GTPase activating protein 19	BC086680|Arhgap19|71085|Rho GTPase activating protein 19	AK044841|Arhgap19|71085|Rho GTPase activating protein 19	AK016763|Arhgap19|71085|Rho GTPase activating protein 19	AK164477|Arhgap19|71085|Rho GTPase activating protein 19	BC139195|Arhgap19|71085|Rho GTPase activating protein 19	NM_001163495|Arhgap19|71085|Rho GTPase activating protein 19	NM_027667|Arhgap19|71085|Rho GTPase activating protein 19
mm9_v1_chrX_+_75233629_75233629	0.449111	SOX2.p2	AK017258|5430402E10Rik|71351|RIKEN cDNA 5430402E10 gene	NM_027768|5430402E10Rik|71351|RIKEN cDNA 5430402E10 gene
mm9_v1_chr4_-_6917628_6917956	0.448704	SOX2.p2	AK161718|Tox|252838|thymocyte selection-associated high mobility group box	AK161578|Tox|252838|thymocyte selection-associated high mobility group box	AF472514|Tox|252838|thymocyte selection-associated high mobility group box	AK029694|Tox|252838|thymocyte selection-associated high mobility group box	AK133397|Tox|252838|thymocyte selection-associated high mobility group box	BC080732|Tox|252838|thymocyte selection-associated high mobility group box	AK038671|Tox|252838|thymocyte selection-associated high mobility group box	NM_145711|Tox|252838|thymocyte selection-associated high mobility group box
mm9_v1_chr6_-_30865541_30865572	0.448508	SOX2.p2	AF294348|Tsga13|116732|testis specific gene A13	AK006265|Tsga13|116732|testis specific gene A13	NM_054073|Tsga13|116732|testis specific gene A13
mm9_v1_chr4_+_155068450_155068511	0.447634	SOX2.p2	AK046537|B930041F14Rik|230991|RIKEN cDNA B930041F14 gene
mm9_v1_chr16_+_10742336_10742473	0.447226	SOX2.p2	AK028051|Clec16a|74374|C-type lectin domain family 16, member A
mm9_v1_chr5_+_95294540_95294551	0.447167	SOX2.p2	AK145705|Gm16367|545762|predicted gene 16367	BC099967|Gm16367|545762|predicted gene 16367	NM_001031622|Gm16367|545762|predicted gene 16367
mm9_v1_chr5_+_95611642_95611653	0.447167	SOX2.p2	AK145705|Gm16367|545762|predicted gene 16367	BC099967|Gm16367|545762|predicted gene 16367	NM_001031622|Gm16367|545762|predicted gene 16367
mm9_v1_chr3_-_81949667_81949798	0.446793	SOX2.p2	BC057327|Gucy1a3|60596|guanylate cyclase 1, soluble, alpha 3	AK031305|Gucy1a3|60596|guanylate cyclase 1, soluble, alpha 3	AK028558|Gucy1a3|60596|guanylate cyclase 1, soluble, alpha 3	AK004815|Gucy1a3|60596|guanylate cyclase 1, soluble, alpha 3	AF297082|Gucy1a3|60596|guanylate cyclase 1, soluble, alpha 3	NM_021896|Gucy1a3|60596|guanylate cyclase 1, soluble, alpha 3
mm9_v1_chr5_+_31829709_31829815	0.446487	SOX2.p2	BC090964|Slc4a1ap|20534|solute carrier family 4 (anion exchanger), member 1, adaptor protein
mm9_v1_chr8_-_59029657_59029687	0.445988	SOX2.p2	
mm9_v1_chr16_-_46010510_46010548	0.445641	SOX2.p2	NM_001134480|Plcxd2|433022|phosphatidylinositol-specific phospholipase C, X domain containing 2
mm9_v1_chr9_-_91260619_91260636	0.445348	SOX2.p2	NM_009573|Zic1|22771|zinc finger protein of the cerebellum 1
mm9_v1_chr8_+_42325093_42325221	0.444327	SOX2.p2	AK133754|Pcm1|18536|pericentriolar material 1	AK011147|Pcm1|18536|pericentriolar material 1	AK141516|Pcm1|18536|pericentriolar material 1	NM_023662|Pcm1|18536|pericentriolar material 1	AF369838|Pcm1|18536|pericentriolar material 1	AB029291|Pcm1|18536|pericentriolar material 1	BC053728|Pcm1|18536|pericentriolar material 1	BC139033|Pcm1|18536|pericentriolar material 1
mm9_v1_chr10_-_85379640_85379767	0.444204	SOX2.p2	AK028414|Prdm4|72843|PR domain containing 4	NM_181650|Prdm4|72843|PR domain containing 4
mm9_v1_chr7_-_118089700_118089700	0.443401	SOX2.p2	NM_010826|Mrvi1|17540|MRV integration site 1	U63408|Mrvi1|17540|MRV integration site 1
mm9_v1_chr14_-_51815597_51815597	0.442821	SOX2.p2	NM_007449|Ang2|11731|angiogenin, ribonuclease A family, member 2
mm9_v1_chr3_-_108692732_108692925	0.441881	SOX2.p2	BC111898|Fndc7|320181|fibronectin type III domain containing 7	BC113188|Fndc7|320181|fibronectin type III domain containing 7	AK053989|Fndc7|320181|fibronectin type III domain containing 7	AK054241|Fndc7|320181|fibronectin type III domain containing 7	NM_001165965|Fndc7|320181|fibronectin type III domain containing 7	NM_177091|Fndc7|320181|fibronectin type III domain containing 7
mm9_v1_chr11_-_96168185_96168223	0.441032	SOX2.p2	AK002860|0610040B09Rik|75395|RIKEN cDNA 0610040B09 gene
mm9_v1_chr3_-_144558974_144558974	0.440836	SOX2.p2	AK139132|Gm6289|622139|predicted gene 6289	NM_001039222|Gm6289|622139|predicted gene 6289
mm9_v1_chr7_+_24919177_24919260	0.440537	SOX2.p2	NM_019941|Zfp235|56525|zinc finger protein 235	AK045726|Zfp235|56525|zinc finger protein 235	AK002713|Zfp235|56525|zinc finger protein 235	AK147833|Zfp235|56525|zinc finger protein 235	AF167321|Zfp235|56525|zinc finger protein 235	AK139127|Zfp235|56525|zinc finger protein 235	BC099965|Zfp235|56525|zinc finger protein 235
mm9_v1_chr14_-_60012348_60012348	0.440188	SOX2.p2	NM_001164289|Gm6907|628705|predicted gene 6907
mm9_v1_chr5_-_115750913_115750938	0.439785	SOX2.p2	BC008106|Dynll1|56455|dynein light chain LC8-type 1	BC034258|Dynll1|56455|dynein light chain LC8-type 1	AF020185|Dynll1|56455|dynein light chain LC8-type 1
mm9_v1_chr7_+_29649474_29649487	0.439671	SOX2.p2	AF038562|Lgals7|16858|lectin, galactose binding, soluble 7
mm9_v1_chr17_-_36408841_36408948	0.439618	SOX2.p2	AB046382|Trim39|79263|tripartite motif-containing 39	NM_024468|Trim39|79263|tripartite motif-containing 39
mm9_v1_chr8_-_125421315_125421317	0.439611	SOX2.p2	
mm9_v1_chr6_-_113550646_113550708	0.439111	SOX2.p2	AK016461|4931417G12Rik|70979|RIKEN cDNA 4931417G12 gene	BC049660|4931417G12Rik|70979|RIKEN cDNA 4931417G12 gene	NM_027633|4931417G12Rik|70979|RIKEN cDNA 4931417G12 gene
mm9_v1_chr16_-_58826586_58826586	0.438668	SOX2.p2	NM_147002|Olfr175-ps1|259004|olfactory receptor 175, pseudogene 1
mm9_v1_chr10_+_59765201_59765253	0.438653	SOX2.p2	
mm9_v1_chr3_-_129525375_129525422	0.434275	SOX2.p2	BC046288|Rrh|20132|retinal pigment epithelium derived rhodopsin homolog	AK044717|Rrh|20132|retinal pigment epithelium derived rhodopsin homolog	AF012271|Rrh|20132|retinal pigment epithelium derived rhodopsin homolog	AK021379|Rrh|20132|retinal pigment epithelium derived rhodopsin homolog	NM_009102|Rrh|20132|retinal pigment epithelium derived rhodopsin homolog
mm9_v1_chr5_-_77544147_77544201	0.434142	SOX2.p2	AF492703|Hopx|74318|HOP homeobox	NM_175606|Hopx|74318|HOP homeobox	AF534182|Hopx|74318|HOP homeobox
mm9_v1_chr15_+_91503687_91503711	0.433736	SOX2.p2	AY792512|Lrrk2|66725|leucine-rich repeat kinase 2
mm9_v1_chr2_-_155878682_155878682	0.433697	SOX2.p2	NM_001136556|Fer1l4|74562|fer-1-like 4 (C. elegans)
mm9_v1_chr18_+_80409068_80409205	0.431871	SOX2.p2	AK183256|Txnl4a|27366|thioredoxin-like 4A
mm9_v1_chr16_+_17276434_17276446	0.429607	SOX2.p2	AB041601|Tmem191c|224019|transmembrane protein 191C
mm9_v1_chr19_+_29038321_29038434	0.429594	SOX2.p2	AK016572|Ppapdc2|74411|phosphatidic acid phosphatase type 2 domain containing 2	NM_028922|Ppapdc2|74411|phosphatidic acid phosphatase type 2 domain containing 2	AK041581|Ppapdc2|74411|phosphatidic acid phosphatase type 2 domain containing 2
mm9_v1_chr3_-_75760820_75760839	0.428489	SOX2.p2	AK149286|Golim4|73124|golgi integral membrane protein 4
mm9_v1_chr16_-_22841914_22841951	0.427414	SOX2.p2	AK179171|Tbccd1|70573|TBCC domain containing 1
mm9_v1_chr16_-_16829386_16829548	0.427113	SOX2.p2	AF173866|Spag6|50525|sperm associated antigen 6	BC090660|Spag6|50525|sperm associated antigen 6	AK053966|Spag6|50525|sperm associated antigen 6	AK005732|Spag6|50525|sperm associated antigen 6	BC100455|Spag6|50525|sperm associated antigen 6	AK054199|Spag6|50525|sperm associated antigen 6	NM_015773|Spag6|50525|sperm associated antigen 6	AK164680|Spag6|50525|sperm associated antigen 6
mm9_v1_chr5_+_76612903_76613006	0.425938	SOX2.p2	NM_011626|Tmem165|21982|transmembrane protein 165	BC037638|Tmem165|21982|transmembrane protein 165	AK004829|Tmem165|21982|transmembrane protein 165	M23568|Tmem165|21982|transmembrane protein 165
mm9_v1_chr10_+_22364816_22364969	0.425272	SOX2.p2	AJ549317|Slc2a12|353169|solute carrier family 2 (facilitated glucose transporter), member 12	NM_178934|Slc2a12|353169|solute carrier family 2 (facilitated glucose transporter), member 12	AK143263|Slc2a12|353169|solute carrier family 2 (facilitated glucose transporter), member 12	AK028970|Slc2a12|353169|solute carrier family 2 (facilitated glucose transporter), member 12	BC096454|Slc2a12|353169|solute carrier family 2 (facilitated glucose transporter), member 12	AK031659|Slc2a12|353169|solute carrier family 2 (facilitated glucose transporter), member 12	AY230881|Slc2a12|353169|solute carrier family 2 (facilitated glucose transporter), member 12	AK035972|Slc2a12|353169|solute carrier family 2 (facilitated glucose transporter), member 12	BC116315|Slc2a12|353169|solute carrier family 2 (facilitated glucose transporter), member 12	BC116314|Slc2a12|353169|solute carrier family 2 (facilitated glucose transporter), member 12	BC138316|Slc2a12|353169|solute carrier family 2 (facilitated glucose transporter), member 12	BC138317|Slc2a12|353169|solute carrier family 2 (facilitated glucose transporter), member 12
mm9_v1_chr1_+_19202046_19202134	0.423584	SOX2.p2	AK032045|Tcfap2b|21419|transcription factor AP-2 beta	NM_001025305|Tcfap2b|21419|transcription factor AP-2 beta
mm9_v1_chr13_+_49600158_49600323	0.421293	SOX2.p2	AK040995|Ecm2|407800|extracellular matrix protein 2, female organ and adipocyte specific	BC089559|Ecm2|407800|extracellular matrix protein 2, female organ and adipocyte specific	NM_001012324|Ecm2|407800|extracellular matrix protein 2, female organ and adipocyte specific	AK134746|Ecm2|407800|extracellular matrix protein 2, female organ and adipocyte specific	AK163501|Ecm2|407800|extracellular matrix protein 2, female organ and adipocyte specific	BC056468|Ecm2|407800|extracellular matrix protein 2, female organ and adipocyte specific	BC065151|Ecm2|407800|extracellular matrix protein 2, female organ and adipocyte specific	AK038812|Ecm2|407800|extracellular matrix protein 2, female organ and adipocyte specific
mm9_v1_chr6_+_57208142_57208142	0.420729	SOX2.p2	BC115501|Vmn1r15|113863|vomeronasal 1 receptor 15	BC115502|Vmn1r15|113863|vomeronasal 1 receptor 15	NM_053236|Vmn1r15|113863|vomeronasal 1 receptor 15
mm9_v1_chr7_+_106614513_106614536	0.420444	SOX2.p2	NM_028145|Klhl35|72184|kelch-like 35 (Drosophila)	AK013012|Klhl35|72184|kelch-like 35 (Drosophila)
mm9_v1_chr7_+_23307985_23307985	0.41929	SOX2.p2	NM_001166738|Vmn1r104|667135|vomeronasal 1 receptor 104	NM_001166752|Vmn1r152|667504|vomeronasal 1 receptor 152
mm9_v1_chr11_+_86940545_86940631	0.418199	SOX2.p2	AK140822|Trim37|68729|tripartite motif-containing 37	BC058678|Trim37|68729|tripartite motif-containing 37	NM_197987|Trim37|68729|tripartite motif-containing 37	BC078416|Trim37|68729|tripartite motif-containing 37	BC059070|Trim37|68729|tripartite motif-containing 37
mm9_v1_chr18_+_43367236_43367350	0.417927	SOX2.p2	AK042599|Stk32a|269019|serine/threonine kinase 32A	BC055002|Stk32a|269019|serine/threonine kinase 32A	AK044474|Stk32a|269019|serine/threonine kinase 32A	AK036266|Stk32a|269019|serine/threonine kinase 32A	NM_178749|Stk32a|269019|serine/threonine kinase 32A
mm9_v1_chr10_+_100055019_100055050	0.416975	SOX2.p2	NM_001081246|1700017N19Rik|66605|RIKEN cDNA 1700017N19 gene	AK014917|1700017N19Rik|66605|RIKEN cDNA 1700017N19 gene	AK006074|1700017N19Rik|66605|RIKEN cDNA 1700017N19 gene
mm9_v1_chr11_-_46202942_46203016	0.416948	SOX2.p2	BC128374|Itk|16428|IL2-inducible T-cell kinase	BC128375|Itk|16428|IL2-inducible T-cell kinase	D14042|Itk|16428|IL2-inducible T-cell kinase	BC028478|Itk|16428|IL2-inducible T-cell kinase	AK020772|Itk|16428|IL2-inducible T-cell kinase	AK079693|Itk|16428|IL2-inducible T-cell kinase	AK153613|Itk|16428|IL2-inducible T-cell kinase	AK153692|Itk|16428|IL2-inducible T-cell kinase	L05631|Itk|16428|IL2-inducible T-cell kinase	L10628|Itk|16428|IL2-inducible T-cell kinase	AK083380|Itk|16428|IL2-inducible T-cell kinase	L00619|Itk|16428|IL2-inducible T-cell kinase	NM_010583|Itk|16428|IL2-inducible T-cell kinase
mm9_v1_chr12_+_58665101_58665119	0.416916	SOX2.p2	BC100489|4921506M07Rik|70846|RIKEN cDNA 4921506M07 gene	NM_001037743|4921506M07Rik|70846|RIKEN cDNA 4921506M07 gene	AK014828|4921506M07Rik|70846|RIKEN cDNA 4921506M07 gene
mm9_v1_chr5_-_116102983_116102996	0.416742	SOX2.p2	AK170295|Ccdc64|75665|coiled-coil domain containing 64
mm9_v1_chr11_-_116332384_116332670	0.416544	SOX2.p2	AK217597|Prpsap1|67763|phosphoribosyl pyrophosphate synthetase-associated protein 1	AK217106|Prpsap1|67763|phosphoribosyl pyrophosphate synthetase-associated protein 1	AK193081|Prpsap1|67763|phosphoribosyl pyrophosphate synthetase-associated protein 1	AK182083|Prpsap1|67763|phosphoribosyl pyrophosphate synthetase-associated protein 1
mm9_v1_chr11_-_69362609_69362611	0.416415	SOX2.p2	NM_001081330|Dnahc2|327954|dynein, axonemal, heavy chain 2	AK051796|Dnahc2|327954|dynein, axonemal, heavy chain 2
mm9_v1_chr6_+_54631644_54631765	0.416355	SOX2.p2	BC042507|2410066E13Rik|68235|RIKEN cDNA 2410066E13 gene	BC052467|2410066E13Rik|68235|RIKEN cDNA 2410066E13 gene	AK019120|2410066E13Rik|68235|RIKEN cDNA 2410066E13 gene	AK019128|2410066E13Rik|68235|RIKEN cDNA 2410066E13 gene	AK043452|2410066E13Rik|68235|RIKEN cDNA 2410066E13 gene	NM_026629|2410066E13Rik|68235|RIKEN cDNA 2410066E13 gene
mm9_v1_chr12_-_32184404_32184480	0.416127	SOX2.p2	BC019529|Cbll1|104836|Casitas B-lineage lymphoma-like 1	NM_134048|Cbll1|104836|Casitas B-lineage lymphoma-like 1	AK049141|Cbll1|104836|Casitas B-lineage lymphoma-like 1	AK051737|Cbll1|104836|Casitas B-lineage lymphoma-like 1	AK166017|Cbll1|104836|Casitas B-lineage lymphoma-like 1	AF167441|Cbll1|104836|Casitas B-lineage lymphoma-like 1
mm9_v1_chr9_-_65972570_65972698	0.416092	SOX2.p2	AK155746|Snx1|56440|sorting nexin 1	AK167993|Snx1|56440|sorting nexin 1	BC066189|Snx1|56440|sorting nexin 1	AK154079|Snx1|56440|sorting nexin 1	AK149850|Snx1|56440|sorting nexin 1	AB019214|Snx1|56440|sorting nexin 1	AK167177|Snx1|56440|sorting nexin 1	BC066044|Snx1|56440|sorting nexin 1	AK161241|Snx1|56440|sorting nexin 1	AK168742|Snx1|56440|sorting nexin 1	AF154120|Snx1|56440|sorting nexin 1	NM_019727|Snx1|56440|sorting nexin 1
mm9_v1_chr1_-_58558259_58558259	0.415795	SOX2.p2	AB190256|Orc2|18393|origin recognition complex, subunit 2	NM_001025378|Orc2|18393|origin recognition complex, subunit 2
mm9_v1_chr2_+_32390780_32390878	0.413651	SOX2.p2	AK131145|Fam102a|98952|family with sequence similarity 102, member A	AK170536|Fam102a|98952|family with sequence similarity 102, member A	AK049032|Fam102a|98952|family with sequence similarity 102, member A	NM_153560|Fam102a|98952|family with sequence similarity 102, member A
mm9_v1_chr5_+_33206352_33206425	0.41365	SOX2.p2	BC072604|Depdc5|277854|DEP domain containing 5	NM_001025426|Depdc5|277854|DEP domain containing 5	NM_001170567|Depdc5|277854|DEP domain containing 5	NM_177786|Depdc5|277854|DEP domain containing 5	AK052458|Depdc5|277854|DEP domain containing 5	AK166366|Depdc5|277854|DEP domain containing 5	AK043137|Depdc5|277854|DEP domain containing 5	AK172587|Depdc5|277854|DEP domain containing 5	AK078771|Depdc5|277854|DEP domain containing 5	AK136321|Depdc5|277854|DEP domain containing 5
mm9_v1_chr3_+_89908053_89908055	0.413165	SOX2.p2	NM_029937|Nup210l|77595|nucleoporin 210-like	AK019752|Nup210l|77595|nucleoporin 210-like
mm9_v1_chr11_+_23978029_23978056	0.410904	SOX2.p2	AK166352|Bcl11a|14025|B-cell CLL/lymphoma 11A (zinc finger protein)	NM_001159289|Bcl11a|14025|B-cell CLL/lymphoma 11A (zinc finger protein)	NM_016707|Bcl11a|14025|B-cell CLL/lymphoma 11A (zinc finger protein)
mm9_v1_chr7_+_21119185_21119185	0.409702	SOX2.p2	NM_001166738|Vmn1r104|667135|vomeronasal 1 receptor 104	NM_001166752|Vmn1r152|667504|vomeronasal 1 receptor 152
mm9_v1_chr15_+_76080159_76080286	0.409629	SOX2.p2	
mm9_v1_chr12_-_81269174_81269180	0.409009	SOX2.p2	AK037382|Actn1|109711|actinin, alpha 1
mm9_v1_chr1_-_155698278_155698324	0.408042	SOX2.p2	BC120491|5830403L16Rik|240817|RIKEN cDNA 5830403L16 gene	BC131905|5830403L16Rik|240817|RIKEN cDNA 5830403L16 gene	AJ554213|5830403L16Rik|240817|RIKEN cDNA 5830403L16 gene	AK136655|5830403L16Rik|240817|RIKEN cDNA 5830403L16 gene	AK136685|5830403L16Rik|240817|RIKEN cDNA 5830403L16 gene	DQ402363|5830403L16Rik|240817|RIKEN cDNA 5830403L16 gene	NM_178243|5830403L16Rik|240817|RIKEN cDNA 5830403L16 gene
mm9_v1_chr2_-_37558794_37558806	0.407797	SOX2.p2	BC014710|Strbp|20744|spermatid perinuclear RNA binding protein
mm9_v1_chr6_+_128325473_128325533	0.407362	SOX2.p2	AK016804|4933413G19Rik|71149|RIKEN cDNA 4933413G19 gene	AK187908|Foxm1|14235|forkhead box M1	AK161342|4933413G19Rik|71149|RIKEN cDNA 4933413G19 gene	NM_027697|4933413G19Rik|71149|RIKEN cDNA 4933413G19 gene	AK218223|Foxm1|14235|forkhead box M1
mm9_v1_chr12_-_88443285_88443488	0.406256	SOX2.p2	AJ245945|Ngb|64242|neuroglobin	AK165775|Ngb|64242|neuroglobin	AK140173|Ngb|64242|neuroglobin	BC024263|Ngb|64242|neuroglobin	NM_022414|Ngb|64242|neuroglobin
mm9_v1_chr11_-_115885714_115885820	0.405944	SOX2.p2	BC092300|H3f3b|15081|H3 histone, family 3B	X13605|H3f3b|15081|H3 histone, family 3B	BC021768|H3f3b|15081|H3 histone, family 3B	BC092043|H3f3b|15081|H3 histone, family 3B	BC002052|H3f3b|15081|H3 histone, family 3B	AK169620|H3f3b|15081|H3 histone, family 3B	BC037730|H3f3b|15081|H3 histone, family 3B	AK167828|H3f3b|15081|H3 histone, family 3B	AK153239|H3f3b|15081|H3 histone, family 3B	AK159615|H3f3b|15081|H3 histone, family 3B	AK166605|H3f3b|15081|H3 histone, family 3B	AK168931|H3f3b|15081|H3 histone, family 3B	AK169042|H3f3b|15081|H3 histone, family 3B	AK044933|H3f3b|15081|H3 histone, family 3B	AK151451|H3f3b|15081|H3 histone, family 3B	AK153189|H3f3b|15081|H3 histone, family 3B	AK151274|H3f3b|15081|H3 histone, family 3B	AK151336|H3f3b|15081|H3 histone, family 3B	AK152026|H3f3b|15081|H3 histone, family 3B	AK153294|H3f3b|15081|H3 histone, family 3B	AK153371|H3f3b|15081|H3 histone, family 3B	AK159338|H3f3b|15081|H3 histone, family 3B	AK169226|H3f3b|15081|H3 histone, family 3B	AK146070|H3f3b|15081|H3 histone, family 3B	AK151658|H3f3b|15081|H3 histone, family 3B	AK151661|H3f3b|15081|H3 histone, family 3B	AK151869|H3f3b|15081|H3 histone, family 3B	AK152453|H3f3b|15081|H3 histone, family 3B	AK152455|H3f3b|15081|H3 histone, family 3B	AK152911|H3f3b|15081|H3 histone, family 3B	AK161675|H3f3b|15081|H3 histone, family 3B	AK162426|H3f3b|15081|H3 histone, family 3B	AK168698|H3f3b|15081|H3 histone, family 3B	AK169039|H3f3b|15081|H3 histone, family 3B	AK163244|H3f3b|15081|H3 histone, family 3B	AK002928|H3f3b|15081|H3 histone, family 3B	AK011431|H3f3b|15081|H3 histone, family 3B	AK159807|H3f3b|15081|H3 histone, family 3B	AK159850|H3f3b|15081|H3 histone, family 3B	AK135839|H3f3b|15081|H3 histone, family 3B	AK151222|H3f3b|15081|H3 histone, family 3B	AK152623|H3f3b|15081|H3 histone, family 3B	AK153530|H3f3b|15081|H3 histone, family 3B	NM_008211|H3f3b|15081|H3 histone, family 3B
mm9_v1_chr7_-_22813915_22813915	0.405176	SOX2.p2	NM_001166746|Vmn1r111|667292|vomeronasal 1 receptor 111	NM_001166839|Gm4172|100043016|predicted gene 4172	NM_001167168|Gm4220|100043088|predicted gene 4220	NM_001167169|Gm4179|100043029|predicted gene 4179
mm9_v1_chr8_-_18741546_18741552	0.405173	SOX2.p2	AK143974|Angpt2|11601|angiopoietin 2	AK019860|Angpt2|11601|angiopoietin 2	NM_007426|Angpt2|11601|angiopoietin 2
mm9_v1_chr7_-_150734970_150735032	0.405082	SOX2.p2	AJ002198|Nap1l4|17955|nucleosome assembly protein 1-like 4	NM_008672|Nap1l4|17955|nucleosome assembly protein 1-like 4	AK156835|Nap1l4|17955|nucleosome assembly protein 1-like 4	BC089018|Nap1l4|17955|nucleosome assembly protein 1-like 4
mm9_v1_chr8_-_25785199_25785226	0.40497	SOX2.p2	BC144841|Adam18|13524|a disintegrin and metallopeptidase domain 18	BC145751|Adam18|13524|a disintegrin and metallopeptidase domain 18	BC051136|Adam18|13524|a disintegrin and metallopeptidase domain 18	AF167405|Adam18|13524|a disintegrin and metallopeptidase domain 18	AK076633|Adam18|13524|a disintegrin and metallopeptidase domain 18	NM_010084|Adam18|13524|a disintegrin and metallopeptidase domain 18
mm9_v1_chr6_+_123122910_123123040	0.4044	SOX2.p2	AK156711|Clec4b2|381809|C-type lectin domain family 4, member b2	AY365133|Clec4b2|381809|C-type lectin domain family 4, member b2	NM_001004159|Clec4b2|381809|C-type lectin domain family 4, member b2
mm9_v1_chr1_+_132762248_132762329	0.401424	SOX2.p2	BC116674|Faim3|69169|Fas apoptotic inhibitory molecule 3	BC118505|Faim3|69169|Fas apoptotic inhibitory molecule 3
mm9_v1_chr7_+_17659388_17659431	0.401075	SOX2.p2	BC030357|Psg16|26436|pregnancy specific glycoprotein 16	NM_007676|Psg16|26436|pregnancy specific glycoprotein 16	U34272|Psg16|26436|pregnancy specific glycoprotein 16
mm9_v1_chr10_+_42550365_42550378	0.400682	SOX2.p2	AK017703|Sec63|140740|SEC63-like (S. cerevisiae)
mm9_v1_chr2_+_165480795_165480797	0.400503	SOX2.p2	BC003755|Eya2|14049|eyes absent 2 homolog (Drosophila)	NM_010165|Eya2|14049|eyes absent 2 homolog (Drosophila)
mm9_v1_chr11_+_120151645_120151699	0.400469	SOX2.p2	BC069995|Bahcc1|268515|BAH domain and coiled-coil containing 1
mm9_v1_chr18_-_24761954_24762029	0.400426	SOX2.p2	BC055012|Slc39a6|106957|solute carrier family 39 (metal ion transporter), member 6
mm9_v1_chr10_-_51351236_51351263	0.399561	SOX2.p2	AY735399|Gprc6a|210198|G protein-coupled receptor, family C, group 6, member A	AY735400|Gprc6a|210198|G protein-coupled receptor, family C, group 6, member A	AY735401|Gprc6a|210198|G protein-coupled receptor, family C, group 6, member A	AY101365|Gprc6a|210198|G protein-coupled receptor, family C, group 6, member A	BC108998|Gprc6a|210198|G protein-coupled receptor, family C, group 6, member A	NM_153071|Gprc6a|210198|G protein-coupled receptor, family C, group 6, member A
mm9_v1_chr8_+_22950397_22950409	0.399346	SOX2.p2	AJ011800|Defb2|13215|defensin beta 2	NM_010030|Defb2|13215|defensin beta 2	BC109129|Defb2|13215|defensin beta 2	BC109130|Defb2|13215|defensin beta 2
mm9_v1_chr11_+_53534295_53534310	0.397589	SOX2.p2	NM_010558|Il5|16191|interleukin 5	X04601|Il5|16191|interleukin 5	X06270|Il5|16191|interleukin 5	BC125366|Il5|16191|interleukin 5	BC132066|Il5|16191|interleukin 5
mm9_v1_chr10_+_56097078_56097350	0.397292	SOX2.p2	AY427554|Gja1|14609|gap junction protein, alpha 1	AY427555|Gja1|14609|gap junction protein, alpha 1	NM_010288|Gja1|14609|gap junction protein, alpha 1	M63801|Gja1|14609|gap junction protein, alpha 1	AK011459|Gja1|14609|gap junction protein, alpha 1	AK036979|Gja1|14609|gap junction protein, alpha 1	AK145692|Gja1|14609|gap junction protein, alpha 1	AK161997|Gja1|14609|gap junction protein, alpha 1	AK171955|Gja1|14609|gap junction protein, alpha 1	AY427560|Gja1|14609|gap junction protein, alpha 1	BC006894|Gja1|14609|gap junction protein, alpha 1	BC055375|Gja1|14609|gap junction protein, alpha 1	AK029291|Gja1|14609|gap junction protein, alpha 1	AK165986|Gja1|14609|gap junction protein, alpha 1	X61576|Gja1|14609|gap junction protein, alpha 1	AY427556|Gja1|14609|gap junction protein, alpha 1	AY427557|Gja1|14609|gap junction protein, alpha 1	AY427558|Gja1|14609|gap junction protein, alpha 1
mm9_v1_chr6_-_49164952_49164952	0.395453	SOX2.p2	AK147140|Igf2bp3|140488|insulin-like growth factor 2 mRNA binding protein 3	NM_023670|Igf2bp3|140488|insulin-like growth factor 2 mRNA binding protein 3
mm9_v1_chr11_+_98725073_98725122	0.394451	SOX2.p2	BC057854|Wipf2|68524|WAS/WASL interacting protein family, member 2
mm9_v1_chr8_-_98331280_98331397	0.393949	SOX2.p2	BC157948|Cnot1|234594|CCR4-NOT transcription complex, subunit 1	BC158073|Cnot1|234594|CCR4-NOT transcription complex, subunit 1	BC172105|Cnot1|234594|CCR4-NOT transcription complex, subunit 1	BC058249|Cnot1|234594|CCR4-NOT transcription complex, subunit 1	AK086041|Cnot1|234594|CCR4-NOT transcription complex, subunit 1	AK169894|Cnot1|234594|CCR4-NOT transcription complex, subunit 1	NM_153164|Cnot1|234594|CCR4-NOT transcription complex, subunit 1	NM_178078|Cnot1|234594|CCR4-NOT transcription complex, subunit 1
mm9_v1_chr6_-_124765218_124765272	0.393729	SOX2.p2	
mm9_v1_chr5_+_89194037_89194113	0.391321	SOX2.p2	NM_007832|Dck|13178|deoxycytidine kinase	BC060062|Dck|13178|deoxycytidine kinase	AK145353|Dck|13178|deoxycytidine kinase	AK145390|Dck|13178|deoxycytidine kinase	BC052004|Dck|13178|deoxycytidine kinase
mm9_v1_chr17_+_24625530_24625580	0.390108	SOX2.p2	AK014376|Caskin1|268932|CASK interacting protein 1
mm9_v1_chr7_-_127288785_127288804	0.389894	SOX2.p2	BC071183|Zp2|22787|zona pellucida glycoprotein 2	AK135903|Zp2|22787|zona pellucida glycoprotein 2	M34148|Zp2|22787|zona pellucida glycoprotein 2	NM_011775|Zp2|22787|zona pellucida glycoprotein 2	AK138699|Zp2|22787|zona pellucida glycoprotein 2
mm9_v1_chr16_-_88774392_88774450	0.389767	SOX2.p2	BC104340|2310057N15Rik|69696|RIKEN cDNA 2310057N15 gene	BC104341|2310057N15Rik|69696|RIKEN cDNA 2310057N15 gene	AK009968|2310057N15Rik|69696|RIKEN cDNA 2310057N15 gene	NM_027170|2310057N15Rik|69696|RIKEN cDNA 2310057N15 gene
mm9_v1_chr15_-_76983985_76984241	0.389558	SOX2.p2	AF387322|Rbfox2|93686|RNA binding protein, fox-1 homolog (C. elegans) 2	AY659951|Rbfox2|93686|RNA binding protein, fox-1 homolog (C. elegans) 2	AY659952|Rbfox2|93686|RNA binding protein, fox-1 homolog (C. elegans) 2	AY659953|Rbfox2|93686|RNA binding protein, fox-1 homolog (C. elegans) 2	DQ017388|Rbfox2|93686|RNA binding protein, fox-1 homolog (C. elegans) 2	DQ017389|Rbfox2|93686|RNA binding protein, fox-1 homolog (C. elegans) 2	BC002124|Rbfox2|93686|RNA binding protein, fox-1 homolog (C. elegans) 2	AF229055|Rbfox2|93686|RNA binding protein, fox-1 homolog (C. elegans) 2	AK044929|Rbfox2|93686|RNA binding protein, fox-1 homolog (C. elegans) 2	NM_001110828|Rbfox2|93686|RNA binding protein, fox-1 homolog (C. elegans) 2	NM_001110829|Rbfox2|93686|RNA binding protein, fox-1 homolog (C. elegans) 2	NM_001110830|Rbfox2|93686|RNA binding protein, fox-1 homolog (C. elegans) 2
mm9_v1_chr8_-_75090050_75090196	0.389492	SOX2.p2	AK215124|9130011J15Rik|66818|RIKEN cDNA 9130011J15 gene	AK217818|9130011J15Rik|66818|RIKEN cDNA 9130011J15 gene	AK207517|9130011J15Rik|66818|RIKEN cDNA 9130011J15 gene
mm9_v1_chr4_+_28740280_28740313	0.389155	SOX2.p2	AK033903|Epha7|13841|Eph receptor A7	NM_001122889|Epha7|13841|Eph receptor A7	NM_010141|Epha7|13841|Eph receptor A7	X79082|Epha7|13841|Eph receptor A7	X79083|Epha7|13841|Eph receptor A7	X79084|Epha7|13841|Eph receptor A7
mm9_v1_chr10_+_63283802_63283803	0.388865	SOX2.p2	AK015241|Ctnna3|216033|catenin (cadherin associated protein), alpha 3	NM_001164519|Ctnna3|216033|catenin (cadherin associated protein), alpha 3	DQ380430|Ctnna3|216033|catenin (cadherin associated protein), alpha 3
mm9_v1_chr7_+_29649467_29649473	0.388738	SOX2.p2	AK009151|Lgals7|16858|lectin, galactose binding, soluble 7	AK003153|Lgals7|16858|lectin, galactose binding, soluble 7	AK008773|Lgals7|16858|lectin, galactose binding, soluble 7
mm9_v1_chr11_+_117710532_117710668	0.388403	SOX2.p2	NM_001012273|Birc5|11799|baculoviral IAP repeat-containing 5	NM_009689|Birc5|11799|baculoviral IAP repeat-containing 5	AB013819|Birc5|11799|baculoviral IAP repeat-containing 5	AK018022|Birc5|11799|baculoviral IAP repeat-containing 5	BC004702|Birc5|11799|baculoviral IAP repeat-containing 5	AK142768|Birc5|11799|baculoviral IAP repeat-containing 5	AF077349|Birc5|11799|baculoviral IAP repeat-containing 5	EU366955|Birc5|11799|baculoviral IAP repeat-containing 5
mm9_v1_chr13_+_55885928_55886022	0.388268	SOX2.p2	BC089518|Catsper3|76856|cation channel, sperm associated 3	AK014942|Catsper3|76856|cation channel, sperm associated 3	NM_029772|Catsper3|76856|cation channel, sperm associated 3	AY263400|Catsper3|76856|cation channel, sperm associated 3	HM179540|Catsper3|76856|cation channel, sperm associated 3	HM179541|Catsper3|76856|cation channel, sperm associated 3
mm9_v1_chr5_-_51848420_51848454	0.387168	SOX2.p2	AK032149|Ppargc1a|19017|peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	AK082685|Ppargc1a|19017|peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	AK043827|Ppargc1a|19017|peroxisome proliferative activated receptor, gamma, coactivator 1 alpha
mm9_v1_chr16_+_33062606_33062616	0.386548	SOX2.p2	AK030463|Lmln|239833|leishmanolysin-like (metallopeptidase M8 family)	BC111899|Lmln|239833|leishmanolysin-like (metallopeptidase M8 family)	BC112428|Lmln|239833|leishmanolysin-like (metallopeptidase M8 family)	NM_172823|Lmln|239833|leishmanolysin-like (metallopeptidase M8 family)
mm9_v1_chr13_-_67738689_67738740	0.386547	SOX2.p2	AK138962|A530054K11Rik|212281|RIKEN cDNA A530054K11 gene	NM_183146|A530054K11Rik|212281|RIKEN cDNA A530054K11 gene	BC098180|A530054K11Rik|212281|RIKEN cDNA A530054K11 gene	AK040978|A530054K11Rik|212281|RIKEN cDNA A530054K11 gene
mm9_v1_chr13_-_70980619_70980688	0.386165	SOX2.p2	AK173338|Adamts16|271127|a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 16	AK031314|Adamts16|271127|a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 16	AK134523|Adamts16|271127|a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 16	NM_172053|Adamts16|271127|a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 16	BC034739|Adamts16|271127|a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 16
mm9_v1_chr5_-_149363989_149364264	0.385931	SOX2.p2	BC025595|Ubl3|24109|ubiquitin-like 3	AK145952|Ubl3|24109|ubiquitin-like 3
mm9_v1_chr7_-_21288567_21288567	0.385612	SOX2.p2	NM_001167154|Gm8693|667543|predicted gene 8693	NM_001167155|Gm4144|100042980|predicted gene 4144
mm9_v1_chr7_+_127883556_127883560	0.385602	SOX2.p2	AK086942|Vwa3a|233813|von Willebrand factor A domain containing 3A	AK136898|Vwa3a|233813|von Willebrand factor A domain containing 3A
mm9_v1_chr7_+_140829388_140829408	0.385563	SOX2.p2	AK144959|2700050L05Rik|214764|RIKEN cDNA 2700050L05 gene	BC072596|2700050L05Rik|214764|RIKEN cDNA 2700050L05 gene	AK144179|2700050L05Rik|214764|RIKEN cDNA 2700050L05 gene
mm9_v1_chr11_+_51817722_51817929	0.384668	SOX2.p2	AK046394|Cdkl3|213084|cyclin-dependent kinase-like 3	NM_001166653|Cdkl3|213084|cyclin-dependent kinase-like 3	NM_001166654|Cdkl3|213084|cyclin-dependent kinase-like 3	NM_001166655|Cdkl3|213084|cyclin-dependent kinase-like 3	NM_001166656|Cdkl3|213084|cyclin-dependent kinase-like 3	NM_001166657|Cdkl3|213084|cyclin-dependent kinase-like 3	NM_153785|Cdkl3|213084|cyclin-dependent kinase-like 3	AK050990|Cdkl3|213084|cyclin-dependent kinase-like 3	AK078804|Cdkl3|213084|cyclin-dependent kinase-like 3	AK090045|Cdkl3|213084|cyclin-dependent kinase-like 3	AK045036|Cdkl3|213084|cyclin-dependent kinase-like 3	AK166428|Cdkl3|213084|cyclin-dependent kinase-like 3	AK045356|Cdkl3|213084|cyclin-dependent kinase-like 3	BC028871|Cdkl3|213084|cyclin-dependent kinase-like 3	AK186403|Cdkl3|213084|cyclin-dependent kinase-like 3	AK210497|Cdkl3|213084|cyclin-dependent kinase-like 3
mm9_v1_chr2_-_25316432_25316473	0.384634	SOX2.p2	AK046066|BC029214|227622|cDNA sequence BC029214
mm9_v1_chr2_+_25036276_25036300	0.384044	SOX2.p2	AY046077|Nrarp|67122|Notch-regulated ankyrin repeat protein	NM_025980|Nrarp|67122|Notch-regulated ankyrin repeat protein	BC020293|Nrarp|67122|Notch-regulated ankyrin repeat protein	BC048088|Nrarp|67122|Notch-regulated ankyrin repeat protein
mm9_v1_chr10_-_100051657_100051858	0.383313	SOX2.p2	AK015251|4930430F08Rik|68281|RIKEN cDNA 4930430F08 gene	AK043358|4930430F08Rik|68281|RIKEN cDNA 4930430F08 gene	BC082587|4930430F08Rik|68281|RIKEN cDNA 4930430F08 gene	AK082894|4930430F08Rik|68281|RIKEN cDNA 4930430F08 gene	AK032226|4930430F08Rik|68281|RIKEN cDNA 4930430F08 gene
mm9_v1_chr10_-_14465464_14465593	0.382743	SOX2.p2	AK209652|Hspa8|15481|heat shock protein 8	AK192102|Hspa8|15481|heat shock protein 8
mm9_v1_chr2_-_180444687_180444716	0.382528	SOX2.p2	BC096662|Dido1|23856|death inducer-obliterator 1	AK129117|Dido1|23856|death inducer-obliterator 1	BC060249|Dido1|23856|death inducer-obliterator 1	NM_177852|Dido1|23856|death inducer-obliterator 1
mm9_v1_chr7_+_21357946_21357946	0.381641	SOX2.p2	NM_001166754|Vmn1r157|667551|vomeronasal 1 receptor 157	NM_001166845|Vmn1r109|100043559|vomeronasal 1 receptor 109
mm9_v1_chrX_-_7709452_7709736	0.381638	SOX2.p2	AF513713|Wdr13|73447|WD repeat domain 13	BC125287|Wdr13|73447|WD repeat domain 13	BC120553|Wdr13|73447|WD repeat domain 13	AK017549|Wdr13|73447|WD repeat domain 13	AF353243|Wdr13|73447|WD repeat domain 13	BC037502|Wdr13|73447|WD repeat domain 13	BC108332|Wdr13|73447|WD repeat domain 13
mm9_v1_chr9_+_109834266_109834307	0.380605	SOX2.p2	NM_008633|Mtap4|17758|microtubule-associated protein 4	AK046825|Mtap4|17758|microtubule-associated protein 4
mm9_v1_chr3_+_92236503_92236517	0.378569	SOX2.p2	AY158995|Sprr2k|20765|small proline-rich protein 2K	NM_011477|Sprr2k|20765|small proline-rich protein 2K	BC116866|Sprr2k|20765|small proline-rich protein 2K	BC116868|Sprr2k|20765|small proline-rich protein 2K
mm9_v1_chr11_-_69575192_69575469	0.378318	SOX2.p2	AF016712|Amac1|56293|acyl-malonyl condensing enzyme 1	BC137893|Amac1|56293|acyl-malonyl condensing enzyme 1	BC137894|Amac1|56293|acyl-malonyl condensing enzyme 1	NM_019871|Amac1|56293|acyl-malonyl condensing enzyme 1	AK077181|Amac1|56293|acyl-malonyl condensing enzyme 1
mm9_v1_chrX_-_148450731_148450837	0.37805	SOX2.p2	AK017461|Ribc1|66611|RIB43A domain with coiled-coils 1	AK084108|Ribc1|66611|RIB43A domain with coiled-coils 1	BC050755|Ribc1|66611|RIB43A domain with coiled-coils 1	AK011592|Ribc1|66611|RIB43A domain with coiled-coils 1	NM_025660|Ribc1|66611|RIB43A domain with coiled-coils 1
mm9_v1_chr1_-_85266715_85266728	0.377869	SOX2.p2	BC007193|C130026I21Rik|620078|RIKEN cDNA C130026I21 gene	BC094285|A530032D15Rik|381287|RIKEN cDNA A530032D15Rik gene
mm9_v1_chr7_+_24002350_24002350	0.376537	SOX2.p2	BC154405|Vmn1r178|232959|vomeronasal 1 receptor 178	NM_001166753|Vmn1r155|667530|vomeronasal 1 receptor 155	NM_001166759|Vmn1r107|673977|vomeronasal 1 receptor 107	NM_001166846|Vmn1r110|100043561|vomeronasal 1 receptor 110	NM_001166848|Vmn1r130|100043596|vomeronasal 1 receptor 130	NM_001166849|Vmn1r137|100043614|vomeronasal 1 receptor 137	NM_001166850|Vmn1r165|100043667|vomeronasal 1 receptor 165
mm9_v1_chr7_+_22779605_22779605	0.376537	SOX2.p2	NM_001166753|Vmn1r155|667530|vomeronasal 1 receptor 155	NM_001166759|Vmn1r107|673977|vomeronasal 1 receptor 107	NM_001166846|Vmn1r110|100043561|vomeronasal 1 receptor 110	NM_001166848|Vmn1r130|100043596|vomeronasal 1 receptor 130	NM_001166849|Vmn1r137|100043614|vomeronasal 1 receptor 137	NM_001166850|Vmn1r165|100043667|vomeronasal 1 receptor 165
mm9_v1_chr7_+_23443036_23443036	0.376049	SOX2.p2	NM_001166753|Vmn1r155|667530|vomeronasal 1 receptor 155	NM_001166759|Vmn1r107|673977|vomeronasal 1 receptor 107	NM_001166846|Vmn1r110|100043561|vomeronasal 1 receptor 110	NM_001166848|Vmn1r130|100043596|vomeronasal 1 receptor 130	NM_001166849|Vmn1r137|100043614|vomeronasal 1 receptor 137	NM_001166850|Vmn1r165|100043667|vomeronasal 1 receptor 165
mm9_v1_chr7_+_21453935_21453935	0.376049	SOX2.p2	NM_001166753|Vmn1r155|667530|vomeronasal 1 receptor 155	NM_001166759|Vmn1r107|673977|vomeronasal 1 receptor 107	NM_001166846|Vmn1r110|100043561|vomeronasal 1 receptor 110	NM_001166848|Vmn1r130|100043596|vomeronasal 1 receptor 130	NM_001166849|Vmn1r137|100043614|vomeronasal 1 receptor 137	NM_001166850|Vmn1r165|100043667|vomeronasal 1 receptor 165
mm9_v1_chr7_+_21254266_21254266	0.376049	SOX2.p2	NM_001166753|Vmn1r155|667530|vomeronasal 1 receptor 155	NM_001166759|Vmn1r107|673977|vomeronasal 1 receptor 107	NM_001166846|Vmn1r110|100043561|vomeronasal 1 receptor 110	NM_001166848|Vmn1r130|100043596|vomeronasal 1 receptor 130	NM_001166849|Vmn1r137|100043614|vomeronasal 1 receptor 137	NM_001166850|Vmn1r165|100043667|vomeronasal 1 receptor 165
mm9_v1_chr11_+_62364951_62365050	0.375942	SOX2.p2	AK007273|Ubb|22187|ubiquitin B	AK003190|Ubb|22187|ubiquitin B	AK010413|Ubb|22187|ubiquitin B	AK010625|Ubb|22187|ubiquitin B	AK012443|Ubb|22187|ubiquitin B	AK013027|Ubb|22187|ubiquitin B	AK132747|Ubb|22187|ubiquitin B	AK165313|Ubb|22187|ubiquitin B	NM_011664|Ubb|22187|ubiquitin B	X51703|Ubb|22187|ubiquitin B	AK160683|Ubb|22187|ubiquitin B	AK013873|Ubb|22187|ubiquitin B	BC019850|Ubb|22187|ubiquitin B	BC100341|Ubb|22187|ubiquitin B
mm9_v1_chr17_-_45705824_45706064	0.374281	SOX2.p2	S46109|Hsp90ab1|15516|heat shock protein 90 alpha (cytosolic), class B member 1
mm9_v1_chr1_-_69732373_69732533	0.373596	SOX2.p2	BC138606|Ikzf2|22779|IKAROS family zinc finger 2	BC138608|Ikzf2|22779|IKAROS family zinc finger 2	AK047925|Ikzf2|22779|IKAROS family zinc finger 2	AF044257|Ikzf2|22779|IKAROS family zinc finger 2	NM_011770|Ikzf2|22779|IKAROS family zinc finger 2
mm9_v1_chr14_+_30791522_30791616	0.373395	SOX2.p2	NM_027493|Actr8|56249|ARP8 actin-related protein 8 homolog (S. cerevisiae)	AK017815|Actr8|56249|ARP8 actin-related protein 8 homolog (S. cerevisiae)	AK045862|Actr8|56249|ARP8 actin-related protein 8 homolog (S. cerevisiae)	BC027281|Actr8|56249|ARP8 actin-related protein 8 homolog (S. cerevisiae)
mm9_v1_chr6_-_29162226_29162288	0.373333	SOX2.p2	BC053416|Impdh1|23917|inosine 5'-phosphate dehydrogenase 1	NM_011829|Impdh1|23917|inosine 5'-phosphate dehydrogenase 1
mm9_v1_chr3_+_89019108_89019113	0.373267	SOX2.p2	NM_013691|Thbs3|21827|thrombospondin 3
mm9_v1_chr7_+_31762061_31762061	0.372712	SOX2.p2	AK028081|Fam187b|76415|family with sequence similarity 187, member B	BC120864|Fam187b|76415|family with sequence similarity 187, member B	BC125560|Fam187b|76415|family with sequence similarity 187, member B	NM_175240|Fam187b|76415|family with sequence similarity 187, member B
mm9_v1_chr1_+_165978346_165978413	0.372445	SOX2.p2	AK153623|Sele|20339|selectin, endothelial cell	M87862|Sele|20339|selectin, endothelial cell	NM_011345|Sele|20339|selectin, endothelial cell	BC119083|Sele|20339|selectin, endothelial cell	BC120795|Sele|20339|selectin, endothelial cell
mm9_v1_chr7_+_16481472_16481519	0.371747	SOX2.p2	AK145701|Crxos1|546024|Crx opposite strand transcript 1	NM_001033638|Crxos1|546024|Crx opposite strand transcript 1	AB472692|Crxos1|546024|Crx opposite strand transcript 1	AB472693|Crxos1|546024|Crx opposite strand transcript 1	AY593966|Crxos1|546024|Crx opposite strand transcript 1
mm9_v1_chr2_-_164104007_164104044	0.371553	SOX2.p2	M35732|Svs4|20941|seminal vesicle secretory protein 4	AK020349|Svs4|20941|seminal vesicle secretory protein 4	BC115604|Svs4|20941|seminal vesicle secretory protein 4	BC115605|Svs4|20941|seminal vesicle secretory protein 4	NM_009300|Svs4|20941|seminal vesicle secretory protein 4
mm9_v1_chr6_-_128776236_128776348	0.371147	SOX2.p2	X64719|Klrb1b|80782|killer cell lectin-like receptor subfamily B member 1B	AF338321|Klrb1b|80782|killer cell lectin-like receptor subfamily B member 1B	AF338322|Klrb1b|80782|killer cell lectin-like receptor subfamily B member 1B	DQ237928|Klrb1b|80782|killer cell lectin-like receptor subfamily B member 1B	AF354259|Klrb1b|80782|killer cell lectin-like receptor subfamily B member 1B	AF354260|Klrb1b|80782|killer cell lectin-like receptor subfamily B member 1B	AK030702|Klrb1b|80782|killer cell lectin-like receptor subfamily B member 1B	BC132126|Klrb1b|80782|killer cell lectin-like receptor subfamily B member 1B	BC132128|Klrb1b|80782|killer cell lectin-like receptor subfamily B member 1B	AF324826|Klrb1b|80782|killer cell lectin-like receptor subfamily B member 1B	AF342896|Klrb1b|80782|killer cell lectin-like receptor subfamily B member 1B	M77677|Klrb1b|80782|killer cell lectin-like receptor subfamily B member 1B	BC055379|Klrb1b|80782|killer cell lectin-like receptor subfamily B member 1B	BC100580|Klrb1b|80782|killer cell lectin-like receptor subfamily B member 1B	AK138766|Klrb1b|80782|killer cell lectin-like receptor subfamily B member 1B	AK041228|Klrb1b|80782|killer cell lectin-like receptor subfamily B member 1B	NM_030599|Klrb1b|80782|killer cell lectin-like receptor subfamily B member 1B	AK169820|Klrb1b|80782|killer cell lectin-like receptor subfamily B member 1B
mm9_v1_chr4_+_154929136_154929270	0.370155	SOX2.p2	AK218112|Gnb1|14688|guanine nucleotide binding protein (G protein), beta 1	AK190349|Gnb1|14688|guanine nucleotide binding protein (G protein), beta 1	AK191980|Gnb1|14688|guanine nucleotide binding protein (G protein), beta 1	AK199789|Gnb1|14688|guanine nucleotide binding protein (G protein), beta 1	AK200062|Gnb1|14688|guanine nucleotide binding protein (G protein), beta 1
mm9_v1_chr2_+_170111212_170111359	0.369928	SOX2.p2	
mm9_v1_chr7_-_19271340_19271380	0.368452	SOX2.p2	NM_054058|Psg20|434540|pregnancy-specific glycoprotein 20	AF113598|Psg28|114871|pregnancy-specific glycoprotein 28
mm9_v1_chr11_-_6328316_6328333	0.368062	SOX2.p2	
mm9_v1_chr2_+_160557441_160557517	0.367022	SOX2.p2	AF027185|Plcg1|18803|phospholipase C, gamma 1
mm9_v1_chr6_-_25639812_25639825	0.366824	SOX2.p2	AK032525|Gpr37|14763|G protein-coupled receptor 37
mm9_v1_chr15_-_81238649_81238728	0.366284	SOX2.p2	BC104396|Dnajb7|57755|DnaJ (Hsp40) homolog, subfamily B, member 7	BC104397|Dnajb7|57755|DnaJ (Hsp40) homolog, subfamily B, member 7	BC119478|Dnajb7|57755|DnaJ (Hsp40) homolog, subfamily B, member 7	BC048738|Dnajb7|57755|DnaJ (Hsp40) homolog, subfamily B, member 7	AB028855|Dnajb7|57755|DnaJ (Hsp40) homolog, subfamily B, member 7	NM_021317|Dnajb7|57755|DnaJ (Hsp40) homolog, subfamily B, member 7	AK006201|Dnajb7|57755|DnaJ (Hsp40) homolog, subfamily B, member 7	AK077186|Dnajb7|57755|DnaJ (Hsp40) homolog, subfamily B, member 7
mm9_v1_chr11_-_35612385_35612385	0.366076	SOX2.p2	NM_001004147|Fbll1|237730|fibrillarin-like 1
mm9_v1_chr17_+_34462609_34462619	0.365758	SOX2.p2	AK157199|H2-Eb2|381091|histocompatibility 2, class II antigen E beta2	AK137912|H2-Eb2|381091|histocompatibility 2, class II antigen E beta2	BC150834|H2-Eb2|381091|histocompatibility 2, class II antigen E beta2	NM_001033978|H2-Eb2|381091|histocompatibility 2, class II antigen E beta2
mm9_v1_chr5_-_135422780_135422780	0.365173	SOX2.p2	BC032172|Cldn4|12740|claudin 4
mm9_v1_chr14_-_68333397_68333419	0.365006	SOX2.p2	BC067009|Cdca2|108912|cell division cycle associated 2
mm9_v1_chr2_-_87875293_87875294	0.364844	SOX2.p2	AB061228|Olfr73|117004|olfactory receptor 73	NM_054090|Olfr73|117004|olfactory receptor 73	BC140145|Olfr73|117004|olfactory receptor 73	BC143167|Olfr73|117004|olfactory receptor 73	BC146832|Olfr73|117004|olfactory receptor 73
mm9_v1_chr17_+_89026108_89026172	0.3646	SOX2.p2	AK077966|Ston1|77057|stonin 1
mm9_v1_chr2_-_66094647_66094696	0.36398	SOX2.p2	BC151199|Ttc21b|73668|tetratricopeptide repeat domain 21B	BC172115|Ttc21b|73668|tetratricopeptide repeat domain 21B	DQ011164|Ttc21b|73668|tetratricopeptide repeat domain 21B	NM_001047604|Ttc21b|73668|tetratricopeptide repeat domain 21B
mm9_v1_chr7_+_20686506_20686506	0.36386	SOX2.p2	NM_001166736|Vmn1r91|667067|vomeronasal 1 receptor 91
mm9_v1_chr11_+_108781661_108781720	0.36293	SOX2.p2	AK142333|Axin2|12006|axin2	NM_015732|Axin2|12006|axin2	BC057338|Axin2|12006|axin2	AK049192|Axin2|12006|axin2
mm9_v1_chr18_+_37164856_37165092	0.362745	SOX2.p2	BC079625|Pcdha10|12943|protocadherin alpha 10	AY013757|Pcdha10|12943|protocadherin alpha 10	NM_009961|Pcdha10|12943|protocadherin alpha 10	AB008178|Pcdha10|12943|protocadherin alpha 10
mm9_v1_chr17_+_35258394_35258523	0.362528	SOX2.p2	NM_001128597|Gpank1|81845|G patch domain and ankyrin repeats 1	AK028189|Gpank1|81845|G patch domain and ankyrin repeats 1	BC057902|Gpank1|81845|G patch domain and ankyrin repeats 1
mm9_v1_chr1_+_137043277_137043554	0.362269	SOX2.p2	BC018479|Arl8a|68724|ADP-ribosylation factor-like 8A	NM_026823|Arl8a|68724|ADP-ribosylation factor-like 8A	AB185207|Arl8a|68724|ADP-ribosylation factor-like 8A
mm9_v1_chr9_+_3335139_3335230	0.361366	SOX2.p2	AK160783|Alkbh8|67667|alkB, alkylation repair homolog 8 (E. coli)	BC050863|Alkbh8|67667|alkB, alkylation repair homolog 8 (E. coli)	NM_026303|Alkbh8|67667|alkB, alkylation repair homolog 8 (E. coli)
mm9_v1_chr19_+_29485408_29485503	0.360971	SOX2.p2	AK089369|Pdcd1lg2|58205|programmed cell death 1 ligand 2	NM_021396|Pdcd1lg2|58205|programmed cell death 1 ligand 2	AF142780|Pdcd1lg2|58205|programmed cell death 1 ligand 2	AK155002|Pdcd1lg2|58205|programmed cell death 1 ligand 2	BC104138|Pdcd1lg2|58205|programmed cell death 1 ligand 2	BC104139|Pdcd1lg2|58205|programmed cell death 1 ligand 2
mm9_v1_chr8_-_108467294_108467304	0.360966	SOX2.p2	AK149476|Lcat|16816|lecithin cholesterol acyltransferase	NM_008490|Lcat|16816|lecithin cholesterol acyltransferase
mm9_v1_chr9_-_21875784_21875847	0.360755	SOX2.p2	AY072705|Zfp653|319601|zinc finger protein 653	BC038037|Zfp653|319601|zinc finger protein 653	NM_177318|Zfp653|319601|zinc finger protein 653	AK171735|Zfp653|319601|zinc finger protein 653
mm9_v1_chr7_-_19751441_19751475	0.360077	SOX2.p2	AK050472|Gipr|381853|gastric inhibitory polypeptide receptor	AK146552|Gipr|381853|gastric inhibitory polypeptide receptor	NM_001080815|Gipr|381853|gastric inhibitory polypeptide receptor
mm9_v1_chr14_+_22808966_22809087	0.359582	SOX2.p2	AK039230|A330001L22Rik|399632|RIKEN cDNA A330001L22 gene
mm9_v1_chr7_+_50817739_50817739	0.358995	SOX2.p2	AK155078|Zfp658|210104|zinc finger protein 658	NM_001008549|Zfp658|210104|zinc finger protein 658
mm9_v1_chr17_+_5975585_5975739	0.358479	SOX2.p2	AK163512|Synj2|20975|synaptojanin 2	NM_001113351|Synj2|20975|synaptojanin 2	NM_011523|Synj2|20975|synaptojanin 2	AF041862|Synj2|20975|synaptojanin 2	BC060214|Synj2|20975|synaptojanin 2
mm9_v1_chr3_-_83844042_83844096	0.358284	SOX2.p2	AY662647|D930015E06Rik|229473|RIKEN cDNA D930015E06 gene	AK053888|D930015E06Rik|229473|RIKEN cDNA D930015E06 gene	AK051240|D930015E06Rik|229473|RIKEN cDNA D930015E06 gene	AK137619|D930015E06Rik|229473|RIKEN cDNA D930015E06 gene	BC062940|D930015E06Rik|229473|RIKEN cDNA D930015E06 gene	AK052409|D930015E06Rik|229473|RIKEN cDNA D930015E06 gene	AK153996|D930015E06Rik|229473|RIKEN cDNA D930015E06 gene	AK154818|D930015E06Rik|229473|RIKEN cDNA D930015E06 gene	NM_172681|D930015E06Rik|229473|RIKEN cDNA D930015E06 gene	AK086232|D930015E06Rik|229473|RIKEN cDNA D930015E06 gene
mm9_v1_chr12_+_70298163_70298251	0.357732	SOX2.p2	AK161156|9330151L19Rik|414085|RIKEN cDNA 9330151L19 gene	AK154174|9330151L19Rik|414085|RIKEN cDNA 9330151L19 gene	AK034052|9330151L19Rik|414085|RIKEN cDNA 9330151L19 gene
mm9_v1_chr13_-_27872632_27872672	0.357641	SOX2.p2	BC099442|Prl7c1|67505|prolactin family 7, subfamily c, member 1	AK014436|Prl7c1|67505|prolactin family 7, subfamily c, member 1	AF525157|Prl7c1|67505|prolactin family 7, subfamily c, member 1	AK005486|Prl7c1|67505|prolactin family 7, subfamily c, member 1	NM_026206|Prl7c1|67505|prolactin family 7, subfamily c, member 1
mm9_v1_chr7_-_23477335_23477335	0.357149	SOX2.p2	NM_001167154|Gm8693|667543|predicted gene 8693	NM_001167155|Gm4144|100042980|predicted gene 4144
mm9_v1_chr9_+_106073523_106073570	0.356458	SOX2.p2	BC031502|Wdr82|77305|WD repeat domain containing 82	EF011615|Wdr82|77305|WD repeat domain containing 82
mm9_v1_chr18_+_11998043_11998097	0.356311	SOX2.p2	AK158396|Cables1|63955|CDK5 and Abl enzyme substrate 1	AF328140|Cables1|63955|CDK5 and Abl enzyme substrate 1
mm9_v1_chr6_+_106068758_106068758	0.355512	SOX2.p2	AK043507|Cntn4|269784|contactin 4	NM_001109751|Cntn4|269784|contactin 4
mm9_v1_chr2_+_71227270_71227349	0.354358	SOX2.p2	AK137648|Hat1|107435|histone aminotransferase 1	AK014330|Hat1|107435|histone aminotransferase 1	AK010715|Hat1|107435|histone aminotransferase 1	AK169315|Hat1|107435|histone aminotransferase 1	AK041700|Hat1|107435|histone aminotransferase 1	NM_026115|Hat1|107435|histone aminotransferase 1	AK018270|Hat1|107435|histone aminotransferase 1	BC055460|Hat1|107435|histone aminotransferase 1
mm9_v1_chr11_-_60727237_60727316	0.353886	SOX2.p2	BC034332|Gm16515|24083|predicted gene, Gm16515	BC038816|Gm16515|24083|predicted gene, Gm16515	AK004720|Gm16515|24083|predicted gene, Gm16515	AK089179|Gm16515|24083|predicted gene, Gm16515	AK080453|Gm16515|24083|predicted gene, Gm16515	NM_025294|Gm16515|24083|predicted gene, Gm16515
mm9_v1_chr13_-_49404519_49404608	0.353466	SOX2.p2	AK157835|Fgd3|30938|FYVE, RhoGEF and PH domain containing 3	NM_015759|Fgd3|30938|FYVE, RhoGEF and PH domain containing 3	AF017369|Fgd3|30938|FYVE, RhoGEF and PH domain containing 3
mm9_v1_chr4_+_140723459_140723541	0.352938	SOX2.p2	AK020135|Fbxo42|213499|F-box protein 42
mm9_v1_chr9_+_108686107_108686181	0.352676	SOX2.p2	AK005166|Ip6k2|76500|inositol hexaphosphate kinase 2	AK050593|Ip6k2|76500|inositol hexaphosphate kinase 2	AK057615|Ip6k2|76500|inositol hexaphosphate kinase 2
mm9_v1_chr7_+_22974395_22974395	0.35249	SOX2.p2	NM_001166750|Vmn1r143|667469|vomeronasal 1 receptor 143	NM_001167538|Vmn1r95|100312475|vomeronasal 1 receptor, 95
mm9_v1_chr2_+_121781736_121781881	0.352349	SOX2.p2	AK163262|Ctdspl2|329506|CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2	AK082646|Ctdspl2|329506|CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2
mm9_v1_chr10_+_111497244_111497244	0.351842	SOX2.p2	AK005860|Glipr1l1|69286|GLI pathogenesis-related 1 like 1	NM_027018|Glipr1l1|69286|GLI pathogenesis-related 1 like 1
mm9_v1_chr9_-_65917524_65917537	0.351392	SOX2.p2	BC138950|Snx22|382083|sorting nexin 22	BC138951|Snx22|382083|sorting nexin 22	AK032028|Snx22|382083|sorting nexin 22	NM_001025612|Snx22|382083|sorting nexin 22
mm9_v1_chr7_-_54387695_54387755	0.351131	SOX2.p2	BC057339|Ptpn5|19259|protein tyrosine phosphatase, non-receptor type 5	BC051975|Ptpn5|19259|protein tyrosine phosphatase, non-receptor type 5	AK038416|Ptpn5|19259|protein tyrosine phosphatase, non-receptor type 5
mm9_v1_chr8_-_108503199_108503328	0.350875	SOX2.p2	AF488553|Dpep3|71854|dipeptidase 3	AK006085|Dpep3|71854|dipeptidase 3	NM_027960|Dpep3|71854|dipeptidase 3	BC051148|Dpep3|71854|dipeptidase 3
mm9_v1_chr15_+_37163001_37163168	0.350741	SOX2.p2	BC055035|Grhl2|252973|grainyhead-like 2 (Drosophila)	AF411213|Grhl2|252973|grainyhead-like 2 (Drosophila)
mm9_v1_chr7_+_20779058_20779058	0.349965	SOX2.p2	NM_001166750|Vmn1r143|667469|vomeronasal 1 receptor 143	NM_001167538|Vmn1r95|100312475|vomeronasal 1 receptor, 95
mm9_v1_chr1_+_187311172_187311232	0.349317	SOX2.p2	AK017151|5033404E19Rik|114668|RIKEN cDNA 5033404E19 gene
mm9_v1_chr2_-_30033944_30034014	0.34931	SOX2.p2	AK044983|D2Wsu81e|227695|DNA segment, Chr 2, Wayne State University 81, expressed	AK036945|D2Wsu81e|227695|DNA segment, Chr 2, Wayne State University 81, expressed	AK147162|D2Wsu81e|227695|DNA segment, Chr 2, Wayne State University 81, expressed	AK046148|D2Wsu81e|227695|DNA segment, Chr 2, Wayne State University 81, expressed	NM_172660|D2Wsu81e|227695|DNA segment, Chr 2, Wayne State University 81, expressed
mm9_v1_chr3_-_63941401_63941401	0.349012	SOX2.p2	NM_001104592|Vmn2r2|100125586|vomeronasal 2, receptor 2
mm9_v1_chr18_+_86882439_86882439	0.348388	SOX2.p2	AK032112|Cbln2|12405|cerebellin 2 precursor protein	NM_172633|Cbln2|12405|cerebellin 2 precursor protein
mm9_v1_chr5_+_94806341_94806364	0.345768	SOX2.p2	AK087752|AA792892|100554|expressed sequence AA792892	BC120516|AA792892|100554|expressed sequence AA792892	BC125434|AA792892|100554|expressed sequence AA792892	NM_178894|AA792892|100554|expressed sequence AA792892
mm9_v1_chr2_+_122573644_122573786	0.345521	SOX2.p2	
mm9_v1_chr10_+_86520790_86520790	0.345497	SOX2.p2	NM_029685|1700113H08Rik|76640|RIKEN cDNA 1700113H08 gene
mm9_v1_chr7_+_28964486_28964515	0.345443	SOX2.p2	BC019545|Dyrk1b|13549|dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1b	NM_001037957|Dyrk1b|13549|dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1b	NM_010092|Dyrk1b|13549|dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1b	Y18280|Dyrk1b|13549|dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1b
mm9_v1_chr1_+_167718811_167718898	0.345389	SOX2.p2	AK138774|Cd247|12503|CD247 antigen	J04967|Cd247|12503|CD247 antigen	NM_001113391|Cd247|12503|CD247 antigen	NM_001113392|Cd247|12503|CD247 antigen	NM_001113393|Cd247|12503|CD247 antigen	NM_001113394|Cd247|12503|CD247 antigen	NM_031162|Cd247|12503|CD247 antigen	AK017904|Cd247|12503|CD247 antigen	AK088087|Cd247|12503|CD247 antigen	L03353|Cd247|12503|CD247 antigen	S51932|Cd247|12503|CD247 antigen	U56258|Cd247|12503|CD247 antigen	X84237|Cd247|12503|CD247 antigen	BC052824|Cd247|12503|CD247 antigen
mm9_v1_chr8_-_74090499_74090547	0.345153	SOX2.p2	BC021911|Nxnl1|234404|nucleoredoxin-like 1	BC017153|Nxnl1|234404|nucleoredoxin-like 1	NM_145598|Nxnl1|234404|nucleoredoxin-like 1
mm9_v1_chr12_+_70269800_70269846	0.344406	SOX2.p2	AK144741|Lrr1|69706|leucine rich repeat protein 1	NM_001081406|Lrr1|69706|leucine rich repeat protein 1	AK010419|Lrr1|69706|leucine rich repeat protein 1	BC075711|Lrr1|69706|leucine rich repeat protein 1	BC117053|Lrr1|69706|leucine rich repeat protein 1	BC117055|Lrr1|69706|leucine rich repeat protein 1	BC022648|Lrr1|69706|leucine rich repeat protein 1
mm9_v1_chr3_+_66789621_66789657	0.343918	SOX2.p2	AK168539|Rsrc1|66880|arginine/serine-rich coiled-coil 1	BC038303|Rsrc1|66880|arginine/serine-rich coiled-coil 1	AK004742|Rsrc1|66880|arginine/serine-rich coiled-coil 1	AK169340|Rsrc1|66880|arginine/serine-rich coiled-coil 1	BC027501|Rsrc1|66880|arginine/serine-rich coiled-coil 1	BC083123|Rsrc1|66880|arginine/serine-rich coiled-coil 1
mm9_v1_chr16_+_49911557_49911575	0.343563	SOX2.p2	AK164165|Cd47|16423|CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	AK021021|Cd47|16423|CD47 antigen (Rh-related antigen, integrin-associated signal transducer)
mm9_v1_chr4_+_137237557_137237628	0.343188	SOX2.p2	NM_001081155|Rap1gap|110351|Rap1 GTPase-activating protein	BC052065|Rap1gap|110351|Rap1 GTPase-activating protein
mm9_v1_chr5_-_100588412_100588450	0.342794	SOX2.p2	AK044702|Tmem150c|231503|transmembrane protein 150C
mm9_v1_chr18_+_37854011_37854154	0.342767	SOX2.p2	AK043161|Pcdhga5|93713|protocadherin gamma subfamily A, 5	BC057404|Pcdhga5|93713|protocadherin gamma subfamily A, 5	AK043491|Pcdhga5|93713|protocadherin gamma subfamily A, 5	AY013799|Pcdhga5|93713|protocadherin gamma subfamily A, 5	NM_033588|Pcdhga5|93713|protocadherin gamma subfamily A, 5
mm9_v1_chr5_-_93611701_93611836	0.342046	SOX2.p2	
mm9_v1_chr8_+_41837561_41837564	0.341897	SOX2.p2	AF167403|Adam25|23793|a disintegrin and metallopeptidase domain 25 (testase 2)	NM_011781|Adam25|23793|a disintegrin and metallopeptidase domain 25 (testase 2)	AK016581|Adam25|23793|a disintegrin and metallopeptidase domain 25 (testase 2)
mm9_v1_chr8_-_113551636_113551700	0.34105	SOX2.p2	AK147499|Ddx19b|234733|DEAD (Asp-Glu-Ala-Asp) box polypeptide 19b	AK013362|Ddx19b|234733|DEAD (Asp-Glu-Ala-Asp) box polypeptide 19b	NM_001190800|Ddx19b|234733|DEAD (Asp-Glu-Ala-Asp) box polypeptide 19b	NM_172284|Ddx19b|234733|DEAD (Asp-Glu-Ala-Asp) box polypeptide 19b
mm9_v1_chr17_-_24781872_24781901	0.340745	SOX2.p2	BC065778|Slc9a3r2|65962|solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 2	AK002557|Slc9a3r2|65962|solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 2	NM_023449|Slc9a3r2|65962|solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 2
mm9_v1_chr1_+_6720087_6720131	0.340704	SOX2.p2	AB097467|St18|240690|suppression of tumorigenicity 18	AJ536155|St18|240690|suppression of tumorigenicity 18	AK032557|St18|240690|suppression of tumorigenicity 18	NM_173868|St18|240690|suppression of tumorigenicity 18
mm9_v1_chr7_-_22331108_22331108	0.34063	SOX2.p2	NM_001166746|Vmn1r111|667292|vomeronasal 1 receptor 111	NM_001166839|Gm4172|100043016|predicted gene 4172	NM_001167168|Gm4220|100043088|predicted gene 4220	NM_001167169|Gm4179|100043029|predicted gene 4179
mm9_v1_chr11_-_68740550_68740582	0.339708	SOX2.p2	AB074438|Odf4|252868|outer dense fiber of sperm tails 4	BC060992|Odf4|252868|outer dense fiber of sperm tails 4	NM_145746|Odf4|252868|outer dense fiber of sperm tails 4
mm9_v1_chr5_-_77524050_77524182	0.339676	SOX2.p2	AF536202|Hopx|74318|HOP homeobox
mm9_v1_chr10_+_33577526_33577529	0.339475	SOX2.p2	AF026075|Sult3a1|57430|sulfotransferase family 3A, member 1	BC125593|Sult3a1|57430|sulfotransferase family 3A, member 1	BC125595|Sult3a1|57430|sulfotransferase family 3A, member 1	NM_020565|Sult3a1|57430|sulfotransferase family 3A, member 1
mm9_v1_chr11_-_99199267_99199279	0.339036	SOX2.p2	BC116672|Krt26|320864|keratin 26	AK132445|Krt26|320864|keratin 26	AK028682|Krt26|320864|keratin 26	AK162718|Krt26|320864|keratin 26	NM_001033397|Krt26|320864|keratin 26	AK028591|Krt26|320864|keratin 26
mm9_v1_chr11_-_3166349_3166433	0.337703	SOX2.p2	BC039649|Drg1|13494|developmentally regulated GTP binding protein 1	AK080814|Drg1|13494|developmentally regulated GTP binding protein 1	D10715|Drg1|13494|developmentally regulated GTP binding protein 1	NM_007879|Drg1|13494|developmentally regulated GTP binding protein 1	AK144438|Drg1|13494|developmentally regulated GTP binding protein 1	AK044194|Drg1|13494|developmentally regulated GTP binding protein 1	AK155061|Drg1|13494|developmentally regulated GTP binding protein 1	AK090156|Drg1|13494|developmentally regulated GTP binding protein 1
mm9_v1_chr17_+_72022598_72022608	0.337072	SOX2.p2	NM_177087|Fam179a|320159|family with sequence similarity 179, member A
mm9_v1_chr6_-_72908018_72908225	0.33622	SOX2.p2	BC089327|Tmsb10|19240|thymosin, beta 10	Z48496|Tmsb10|19240|thymosin, beta 10	NM_001039392|Tmsb10|19240|thymosin, beta 10
mm9_v1_chr4_-_124742875_124742900	0.335711	SOX2.p2	BC118619|Dnali1|75563|dynein, axonemal, light intermediate polypeptide 1	BC122552|Dnali1|75563|dynein, axonemal, light intermediate polypeptide 1	AK077109|Dnali1|75563|dynein, axonemal, light intermediate polypeptide 1	NM_175223|Dnali1|75563|dynein, axonemal, light intermediate polypeptide 1
mm9_v1_chr1_-_65003291_65003407	0.335577	SOX2.p2	AK034959|Plekhm3|241075|pleckstrin homology domain containing, family M, member 3	BC063098|Plekhm3|241075|pleckstrin homology domain containing, family M, member 3	NM_001039493|Plekhm3|241075|pleckstrin homology domain containing, family M, member 3
mm9_v1_chr2_+_181336020_181336108	0.335575	SOX2.p2	AK145461|Prpf6|68879|PRP6 pre-mRNA splicing factor 6 homolog (yeast)	NM_133701|Prpf6|68879|PRP6 pre-mRNA splicing factor 6 homolog (yeast)	AK166890|Prpf6|68879|PRP6 pre-mRNA splicing factor 6 homolog (yeast)	BC025030|Prpf6|68879|PRP6 pre-mRNA splicing factor 6 homolog (yeast)	AK011639|Prpf6|68879|PRP6 pre-mRNA splicing factor 6 homolog (yeast)	AK081998|Prpf6|68879|PRP6 pre-mRNA splicing factor 6 homolog (yeast)	BC014869|Prpf6|68879|PRP6 pre-mRNA splicing factor 6 homolog (yeast)	BC023691|Prpf6|68879|PRP6 pre-mRNA splicing factor 6 homolog (yeast)
mm9_v1_chr17_+_72131286_72131286	0.335547	SOX2.p2	BC035226|Clip4|78785|CAP-GLY domain containing linker protein family, member 4	NM_030179|Clip4|78785|CAP-GLY domain containing linker protein family, member 4
mm9_v1_chr3_+_66789859_66789903	0.335105	SOX2.p2	BC043045|Rsrc1|66880|arginine/serine-rich coiled-coil 1
mm9_v1_chr4_-_108311676_108311740	0.334854	SOX2.p2	
mm9_v1_chr8_+_34842304_34842440	0.334758	SOX2.p2	AK158783|Gtf2e2|68153|general transcription factor II E, polypeptide 2 (beta subunit)	NM_001167921|Gtf2e2|68153|general transcription factor II E, polypeptide 2 (beta subunit)	AK150415|Gtf2e2|68153|general transcription factor II E, polypeptide 2 (beta subunit)	AK153370|Gtf2e2|68153|general transcription factor II E, polypeptide 2 (beta subunit)
mm9_v1_chr9_+_90057930_90058082	0.334604	SOX2.p2	BC076575|Adamts7|108153|a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 7	BC141173|Adamts7|108153|a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 7	BC145491|Adamts7|108153|a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 7	AY551090|Adamts7|108153|a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 7
mm9_v1_chr6_-_129573858_129573881	0.333997	SOX2.p2	AF030313|Klrk1|27007|killer cell lectin-like receptor subfamily K, member 1	NM_001083322|Klrk1|27007|killer cell lectin-like receptor subfamily K, member 1	AK170499|Klrk1|27007|killer cell lectin-like receptor subfamily K, member 1
mm9_v1_chr6_+_89971881_89971882	0.333908	SOX2.p2	NM_053219|Vmn1r47|113846|vomeronasal 1 receptor 47	BC111822|Vmn1r47|113846|vomeronasal 1 receptor 47
mm9_v1_chr5_+_89956453_89956453	0.333898	SOX2.p2	AK050939|Npffr2|104443|neuropeptide FF receptor 2	NM_133192|Npffr2|104443|neuropeptide FF receptor 2
mm9_v1_chr5_-_88128419_88128445	0.33382	SOX2.p2	BC019114|Csn2|12991|casein beta	BC013332|Csn2|12991|casein beta	BC092098|Csn2|12991|casein beta	BC020356|Csn2|12991|casein beta	BC050270|Csn2|12991|casein beta	BC020383|Csn2|12991|casein beta	BC021153|Csn2|12991|casein beta	BC057671|Csn2|12991|casein beta	BC080709|Csn2|12991|casein beta	AK164792|Csn2|12991|casein beta	AK164793|Csn2|12991|casein beta	AK085729|Csn2|12991|casein beta	AK021324|Csn2|12991|casein beta	AK021328|Csn2|12991|casein beta	AK052803|Csn2|12991|casein beta	AK052805|Csn2|12991|casein beta	AK052822|Csn2|12991|casein beta	AK085678|Csn2|12991|casein beta	AK085694|Csn2|12991|casein beta	AK085698|Csn2|12991|casein beta	AK085756|Csn2|12991|casein beta	AK142616|Csn2|12991|casein beta	AK142620|Csn2|12991|casein beta	AK142631|Csn2|12991|casein beta	AK142635|Csn2|12991|casein beta	AK164747|Csn2|12991|casein beta	AK164761|Csn2|12991|casein beta	AK164791|Csn2|12991|casein beta	AK164794|Csn2|12991|casein beta	NM_009972|Csn2|12991|casein beta	X04490|Csn2|12991|casein beta
mm9_v1_chr17_-_80879792_80879792	0.333728	SOX2.p2	AK140310|Sos1|20662|son of sevenless homolog 1 (Drosophila)	NM_009231|Sos1|20662|son of sevenless homolog 1 (Drosophila)
mm9_v1_chr2_-_148676641_148676677	0.333598	SOX2.p2	BC104302|9230104L09Rik|77705|RIKEN cDNA 9230104L09 gene	BC104303|9230104L09Rik|77705|RIKEN cDNA 9230104L09 gene	AK020314|9230104L09Rik|77705|RIKEN cDNA 9230104L09 gene	NM_029960|9230104L09Rik|77705|RIKEN cDNA 9230104L09 gene
mm9_v1_chr9_+_98886784_98886846	0.332088	SOX2.p2	AK005762|Faim|23873|Fas apoptotic inhibitory molecule	NM_001122851|Faim|23873|Fas apoptotic inhibitory molecule	NM_011810|Faim|23873|Fas apoptotic inhibitory molecule	AK044452|Faim|23873|Fas apoptotic inhibitory molecule	AK156341|Faim|23873|Fas apoptotic inhibitory molecule	AK149335|Faim|23873|Fas apoptotic inhibitory molecule
mm9_v1_chr2_-_152223710_152223930	0.3305	SOX2.p2	BC067019|Sox12|20667|SRY-box containing gene 12	NM_011438|Sox12|20667|SRY-box containing gene 12
mm9_v1_chr2_+_84820615_84820637	0.330435	SOX2.p2	AK156715|Prg2|19074|proteoglycan 2, bone marrow	AK010901|Prg2|19074|proteoglycan 2, bone marrow	NM_008920|Prg2|19074|proteoglycan 2, bone marrow	BC109348|Prg2|19074|proteoglycan 2, bone marrow
mm9_v1_chr7_-_111291762_111291785	0.32968	SOX2.p2	BC100419|Ubqln3|244178|ubiquilin 3	AK077072|Ubqln3|244178|ubiquilin 3	NM_198623|Ubqln3|244178|ubiquilin 3
mm9_v1_chrX_-_70905062_70905211	0.329228	SOX2.p2	AK134665|Pnck|93843|pregnancy upregulated non-ubiquitously expressed CaM kinase	AF181984|Pnck|93843|pregnancy upregulated non-ubiquitously expressed CaM kinase	NM_012040|Pnck|93843|pregnancy upregulated non-ubiquitously expressed CaM kinase
mm9_v1_chr3_+_55265654_55265683	0.328967	SOX2.p2	NM_001111051|Dclk1|13175|doublecortin-like kinase 1	NM_001111052|Dclk1|13175|doublecortin-like kinase 1	NM_001195539|Dclk1|13175|doublecortin-like kinase 1	NM_001195540|Dclk1|13175|doublecortin-like kinase 1
mm9_v1_chr5_-_86539474_86539529	0.328909	SOX2.p2	AK017687|Uba6|231380|ubiquitin-like modifier activating enzyme 6
mm9_v1_chr14_-_68333427_68333447	0.328861	SOX2.p2	AK160223|Cdca2|108912|cell division cycle associated 2	AK031083|Cdca2|108912|cell division cycle associated 2	AK166952|Cdca2|108912|cell division cycle associated 2	BC037136|Cdca2|108912|cell division cycle associated 2
mm9_v1_chr5_+_115777174_115777309	0.328253	SOX2.p2	BC012217|Srsf9|108014|serine/arginine-rich splicing factor 9	NM_025573|Srsf9|108014|serine/arginine-rich splicing factor 9	AK159190|Srsf9|108014|serine/arginine-rich splicing factor 9	AK011621|Srsf9|108014|serine/arginine-rich splicing factor 9
mm9_v1_chr9_+_45214037_45214172	0.328117	SOX2.p2	AY626243|Fxyd2|11936|FXYD domain-containing ion transport regulator 2	AY626245|Fxyd2|11936|FXYD domain-containing ion transport regulator 2	AK002228|Fxyd2|11936|FXYD domain-containing ion transport regulator 2	NM_007503|Fxyd2|11936|FXYD domain-containing ion transport regulator 2	BC024614|Fxyd2|11936|FXYD domain-containing ion transport regulator 2	AK002215|Fxyd2|11936|FXYD domain-containing ion transport regulator 2
mm9_v1_chr14_+_34402392_34402458	0.327973	SOX2.p2	AK017003|Ptpn20|19256|protein tyrosine phosphatase, non-receptor type 20	NM_008978|Ptpn20|19256|protein tyrosine phosphatase, non-receptor type 20	AK029493|Ptpn20|19256|protein tyrosine phosphatase, non-receptor type 20
mm9_v1_chr10_+_59569084_59569159	0.327812	SOX2.p2	AK140483|Spock2|94214|sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2	AK162941|Spock2|94214|sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2
mm9_v1_chrX_+_7156801_7156818	0.327331	SOX2.p2	AK157447|Foxp3|20371|forkhead box P3	DQ387959|Foxp3|20371|forkhead box P3	AF277992|Foxp3|20371|forkhead box P3	NM_054039|Foxp3|20371|forkhead box P3
mm9_v1_chr3_+_32607582_32607695	0.327309	SOX2.p2	AF041476|Actl6a|56456|actin-like 6A	AK169278|Actl6a|56456|actin-like 6A	AK090154|Actl6a|56456|actin-like 6A	AK167905|Actl6a|56456|actin-like 6A	BC094498|Actl6a|56456|actin-like 6A	AK002724|Actl6a|56456|actin-like 6A	BC001994|Actl6a|56456|actin-like 6A
mm9_v1_chr8_+_55686133_55686133	0.326867	SOX2.p2	AF395083|Spata4|69281|spermatogenesis associated 4	AF530515|Spata4|69281|spermatogenesis associated 4	AK005612|Spata4|69281|spermatogenesis associated 4	BC048650|Spata4|69281|spermatogenesis associated 4	NM_133711|Spata4|69281|spermatogenesis associated 4
mm9_v1_chr18_-_34666454_34666491	0.32558	SOX2.p2	AK029766|Fam13b|225358|family with sequence similarity 13, member B	BC031465|Fam13b|225358|family with sequence similarity 13, member B	NM_146084|Fam13b|225358|family with sequence similarity 13, member B	AK084711|Fam13b|225358|family with sequence similarity 13, member B
mm9_v1_chr3_-_153388047_153388152	0.32507	SOX2.p2	BC131987|St6galnac3|20447|ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	BC132317|St6galnac3|20447|ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	BC058387|St6galnac3|20447|ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	AK034804|St6galnac3|20447|ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	NM_011372|St6galnac3|20447|ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	Y11342|St6galnac3|20447|ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3
mm9_v1_chr5_+_95939760_95939760	0.324582	SOX2.p2	AK145737|Gm3286|100041354|predicted gene 3286	NM_001122678|Gm3286|100041354|predicted gene 3286	NM_001167792|Gm3286|100041354|predicted gene 3286	NM_001167793|Gm3286|100041354|predicted gene 3286
mm9_v1_chr7_-_137663020_137663074	0.324263	SOX2.p2	BC050948|Ate1|11907|arginyltransferase 1	NM_001136054|Ate1|11907|arginyltransferase 1	AK167591|Ate1|11907|arginyltransferase 1	BC042601|Ate1|11907|arginyltransferase 1	NM_013799|Ate1|11907|arginyltransferase 1	AK148442|Ate1|11907|arginyltransferase 1
mm9_v1_chr8_-_10928326_10928456	0.324176	SOX2.p2	AK014460|3930402G23Rik|665306|RIKEN cDNA 3930402G23 gene
mm9_v1_chr9_-_57613666_57613666	0.323422	SOX2.p2	AK146942|Clk3|102414|CDC-like kinase 3	AK167300|Clk3|102414|CDC-like kinase 3	NM_007713|Clk3|102414|CDC-like kinase 3
mm9_v1_chr11_-_100511964_100512006	0.322891	SOX2.p2	BC116726|Zfp385c|278304|zinc finger protein 385C	AK044299|Zfp385c|278304|zinc finger protein 385C	NM_177790|Zfp385c|278304|zinc finger protein 385C
mm9_v1_chr16_-_45724422_45724643	0.322752	SOX2.p2	BC043027|Tagln3|56370|transgelin 3	AB031291|Tagln3|56370|transgelin 3	AK013484|Tagln3|56370|transgelin 3	BC055338|Tagln3|56370|transgelin 3	NM_019754|Tagln3|56370|transgelin 3
mm9_v1_chr5_+_53440591_53440620	0.322744	SOX2.p2	AK164786|Slc34a2|20531|solute carrier family 34 (sodium phosphate), member 2	NM_011402|Slc34a2|20531|solute carrier family 34 (sodium phosphate), member 2	AK004832|Slc34a2|20531|solute carrier family 34 (sodium phosphate), member 2	AK145599|Slc34a2|20531|solute carrier family 34 (sodium phosphate), member 2	AF081499|Slc34a2|20531|solute carrier family 34 (sodium phosphate), member 2	BC096369|Slc34a2|20531|solute carrier family 34 (sodium phosphate), member 2
mm9_v1_chr4_-_41644071_41644122	0.322452	SOX2.p2	AF068615|Cntfr|12804|ciliary neurotrophic factor receptor	AK015675|Cntfr|12804|ciliary neurotrophic factor receptor	NM_001146080|Cntfr|12804|ciliary neurotrophic factor receptor	NM_016673|Cntfr|12804|ciliary neurotrophic factor receptor
mm9_v1_chr13_-_101262544_101262571	0.321713	SOX2.p2	NM_022011|Gtf2h2|23894|general transcription factor II H, polypeptide 2
mm9_v1_chr8_+_86132073_86132203	0.321597	SOX2.p2	NM_018808|Dnajb1|81489|DnaJ (Hsp40) homolog, subfamily B, member 1	AB028272|Dnajb1|81489|DnaJ (Hsp40) homolog, subfamily B, member 1	AK146657|Dnajb1|81489|DnaJ (Hsp40) homolog, subfamily B, member 1	AK164392|Dnajb1|81489|DnaJ (Hsp40) homolog, subfamily B, member 1	AK168220|Dnajb1|81489|DnaJ (Hsp40) homolog, subfamily B, member 1	AK168291|Dnajb1|81489|DnaJ (Hsp40) homolog, subfamily B, member 1	AK002290|Dnajb1|81489|DnaJ (Hsp40) homolog, subfamily B, member 1	AK160924|Dnajb1|81489|DnaJ (Hsp40) homolog, subfamily B, member 1	AK167718|Dnajb1|81489|DnaJ (Hsp40) homolog, subfamily B, member 1	BC012962|Dnajb1|81489|DnaJ (Hsp40) homolog, subfamily B, member 1
mm9_v1_chr6_+_129462572_129462636	0.321028	SOX2.p2	AK085389|D630042F21Rik|330428|RIKEN cDNA D630042F21 gene	NM_001081186|D630042F21Rik|330428|RIKEN cDNA D630042F21 gene	AK085571|D630042F21Rik|330428|RIKEN cDNA D630042F21 gene
mm9_v1_chr15_+_82000246_82000509	0.320569	SOX2.p2	BC023333|Srebf2|20788|sterol regulatory element binding factor 2
mm9_v1_chr7_+_5031809_5032021	0.319864	SOX2.p2	AK155033|Epn1|13854|epsin 1	BC067206|Epn1|13854|epsin 1	BC099682|Epn1|13854|epsin 1	NM_010147|Epn1|13854|epsin 1
mm9_v1_chr1_-_4350323_4350394	0.31954	SOX2.p2	BC038794|Rp1|19888|retinitis pigmentosa 1 (human)	BC120927|Rp1|19888|retinitis pigmentosa 1 (human)	BC120928|Rp1|19888|retinitis pigmentosa 1 (human)	AF155141|Rp1|19888|retinitis pigmentosa 1 (human)	AK044413|Rp1|19888|retinitis pigmentosa 1 (human)	BC096607|Rp1|19888|retinitis pigmentosa 1 (human)	NM_011283|Rp1|19888|retinitis pigmentosa 1 (human)
mm9_v1_chr6_-_129335520_129335520	0.319376	SOX2.p2	AK016908|Clec12b|71183|C-type lectin domain family 12, member B	NM_027709|Clec12b|71183|C-type lectin domain family 12, member B
mm9_v1_chr1_+_31279683_31279691	0.319001	SOX2.p2	AK015858|4930521A18Rik|74708|RIKEN cDNA 4930521A18 gene	NM_029062|4930521A18Rik|74708|RIKEN cDNA 4930521A18 gene	BC107262|4930521A18Rik|74708|RIKEN cDNA 4930521A18 gene
mm9_v1_chr8_+_74432504_74432561	0.318931	SOX2.p2	NM_001166645|Zfp882|382019|zinc finger protein 882	AK040385|Zfp882|382019|zinc finger protein 882	BC080687|Zfp882|382019|zinc finger protein 882
mm9_v1_chr2_+_25719373_25719373	0.318792	SOX2.p2	FJ628361|Kcnt1|227632|potassium channel, subfamily T, member 1	NM_001145403|Kcnt1|227632|potassium channel, subfamily T, member 1
mm9_v1_chr4_+_108132677_108132756	0.318759	SOX2.p2	BC145507|Zcchc11|230594|zinc finger, CCHC domain containing 11	BC150791|Zcchc11|230594|zinc finger, CCHC domain containing 11
mm9_v1_chr11_+_115015491_115015512	0.318623	SOX2.p2	BC050757|Rab37|58222|RAB37, member of RAS oncogene family	NM_021411|Rab37|58222|RAB37, member of RAS oncogene family	AK040216|Rab37|58222|RAB37, member of RAS oncogene family	AK039716|Rab37|58222|RAB37, member of RAS oncogene family	AK050483|Rab37|58222|RAB37, member of RAS oncogene family	BC128020|Rab37|58222|RAB37, member of RAS oncogene family	AB232633|Rab37|58222|RAB37, member of RAS oncogene family	AF233582|Rab37|58222|RAB37, member of RAS oncogene family
mm9_v1_chr16_+_21423190_21423247	0.318462	SOX2.p2	NM_001081366|Vps8|209018|vacuolar protein sorting 8 homolog (S. cerevisiae)	AK122375|Vps8|209018|vacuolar protein sorting 8 homolog (S. cerevisiae)
mm9_v1_chr17_+_34766489_34766633	0.318427	SOX2.p2	BC128489|Prrt1|260297|proline-rich transmembrane protein 1	NM_030890|Prrt1|260297|proline-rich transmembrane protein 1	BC115512|Prrt1|260297|proline-rich transmembrane protein 1	BC115513|Prrt1|260297|proline-rich transmembrane protein 1
mm9_v1_chr17_+_73186891_73186925	0.317573	SOX2.p2	AK154461|Ypel5|383295|yippee-like 5 (Drosophila)
mm9_v1_chr8_+_91220959_91220964	0.317479	SOX2.p2	AK042764|Cyld|74256|cylindromatosis (turban tumor syndrome)	AK167424|Cyld|74256|cylindromatosis (turban tumor syndrome)	AK133479|Cyld|74256|cylindromatosis (turban tumor syndrome)
mm9_v1_chr11_+_89892027_89892040	0.317067	SOX2.p2	AK003574|Tmem100|67888|transmembrane protein 100	AK033406|Tmem100|67888|transmembrane protein 100
mm9_v1_chr9_-_21875603_21875617	0.317052	SOX2.p2	AK089104|Zfp653|319601|zinc finger protein 653
mm9_v1_chr12_-_70458134_70458151	0.316008	SOX2.p2	AK005212|Nemf|66244|nuclear export mediator factor	AK041458|Nemf|66244|nuclear export mediator factor	AK171652|Nemf|66244|nuclear export mediator factor	BC080716|Nemf|66244|nuclear export mediator factor
mm9_v1_chr13_+_78337168_78337277	0.315709	SOX2.p2	AK082108|A830082K12Rik|320174|RIKEN cDNA A830082K12 gene
mm9_v1_chr14_-_122314994_122315068	0.315658	SOX2.p2	AK172401|Gpr18|110168|G protein-coupled receptor 18	BC034872|Gpr18|110168|G protein-coupled receptor 18	NM_182806|Gpr18|110168|G protein-coupled receptor 18	AK157029|Gpr18|110168|G protein-coupled receptor 18	AK156868|Gpr18|110168|G protein-coupled receptor 18	AK156039|Gpr18|110168|G protein-coupled receptor 18
mm9_v1_chr14_-_64035873_64036023	0.315583	SOX2.p2	BC030668|Blk|12143|B lymphoid kinase	M30903|Blk|12143|B lymphoid kinase	AK171640|Blk|12143|B lymphoid kinase	AK089888|Blk|12143|B lymphoid kinase	NM_007549|Blk|12143|B lymphoid kinase
mm9_v1_chr2_+_3035629_3035684	0.314969	SOX2.p2	NM_001081161|Fam171a1|269233|family with sequence similarity 171, member A1	AK032237|Fam171a1|269233|family with sequence similarity 171, member A1
mm9_v1_chr6_-_25639835_25639849	0.314882	SOX2.p2	BC031918|Gpr37|14763|G protein-coupled receptor 37
mm9_v1_chr19_-_47538692_47538733	0.314441	SOX2.p2	BC118022|Sh3pxd2a|14218|SH3 and PX domains 2A
mm9_v1_chr4_+_140258090_140258179	0.313882	SOX2.p2	AK186216|Rcc2|108911|regulator of chromosome condensation 2	AK129370|Rcc2|108911|regulator of chromosome condensation 2
mm9_v1_chr3_+_89019126_89019154	0.313624	SOX2.p2	L04302|Thbs3|21827|thrombospondin 3	L24434|Thbs3|21827|thrombospondin 3	BC060104|Thbs3|21827|thrombospondin 3	BC053023|Thbs3|21827|thrombospondin 3
mm9_v1_chr4_+_101659444_101659444	0.313363	SOX2.p2	NM_001085520|Gm12789|381536|predicted gene 12789
mm9_v1_chr7_-_54387915_54388047	0.313291	SOX2.p2	NM_001163565|Ptpn5|19259|protein tyrosine phosphatase, non-receptor type 5	BC079592|Ptpn5|19259|protein tyrosine phosphatase, non-receptor type 5
mm9_v1_chrX_-_6618729_6618744	0.313179	SOX2.p2	AJ555465|Ccnb3|209091|cyclin B3	AJ555464|Ccnb3|209091|cyclin B3	NM_183015|Ccnb3|209091|cyclin B3
mm9_v1_chr7_+_17460697_17460886	0.313067	SOX2.p2	AB073971|Dact3|629378|dapper homolog 3, antagonist of beta-catenin (xenopus)
mm9_v1_chr14_-_51301319_51301319	0.312505	SOX2.p2	NM_207156|Olfr747|258264|olfactory receptor 747
mm9_v1_chr15_-_75397243_75397344	0.312386	SOX2.p2	AF127091|Ly6h|23934|lymphocyte antigen 6 complex, locus H	BC028758|Ly6h|23934|lymphocyte antigen 6 complex, locus H	NM_001135688|Ly6h|23934|lymphocyte antigen 6 complex, locus H	AK021002|Ly6h|23934|lymphocyte antigen 6 complex, locus H
mm9_v1_chr6_-_51413182_51413233	0.311422	SOX2.p2	AK049735|Hnrnpa2b1|53379|heterogeneous nuclear ribonucleoprotein A2/B1
mm9_v1_chr12_+_70397702_70397722	0.310733	SOX2.p2	AK082528|Klhdc2|69554|kelch domain containing 2	AY513272|Klhdc2|69554|kelch domain containing 2
mm9_v1_chr6_+_57087346_57087346	0.310436	SOX2.p2	BC104398|Vmn1r11|113860|vomeronasal 1 receptor 11	BC104399|Vmn1r11|113860|vomeronasal 1 receptor 11	NM_053233|Vmn1r11|113860|vomeronasal 1 receptor 11
mm9_v1_chr11_-_42134509_42134538	0.310101	SOX2.p2	X51986|Gabra6|14399|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 6
mm9_v1_chr3_+_66789587_66789619	0.309765	SOX2.p2	AK012100|Rsrc1|66880|arginine/serine-rich coiled-coil 1	NM_025822|Rsrc1|66880|arginine/serine-rich coiled-coil 1	AK005242|Rsrc1|66880|arginine/serine-rich coiled-coil 1	AK043731|Rsrc1|66880|arginine/serine-rich coiled-coil 1	AK045433|Rsrc1|66880|arginine/serine-rich coiled-coil 1
mm9_v1_chr10_+_39089594_39089612	0.309742	SOX2.p2	AK156584|Fyn|14360|Fyn proto-oncogene	AK171646|Fyn|14360|Fyn proto-oncogene	NM_001122892|Fyn|14360|Fyn proto-oncogene	NM_001122893|Fyn|14360|Fyn proto-oncogene	NM_008054|Fyn|14360|Fyn proto-oncogene	BC092217|Fyn|14360|Fyn proto-oncogene
mm9_v1_chr13_-_55431027_55431105	0.308895	SOX2.p2	U32394|Mxd3|17121|Max dimerization protein 3	AK138742|Mxd3|17121|Max dimerization protein 3	NM_016662|Mxd3|17121|Max dimerization protein 3	AK086190|Mxd3|17121|Max dimerization protein 3	BC051970|Mxd3|17121|Max dimerization protein 3	AK014516|Mxd3|17121|Max dimerization protein 3
mm9_v1_chr7_+_19876447_19876478	0.308616	SOX2.p2	NM_001025364|Rtn2|20167|reticulon 2 (Z-band associated protein)	AK160500|Rtn2|20167|reticulon 2 (Z-band associated protein)	AF038539|Rtn2|20167|reticulon 2 (Z-band associated protein)
mm9_v1_chr5_+_89194155_89194268	0.308115	SOX2.p2	AK048347|Dck|13178|deoxycytidine kinase	AK088195|Dck|13178|deoxycytidine kinase	AK151851|Dck|13178|deoxycytidine kinase	AK004592|Dck|13178|deoxycytidine kinase	AK010700|Dck|13178|deoxycytidine kinase	X77731|Dck|13178|deoxycytidine kinase
mm9_v1_chr13_-_56236756_56236903	0.308107	SOX2.p2	AK143498|H2afy|26914|H2A histone family, member Y	AB071988|H2afy|26914|H2A histone family, member Y	BC006955|H2afy|26914|H2A histone family, member Y	AF171080|H2afy|26914|H2A histone family, member Y	AK039274|H2afy|26914|H2A histone family, member Y
mm9_v1_chr18_+_37906668_37906697	0.307943	SOX2.p2	BC035540|Pcdhga10|93722|protocadherin gamma subfamily A, 10
mm9_v1_chr16_+_43321404_43321450	0.307673	SOX2.p2	
mm9_v1_chr7_-_14708338_14708398	0.307477	SOX2.p2	NM_001101586|Sult2a3|629203|sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 3
mm9_v1_chr7_+_29649404_29649463	0.307445	SOX2.p2	NM_008496|Lgals7|16858|lectin, galactose binding, soluble 7	BC116838|Lgals7|16858|lectin, galactose binding, soluble 7	BC116840|Lgals7|16858|lectin, galactose binding, soluble 7
mm9_v1_chr1_+_167225896_167225919	0.307154	SOX2.p2	NM_001081126|Gpr161|240888|G protein-coupled receptor 161	BC137659|Gpr161|240888|G protein-coupled receptor 161
mm9_v1_chr12_-_102267159_102267268	0.3071	SOX2.p2	AY339881|Ccdc88c|68339|coiled-coil domain containing 88C	NM_026681|Ccdc88c|68339|coiled-coil domain containing 88C	BC043115|Ccdc88c|68339|coiled-coil domain containing 88C	BC063255|Ccdc88c|68339|coiled-coil domain containing 88C
mm9_v1_chr9_+_7558428_7558469	0.306896	SOX2.p2	NM_008611|Mmp8|17394|matrix metallopeptidase 8	BC042742|Mmp8|17394|matrix metallopeptidase 8	AK089336|Mmp8|17394|matrix metallopeptidase 8	AK155901|Mmp8|17394|matrix metallopeptidase 8	AK171613|Mmp8|17394|matrix metallopeptidase 8	AK089234|Mmp8|17394|matrix metallopeptidase 8	AK154937|Mmp8|17394|matrix metallopeptidase 8	AK089381|Mmp8|17394|matrix metallopeptidase 8	AK137468|Mmp8|17394|matrix metallopeptidase 8	AK155740|Mmp8|17394|matrix metallopeptidase 8	AK155832|Mmp8|17394|matrix metallopeptidase 8	AK170177|Mmp8|17394|matrix metallopeptidase 8	AK170388|Mmp8|17394|matrix metallopeptidase 8	AK170760|Mmp8|17394|matrix metallopeptidase 8	AK171168|Mmp8|17394|matrix metallopeptidase 8	U96696|Mmp8|17394|matrix metallopeptidase 8	AK089516|Mmp8|17394|matrix metallopeptidase 8
mm9_v1_chr11_+_117658973_117659056	0.306048	SOX2.p2	NM_029964|6030468B19Rik|77727|RIKEN cDNA 6030468B19 gene	AK020081|6030468B19Rik|77727|RIKEN cDNA 6030468B19 gene
mm9_v1_chr6_-_40949477_40949477	0.305076	SOX2.p2	NM_001102660|Gm2663|100040208|predicted gene 2663
mm9_v1_chrX_+_137442146_137442190	0.304865	SOX2.p2	AK132956|Vsig1|78789|V-set and immunoglobulin domain containing 1	NM_030181|Vsig1|78789|V-set and immunoglobulin domain containing 1	AK019565|Vsig1|78789|V-set and immunoglobulin domain containing 1	DQ007336|Vsig1|78789|V-set and immunoglobulin domain containing 1	AK160478|Vsig1|78789|V-set and immunoglobulin domain containing 1	AK136562|Vsig1|78789|V-set and immunoglobulin domain containing 1	BC120675|Vsig1|78789|V-set and immunoglobulin domain containing 1	BC125278|Vsig1|78789|V-set and immunoglobulin domain containing 1	BC145050|Vsig1|78789|V-set and immunoglobulin domain containing 1
mm9_v1_chr7_+_23198601_23198601	0.30484	SOX2.p2	NM_001166844|Vmn1r100|100043536|vomeronasal 1 receptor 100
mm9_v1_chr16_+_88729106_88729106	0.304746	SOX2.p2	BC027551|Krtap13-1|268905|keratin associated protein 13-1	NM_183189|Krtap13-1|268905|keratin associated protein 13-1
mm9_v1_chr9_-_114549261_114549332	0.304569	SOX2.p2	BC036179|Cnot10|78893|CCR4-NOT transcription complex, subunit 10	BC039183|Cnot10|78893|CCR4-NOT transcription complex, subunit 10	AK171701|Cnot10|78893|CCR4-NOT transcription complex, subunit 10	AK161842|Cnot10|78893|CCR4-NOT transcription complex, subunit 10
mm9_v1_chr17_+_23949101_23949124	0.304397	SOX2.p2	AK081577|Srrm2|75956|serine/arginine repetitive matrix 2
mm9_v1_chr16_-_76288569_76288581	0.30397	SOX2.p2	BC062260|Nrip1|268903|nuclear receptor interacting protein 1
mm9_v1_chr11_+_9091944_9091944	0.303849	SOX2.p2	AK036546|Abca13|268379|ATP-binding cassette, sub-family A (ABC1), member 13	NM_178259|Abca13|268379|ATP-binding cassette, sub-family A (ABC1), member 13
mm9_v1_chr1_+_135142673_135142702	0.302535	SOX2.p2	NM_001160268|Plekha6|240753|pleckstrin homology domain containing, family A member 6	NM_182930|Plekha6|240753|pleckstrin homology domain containing, family A member 6	BC054547|Plekha6|240753|pleckstrin homology domain containing, family A member 6	AK173074|Plekha6|240753|pleckstrin homology domain containing, family A member 6
mm9_v1_chr7_+_25292375_25292405	0.302311	SOX2.p2	AK139174|Zfp428|232969|zinc finger protein 428
mm9_v1_chr9_+_90057741_90057815	0.301055	SOX2.p2	NM_001003911|Adamts7|108153|a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 7
mm9_v1_chr7_-_19017274_19017403	0.300723	SOX2.p2	BC099403|Psg28|114871|pregnancy-specific glycoprotein 28	BC141038|Psg28|114871|pregnancy-specific glycoprotein 28	BC099402|Psg28|114871|pregnancy-specific glycoprotein 28	NM_054063|Psg28|114871|pregnancy-specific glycoprotein 28
mm9_v1_chr8_+_72897445_72897456	0.300158	SOX2.p2	NM_016685|Comp|12845|cartilage oligomeric matrix protein	AF033530|Comp|12845|cartilage oligomeric matrix protein	BC128368|Comp|12845|cartilage oligomeric matrix protein	BC128369|Comp|12845|cartilage oligomeric matrix protein
mm9_v1_chr10_-_81704017_81704063	0.299377	SOX2.p2	BC040349|Zfp938|237411|zinc finger protein 938	NM_001105557|Zfp938|237411|zinc finger protein 938	AK045871|Zfp938|237411|zinc finger protein 938
mm9_v1_chr13_+_23635920_23635920	0.299258	SOX2.p2	BC101954|Hist1h3f|260423|histone cluster 1, H3f	BC101955|Hist1h3f|260423|histone cluster 1, H3f	BC101956|Hist1h3f|260423|histone cluster 1, H3f	BC103549|Hist1h3f|260423|histone cluster 1, H3f	NM_013548|Hist1h3f|260423|histone cluster 1, H3f
mm9_v1_chr7_+_50663608_50663649	0.299018	SOX2.p2	AK156766|Siglecg|243958|sialic acid binding Ig-like lectin G	AK036698|Siglecg|243958|sialic acid binding Ig-like lectin G	BC114981|Siglecg|243958|sialic acid binding Ig-like lectin G	AK042488|Siglecg|243958|sialic acid binding Ig-like lectin G	NM_172900|Siglecg|243958|sialic acid binding Ig-like lectin G
mm9_v1_chr7_+_52151432_52151509	0.297686	SOX2.p2	NM_027376|Fuz|70300|fuzzy homolog (Drosophila)	AK134650|Fuz|70300|fuzzy homolog (Drosophila)	AK168939|Fuz|70300|fuzzy homolog (Drosophila)	AK045745|Fuz|70300|fuzzy homolog (Drosophila)	AK033247|Fuz|70300|fuzzy homolog (Drosophila)	BC045601|Fuz|70300|fuzzy homolog (Drosophila)	AK011195|Fuz|70300|fuzzy homolog (Drosophila)
mm9_v1_chr11_+_59918407_59918514	0.297103	SOX2.p2	BC049785|Rai1|19377|retinoic acid induced 1	NM_009021|Rai1|19377|retinoic acid induced 1
mm9_v1_chr14_-_122364309_122364416	0.2969	SOX2.p2	BC052868|Gpr183|321019|G protein-coupled receptor 183	AK141593|Gpr183|321019|G protein-coupled receptor 183	AK153216|Gpr183|321019|G protein-coupled receptor 183	AK087951|Gpr183|321019|G protein-coupled receptor 183	AK156005|Gpr183|321019|G protein-coupled receptor 183	AK156289|Gpr183|321019|G protein-coupled receptor 183	NM_183031|Gpr183|321019|G protein-coupled receptor 183	AK138693|Gpr183|321019|G protein-coupled receptor 183
mm9_v1_chr11_+_105898183_105898284	0.296465	SOX2.p2	AK047435|Dcaf7|71833|DDB1 and CUL4 associated factor 7	NM_027946|Dcaf7|71833|DDB1 and CUL4 associated factor 7	AK005902|Dcaf7|71833|DDB1 and CUL4 associated factor 7	AK154757|Dcaf7|71833|DDB1 and CUL4 associated factor 7	AK165674|Dcaf7|71833|DDB1 and CUL4 associated factor 7	AK080823|Dcaf7|71833|DDB1 and CUL4 associated factor 7	AK137813|Dcaf7|71833|DDB1 and CUL4 associated factor 7	BC048722|Dcaf7|71833|DDB1 and CUL4 associated factor 7	BC048165|Dcaf7|71833|DDB1 and CUL4 associated factor 7
mm9_v1_chr11_-_53448203_53448203	0.295774	SOX2.p2	M23504|Il13|16163|interleukin 13	NM_008355|Il13|16163|interleukin 13
mm9_v1_chr14_+_69789858_69790075	0.295724	SOX2.p2	AF045150|Nkx2-6|18092|NK2 transcription factor related, locus 6 (Drosophila)	BC132558|Nkx2-6|18092|NK2 transcription factor related, locus 6 (Drosophila)	BC139035|Nkx2-6|18092|NK2 transcription factor related, locus 6 (Drosophila)	AK006401|Nkx2-6|18092|NK2 transcription factor related, locus 6 (Drosophila)	BC100425|Nkx2-6|18092|NK2 transcription factor related, locus 6 (Drosophila)	AF030113|Nkx2-6|18092|NK2 transcription factor related, locus 6 (Drosophila)	AK007304|Nkx2-6|18092|NK2 transcription factor related, locus 6 (Drosophila)	NM_010920|Nkx2-6|18092|NK2 transcription factor related, locus 6 (Drosophila)
mm9_v1_chr2_-_27330682_27330707	0.295616	SOX2.p2	BC031536|Brd3|67382|bromodomain containing 3
mm9_v1_chr7_-_24993103_24993167	0.294059	SOX2.p2	BC005456|Zfp111|56707|zinc finger protein 111	AK135436|Zfp111|56707|zinc finger protein 111	NM_019940|Zfp111|56707|zinc finger protein 111
mm9_v1_chr3_+_17954324_17954405	0.293957	SOX2.p2	BC053007|Bhlhe22|59058|basic helix-loop-helix family, member e22	NM_021560|Bhlhe22|59058|basic helix-loop-helix family, member e22	AK076228|Bhlhe22|59058|basic helix-loop-helix family, member e22
mm9_v1_chr4_-_150418704_150418793	0.292836	SOX2.p2	NM_011067|Per3|18628|period homolog 3 (Drosophila)	AK166514|Per3|18628|period homolog 3 (Drosophila)
mm9_v1_chr3_-_103545641_103545788	0.292691	SOX2.p2	AK159746|Hipk1|15257|homeodomain interacting protein kinase 1	AK076611|Hipk1|15257|homeodomain interacting protein kinase 1
mm9_v1_chr17_+_6910178_6910178	0.291252	SOX2.p2	NM_183368|Sytl3|83672|synaptotagmin-like 3
mm9_v1_chr16_+_17276720_17276769	0.290812	SOX2.p2	BC058760|Tmem191c|224019|transmembrane protein 191C
mm9_v1_chr15_+_39577477_39577489	0.28991	SOX2.p2	AB109560|Tm7sf4|75766|transmembrane 7 superfamily member 4	AB109561|Tm7sf4|75766|transmembrane 7 superfamily member 4	AK014697|Tm7sf4|75766|transmembrane 7 superfamily member 4	AK154384|Tm7sf4|75766|transmembrane 7 superfamily member 4	AY517483|Tm7sf4|75766|transmembrane 7 superfamily member 4	AY517484|Tm7sf4|75766|transmembrane 7 superfamily member 4	AY517485|Tm7sf4|75766|transmembrane 7 superfamily member 4	NM_029422|Tm7sf4|75766|transmembrane 7 superfamily member 4	BC139146|Tm7sf4|75766|transmembrane 7 superfamily member 4	BC145557|Tm7sf4|75766|transmembrane 7 superfamily member 4	BC145558|Tm7sf4|75766|transmembrane 7 superfamily member 4
mm9_v1_chr10_+_39089853_39089891	0.289182	SOX2.p2	M27266|Fyn|14360|Fyn proto-oncogene	U70324|Fyn|14360|Fyn proto-oncogene
mm9_v1_chr7_-_27980727_27980786	0.289139	SOX2.p2	NM_001046637|Snrpa|53607|small nuclear ribonucleoprotein polypeptide A
mm9_v1_chr7_-_19242050_19242073	0.289084	SOX2.p2	BC100324|Psg21|72242|pregnancy-specific glycoprotein 21	BC100325|Psg21|72242|pregnancy-specific glycoprotein 21	AK005540|Psg21|72242|pregnancy-specific glycoprotein 21	AK005492|Psg21|72242|pregnancy-specific glycoprotein 21	AK005545|Psg21|72242|pregnancy-specific glycoprotein 21	AK131670|Psg21|72242|pregnancy-specific glycoprotein 21	NM_027403|Psg21|72242|pregnancy-specific glycoprotein 21
mm9_v1_chr3_+_122432075_122432112	0.288441	SOX2.p2	AF541937|Pde5a|242202|phosphodiesterase 5A, cGMP-specific	NM_153422|Pde5a|242202|phosphodiesterase 5A, cGMP-specific	BC119137|Pde5a|242202|phosphodiesterase 5A, cGMP-specific	BC120486|Pde5a|242202|phosphodiesterase 5A, cGMP-specific
mm9_v1_chr8_-_90483392_90483493	0.288282	SOX2.p2	AY256893|Zfp423|94187|zinc finger protein 423	AK122365|Zfp423|94187|zinc finger protein 423	NM_033327|Zfp423|94187|zinc finger protein 423
mm9_v1_chr19_+_26822892_26822948	0.287932	SOX2.p2	NM_026003|Smarca2|67155|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	AK011935|Smarca2|67155|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2
mm9_v1_chr7_-_21488234_21488234	0.287868	SOX2.p2	NM_001166746|Vmn1r111|667292|vomeronasal 1 receptor 111	NM_001166839|Gm4172|100043016|predicted gene 4172	NM_001167168|Gm4220|100043088|predicted gene 4220	NM_001167169|Gm4179|100043029|predicted gene 4179
mm9_v1_chr7_-_24036700_24036700	0.287868	SOX2.p2	NM_001166746|Vmn1r111|667292|vomeronasal 1 receptor 111	NM_001166839|Gm4172|100043016|predicted gene 4172	NM_001167168|Gm4220|100043088|predicted gene 4220	NM_001167169|Gm4179|100043029|predicted gene 4179
mm9_v1_chr5_-_130214385_130214385	0.287571	SOX2.p2	NM_028826|Sept14|74222|septin 14
mm9_v1_chr3_+_136598184_136598389	0.287494	SOX2.p2	AK218972|Ppp3ca|19055|protein phosphatase 3, catalytic subunit, alpha isoform	AK179617|Ppp3ca|19055|protein phosphatase 3, catalytic subunit, alpha isoform	AK145309|Ppp3ca|19055|protein phosphatase 3, catalytic subunit, alpha isoform
mm9_v1_chr7_+_21003290_21003290	0.287494	SOX2.p2	NM_001166844|Vmn1r100|100043536|vomeronasal 1 receptor 100
mm9_v1_chr10_+_90545796_90545821	0.28718	SOX2.p2	AK006283|Ikbip|67454|IKBKB interacting protein	BC034890|Ikbip|67454|IKBKB interacting protein
mm9_v1_chr2_+_181572558_181572632	0.286791	SOX2.p2	AK031335|Pcmtd2|245867|protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2	BC040385|Pcmtd2|245867|protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2	NM_153594|Pcmtd2|245867|protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2	AK146080|Pcmtd2|245867|protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2	AB182640|Pcmtd2|245867|protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2	AK088800|Pcmtd2|245867|protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2
mm9_v1_chr13_+_64533703_64533885	0.286654	SOX2.p2	AY005133|Cdk20|105278|cyclin-dependent kinase 20	BC031907|Cdk20|105278|cyclin-dependent kinase 20	NM_053180|Cdk20|105278|cyclin-dependent kinase 20	BC058353|Cdk20|105278|cyclin-dependent kinase 20
mm9_v1_chr13_+_21826902_21826964	0.286059	SOX2.p2	BC139425|Hist1h4m|100041230|histone cluster 1, H4m	BC139437|Hist1h4m|100041230|histone cluster 1, H4m	AK010085|Hist1h4j|319159|histone cluster 1, H4j	NM_178210|Hist1h4j|319159|histone cluster 1, H4j
mm9_v1_chr9_-_71326587_71326617	0.2859	SOX2.p2	
mm9_v1_chrX_-_65174607_65174624	0.285849	SOX2.p2	AK016292|4933436I01Rik|66780|RIKEN cDNA 4933436I01 gene	BC125317|4933436I01Rik|66780|RIKEN cDNA 4933436I01 gene	BC138016|4933436I01Rik|66780|RIKEN cDNA 4933436I01 gene	AK017084|4933436I01Rik|66780|RIKEN cDNA 4933436I01 gene	NM_025763|4933436I01Rik|66780|RIKEN cDNA 4933436I01 gene
mm9_v1_chr10_-_120416369_120416397	0.285588	SOX2.p2	AF112300|Lemd3|380664|LEM domain containing 3	NM_001081193|Lemd3|380664|LEM domain containing 3
mm9_v1_chr14_-_79647102_79647173	0.285316	SOX2.p2	AK139686|Zfp957|105590|zinc finger protein 957	NM_001033215|Zfp957|105590|zinc finger protein 957
mm9_v1_chr3_+_7366586_7366727	0.284547	SOX2.p2	NM_008862|Pkia|18767|protein kinase inhibitor, alpha	BC048244|Pkia|18767|protein kinase inhibitor, alpha	AK139347|Pkia|18767|protein kinase inhibitor, alpha
mm9_v1_chrX_+_160346948_160347157	0.284429	SOX2.p2	AK045558|Ap1s2|108012|adaptor-related protein complex 1, sigma 2 subunit	AK047724|Ap1s2|108012|adaptor-related protein complex 1, sigma 2 subunit	AK167690|Ap1s2|108012|adaptor-related protein complex 1, sigma 2 subunit	AK053941|Ap1s2|108012|adaptor-related protein complex 1, sigma 2 subunit	AK005223|Ap1s2|108012|adaptor-related protein complex 1, sigma 2 subunit	BC046964|Ap1s2|108012|adaptor-related protein complex 1, sigma 2 subunit	NM_026887|Ap1s2|108012|adaptor-related protein complex 1, sigma 2 subunit	AK043776|Ap1s2|108012|adaptor-related protein complex 1, sigma 2 subunit
mm9_v1_chr7_+_22057197_22057197	0.284058	SOX2.p2	NM_001166740|Vmn1r125|667215|vomeronasal 1 receptor 125
mm9_v1_chr2_-_156688501_156688698	0.28355	SOX2.p2	BC042697|5430405H02Rik|74487|RIKEN cDNA 5430405H02 gene	AK134962|5430405H02Rik|74487|RIKEN cDNA 5430405H02 gene	AK134903|5430405H02Rik|74487|RIKEN cDNA 5430405H02 gene	AK012005|5430405H02Rik|74487|RIKEN cDNA 5430405H02 gene	AK017271|5430405H02Rik|74487|RIKEN cDNA 5430405H02 gene
mm9_v1_chr6_+_122503826_122503835	0.283517	SOX2.p2	NM_009645|Aicda|11628|activation-induced cytidine deaminase	AF132979|Aicda|11628|activation-induced cytidine deaminase
mm9_v1_chr9_+_47338255_47338425	0.283485	SOX2.p2	BC090970|Cadm1|54725|cell adhesion molecule 1	AF434663|Cadm1|54725|cell adhesion molecule 1	AK013911|Cadm1|54725|cell adhesion molecule 1
mm9_v1_chr10_-_116675736_116675742	0.283475	SOX2.p2	NM_029906|9530003J23Rik|77397|RIKEN cDNA 9530003J23 gene
mm9_v1_chr2_+_118872854_118872888	0.283424	SOX2.p2	AK009772|Casc5|76464|cancer susceptibility candidate 5	NM_029617|Casc5|76464|cancer susceptibility candidate 5	BC080815|Casc5|76464|cancer susceptibility candidate 5	AK033132|Casc5|76464|cancer susceptibility candidate 5
mm9_v1_chr14_-_66899764_66899954	0.283133	SOX2.p2	AK158980|Ptk2b|19229|PTK2 protein tyrosine kinase 2 beta	AK054002|Ptk2b|19229|PTK2 protein tyrosine kinase 2 beta	AK150105|Ptk2b|19229|PTK2 protein tyrosine kinase 2 beta	AK041878|Ptk2b|19229|PTK2 protein tyrosine kinase 2 beta	AK088696|Ptk2b|19229|PTK2 protein tyrosine kinase 2 beta	NM_001162365|Ptk2b|19229|PTK2 protein tyrosine kinase 2 beta	NM_172498|Ptk2b|19229|PTK2 protein tyrosine kinase 2 beta
mm9_v1_chr10_-_44786779_44786797	0.282707	SOX2.p2	AK007865|2310075K07Rik|100125933|RIKEN cDNA 2310075K07 gene
mm9_v1_chr1_-_184679281_184679310	0.282388	SOX2.p2	BC150917|4922505E12Rik|433386|RIKEN cDNA 4922505E12 gene	AK132754|4922505E12Rik|433386|RIKEN cDNA 4922505E12 gene	NM_001033547|4922505E12Rik|433386|RIKEN cDNA 4922505E12 gene
mm9_v1_chr7_-_25917458_25917515	0.282198	SOX2.p2	AY746974|Pou2f2|18987|POU domain, class 2, transcription factor 2	BC104488|Pou2f2|18987|POU domain, class 2, transcription factor 2	BC105647|Pou2f2|18987|POU domain, class 2, transcription factor 2	BC105920|Pou2f2|18987|POU domain, class 2, transcription factor 2	BC105921|Pou2f2|18987|POU domain, class 2, transcription factor 2	NM_001163554|Pou2f2|18987|POU domain, class 2, transcription factor 2	NM_001163555|Pou2f2|18987|POU domain, class 2, transcription factor 2	NM_001163556|Pou2f2|18987|POU domain, class 2, transcription factor 2	NM_011138|Pou2f2|18987|POU domain, class 2, transcription factor 2	X57936|Pou2f2|18987|POU domain, class 2, transcription factor 2	X57937|Pou2f2|18987|POU domain, class 2, transcription factor 2	X57938|Pou2f2|18987|POU domain, class 2, transcription factor 2	X57939|Pou2f2|18987|POU domain, class 2, transcription factor 2	X57940|Pou2f2|18987|POU domain, class 2, transcription factor 2	X57941|Pou2f2|18987|POU domain, class 2, transcription factor 2	AK156322|Pou2f2|18987|POU domain, class 2, transcription factor 2	BC050258|Pou2f2|18987|POU domain, class 2, transcription factor 2	AY746973|Pou2f2|18987|POU domain, class 2, transcription factor 2
mm9_v1_chr12_-_80292830_80292851	0.282068	SOX2.p2	BC018261|Rdh11|17252|retinol dehydrogenase 11	BC036273|Rdh11|17252|retinol dehydrogenase 11	AK012056|Rdh11|17252|retinol dehydrogenase 11	AK135443|Rdh11|17252|retinol dehydrogenase 11	AF474027|Rdh11|17252|retinol dehydrogenase 11
mm9_v1_chr9_-_35075338_35075393	0.282051	SOX2.p2	BC051180|Fam118b|109229|family with sequence similarity 118, member B	NM_194257|Fam118b|109229|family with sequence similarity 118, member B	AK079397|Fam118b|109229|family with sequence similarity 118, member B	AK168168|Fam118b|109229|family with sequence similarity 118, member B	AK009486|Fam118b|109229|family with sequence similarity 118, member B	AK081206|Fam118b|109229|family with sequence similarity 118, member B	AK153897|Fam118b|109229|family with sequence similarity 118, member B	AK169810|Fam118b|109229|family with sequence similarity 118, member B	NM_175411|Fam118b|109229|family with sequence similarity 118, member B
mm9_v1_chr13_+_23667631_23667670	0.281782	SOX2.p2	AK020421|Hist1h3d|319149|histone cluster 1, H3d	NM_178204|Hist1h3d|319149|histone cluster 1, H3d
mm9_v1_chr13_-_27673996_27674039	0.280894	SOX2.p2	AF525158|Prl8a1|73244|prolactin family 8, subfamily a, member 1	BC109185|Prl8a1|73244|prolactin family 8, subfamily a, member 1	BC109186|Prl8a1|73244|prolactin family 8, subfamily a, member 1	AK005485|Prl8a1|73244|prolactin family 8, subfamily a, member 1	AK014414|Prl8a1|73244|prolactin family 8, subfamily a, member 1	NM_028477|Prl8a1|73244|prolactin family 8, subfamily a, member 1
mm9_v1_chr9_+_99476204_99476272	0.279251	SOX2.p2	AK050090|Dbr1|83703|debranching enzyme homolog 1 (S. cerevisiae)	NM_031403|Dbr1|83703|debranching enzyme homolog 1 (S. cerevisiae)	BC006661|Dbr1|83703|debranching enzyme homolog 1 (S. cerevisiae)	AK139631|Dbr1|83703|debranching enzyme homolog 1 (S. cerevisiae)	AK090351|Dbr1|83703|debranching enzyme homolog 1 (S. cerevisiae)
mm9_v1_chr5_-_46030523_46030852	0.278418	SOX2.p2	AK081567|Fam184b|58227|family with sequence similarity 184, member B	BC056379|Fam184b|58227|family with sequence similarity 184, member B	NM_021416|Fam184b|58227|family with sequence similarity 184, member B	AB257856|Fam184b|58227|family with sequence similarity 184, member B
mm9_v1_chr9_+_99143756_99143900	0.277366	SOX2.p2	AK021095|Cep70|68121|centrosomal protein 70	AK020622|Cep70|68121|centrosomal protein 70	AF242319|Cep70|68121|centrosomal protein 70	AK049326|Cep70|68121|centrosomal protein 70	AK133048|Cep70|68121|centrosomal protein 70	BC071260|Cep70|68121|centrosomal protein 70	NM_023873|Cep70|68121|centrosomal protein 70	BC050819|Cep70|68121|centrosomal protein 70	AK020174|Cep70|68121|centrosomal protein 70
mm9_v1_chr15_+_38591604_38591751	0.27705	SOX2.p2	NM_025494|Atp6v1c1|66335|ATPase, H+ transporting, lysosomal V1 subunit C1	AK075779|Atp6v1c1|66335|ATPase, H+ transporting, lysosomal V1 subunit C1	AK129007|Atp6v1c1|66335|ATPase, H+ transporting, lysosomal V1 subunit C1	AK151237|Atp6v1c1|66335|ATPase, H+ transporting, lysosomal V1 subunit C1	AK006323|Atp6v1c1|66335|ATPase, H+ transporting, lysosomal V1 subunit C1	AK168914|Atp6v1c1|66335|ATPase, H+ transporting, lysosomal V1 subunit C1	BC010217|Atp6v1c1|66335|ATPase, H+ transporting, lysosomal V1 subunit C1	AB088407|Atp6v1c1|66335|ATPase, H+ transporting, lysosomal V1 subunit C1	U13839|Atp6v1c1|66335|ATPase, H+ transporting, lysosomal V1 subunit C1
mm9_v1_chr14_-_66539632_66539775	0.27703	SOX2.p2	AK035740|Scara3|219151|scavenger receptor class A, member 3
mm9_v1_chr14_-_56563373_56563441	0.275852	SOX2.p2	M68898|Cma1|17228|chymase 1, mast cell	M73759|Cma1|17228|chymase 1, mast cell	BC139759|Cma1|17228|chymase 1, mast cell
mm9_v1_chr2_+_31951149_31951239	0.275505	SOX2.p2	AK052883|Ppapdc3|227721|phosphatidic acid phosphatase type 2 domain containing 3	NM_145521|Ppapdc3|227721|phosphatidic acid phosphatase type 2 domain containing 3	BC016136|Ppapdc3|227721|phosphatidic acid phosphatase type 2 domain containing 3
mm9_v1_chr18_+_37607310_37607496	0.273683	SOX2.p2	AK032156|Pcdhb14|93885|protocadherin beta 14	NM_053139|Pcdhb14|93885|protocadherin beta 14	AK008662|Pcdhb14|93885|protocadherin beta 14	BC059821|Pcdhb14|93885|protocadherin beta 14	AK083065|Pcdhb14|93885|protocadherin beta 14	AY013775|Pcdhb14|93885|protocadherin beta 14
mm9_v1_chr6_+_105627738_105627848	0.27307	SOX2.p2	NM_001109749|Cntn4|269784|contactin 4	NM_173004|Cntn4|269784|contactin 4	AK036262|Cntn4|269784|contactin 4	BC115766|Cntn4|269784|contactin 4
mm9_v1_chr7_+_50432957_50432973	0.272213	SOX2.p2	AK145615|Zfp936|668620|zinc finger protein 936	NM_001034893|Zfp936|668620|zinc finger protein 936	BC066874|Zfp936|668620|zinc finger protein 936
mm9_v1_chr9_+_38280332_38280333	0.271875	SOX2.p2	BC150476|Olfr905|258800|olfactory receptor 905	NM_146804|Olfr905|258800|olfactory receptor 905
mm9_v1_chr14_+_61757271_61757327	0.2711	SOX2.p2	AK160797|Sacs|50720|sacsin	NM_172809|Sacs|50720|sacsin	AK046501|Sacs|50720|sacsin
mm9_v1_chr12_-_70458116_70458130	0.270024	SOX2.p2	BC037106|Nemf|66244|nuclear export mediator factor	AK039497|Nemf|66244|nuclear export mediator factor
mm9_v1_chr14_-_34965604_34965674	0.26935	SOX2.p2	BC132395|Ppyr1|19065|pancreatic polypeptide receptor 1	BC145981|Ppyr1|19065|pancreatic polypeptide receptor 1	NM_008919|Ppyr1|19065|pancreatic polypeptide receptor 1	AK144461|Ppyr1|19065|pancreatic polypeptide receptor 1	AK035505|Ppyr1|19065|pancreatic polypeptide receptor 1
mm9_v1_chr1_-_10710010_10710025	0.268118	SOX2.p2	BC119559|Cpa6|329093|carboxypeptidase A6	BC119560|Cpa6|329093|carboxypeptidase A6	AY773477|Cpa6|329093|carboxypeptidase A6	NM_177834|Cpa6|329093|carboxypeptidase A6	AK078883|Cpa6|329093|carboxypeptidase A6
mm9_v1_chr4_+_150302107_150302108	0.267718	SOX2.p2	NM_001077509|Tnfrsf9|21942|tumor necrosis factor receptor superfamily, member 9	AK154625|Tnfrsf9|21942|tumor necrosis factor receptor superfamily, member 9
mm9_v1_chr6_-_47544925_47545028	0.267542	SOX2.p2	BC003772|Ezh2|14056|enhancer of zeste homolog 2 (Drosophila)	BC016391|Ezh2|14056|enhancer of zeste homolog 2 (Drosophila)	BC079538|Ezh2|14056|enhancer of zeste homolog 2 (Drosophila)	AK220174|Ezh2|14056|enhancer of zeste homolog 2 (Drosophila)	U52951|Ezh2|14056|enhancer of zeste homolog 2 (Drosophila)	AK157853|Ezh2|14056|enhancer of zeste homolog 2 (Drosophila)	NM_001146689|Ezh2|14056|enhancer of zeste homolog 2 (Drosophila)	NM_007971|Ezh2|14056|enhancer of zeste homolog 2 (Drosophila)
mm9_v1_chr7_-_111001598_111001720	0.267507	SOX2.p2	V00857|Hbb-y|15135|hemoglobin Y, beta-like embryonic chain	M26897|Hbb-y|15135|hemoglobin Y, beta-like embryonic chain	BC057014|Hbb-y|15135|hemoglobin Y, beta-like embryonic chain	AK011619|Hbb-y|15135|hemoglobin Y, beta-like embryonic chain	AK012501|Hbb-y|15135|hemoglobin Y, beta-like embryonic chain	AK012897|Hbb-y|15135|hemoglobin Y, beta-like embryonic chain	NM_008221|Hbb-y|15135|hemoglobin Y, beta-like embryonic chain
mm9_v1_chr18_+_37581071_37581102	0.267036	SOX2.p2	AK078189|Pcdhb11|93882|protocadherin beta 11	NM_053136|Pcdhb11|93882|protocadherin beta 11	AK160803|Pcdhb11|93882|protocadherin beta 11
mm9_v1_chr6_-_123803207_123803207	0.266932	SOX2.p2	NM_001104641|Vmn2r25|545874|vomeronasal 2, receptor 25
mm9_v1_chr2_+_31951030_31951062	0.26667	SOX2.p2	AK134638|Ppapdc3|227721|phosphatidic acid phosphatase type 2 domain containing 3
mm9_v1_chr6_+_81873662_81873720	0.266508	SOX2.p2	NM_177884|AW146020|330361|expressed sequence AW146020	AK038369|AW146020|330361|expressed sequence AW146020	AK077263|AW146020|330361|expressed sequence AW146020	AK078171|AW146020|330361|expressed sequence AW146020	AK050789|AW146020|330361|expressed sequence AW146020
mm9_v1_chr6_-_71582562_71582698	0.265401	SOX2.p2	BC059264|Kdm3a|104263|lysine (K)-specific demethylase 3A	AK144825|Kdm3a|104263|lysine (K)-specific demethylase 3A	NM_173001|Kdm3a|104263|lysine (K)-specific demethylase 3A
mm9_v1_chr3_-_37131486_37131557	0.265384	SOX2.p2	AY428162|Il21|60505|interleukin 21	DQ645418|Il21|60505|interleukin 21	BC125414|Il21|60505|interleukin 21	BC125416|Il21|60505|interleukin 21	AF254070|Il21|60505|interleukin 21	NM_021782|Il21|60505|interleukin 21
mm9_v1_chr17_+_18561067_18561067	0.265369	SOX2.p2	NM_001102581|Vmn2r95|328759|vomeronasal 2, receptor 95
mm9_v1_chr3_-_122687238_122687429	0.264088	SOX2.p2	AK040332|Usp53|99526|ubiquitin specific peptidase 53	AK140453|Usp53|99526|ubiquitin specific peptidase 53	BC096383|Usp53|99526|ubiquitin specific peptidase 53	AK036876|Usp53|99526|ubiquitin specific peptidase 53	NM_133857|Usp53|99526|ubiquitin specific peptidase 53	AK030317|Usp53|99526|ubiquitin specific peptidase 53	AK045953|Usp53|99526|ubiquitin specific peptidase 53
mm9_v1_chr13_+_93195850_93196061	0.264032	SOX2.p2	AK078203|Ankrd34b|218440|ankyrin repeat domain 34B	AK090387|Ankrd34b|218440|ankyrin repeat domain 34B	NM_175455|Ankrd34b|218440|ankyrin repeat domain 34B	BC096609|Ankrd34b|218440|ankyrin repeat domain 34B	BC119312|Ankrd34b|218440|ankyrin repeat domain 34B	BC119314|Ankrd34b|218440|ankyrin repeat domain 34B
mm9_v1_chr7_+_56214442_56214485	0.263999	SOX2.p2	AK019901|Nav2|78286|neuron navigator 2	NM_001111016|Nav2|78286|neuron navigator 2	AK084063|Nav2|78286|neuron navigator 2	AK162444|Nav2|78286|neuron navigator 2
mm9_v1_chr4_+_135979438_135979444	0.263956	SOX2.p2	AK082016|Htr1d|15552|5-hydroxytryptamine (serotonin) receptor 1D	NM_008309|Htr1d|15552|5-hydroxytryptamine (serotonin) receptor 1D	BC103532|Htr1d|15552|5-hydroxytryptamine (serotonin) receptor 1D	BC103536|Htr1d|15552|5-hydroxytryptamine (serotonin) receptor 1D	BC103535|Htr1d|15552|5-hydroxytryptamine (serotonin) receptor 1D
mm9_v1_chr5_+_130384409_130384452	0.263929	SOX2.p2	BC100444|4930579G22Rik|69034|RIKEN cDNA 4930579G22 gene	NM_026916|4930579G22Rik|69034|RIKEN cDNA 4930579G22 gene	AK016320|4930579G22Rik|69034|RIKEN cDNA 4930579G22 gene	AK007417|4930579G22Rik|69034|RIKEN cDNA 4930579G22 gene	AK135384|4930579G22Rik|69034|RIKEN cDNA 4930579G22 gene	AK148362|4930579G22Rik|69034|RIKEN cDNA 4930579G22 gene
mm9_v1_chr16_-_20426357_20426468	0.263022	SOX2.p2	BC042581|Abcc5|27416|ATP-binding cassette, sub-family C (CFTR/MRP), member 5	AB019003|Abcc5|27416|ATP-binding cassette, sub-family C (CFTR/MRP), member 5	BC090629|Abcc5|27416|ATP-binding cassette, sub-family C (CFTR/MRP), member 5	BC061132|Abcc5|27416|ATP-binding cassette, sub-family C (CFTR/MRP), member 5	NM_013790|Abcc5|27416|ATP-binding cassette, sub-family C (CFTR/MRP), member 5	NM_176839|Abcc5|27416|ATP-binding cassette, sub-family C (CFTR/MRP), member 5
mm9_v1_chr1_-_30920095_30920100	0.262931	SOX2.p2	BC011226|Phf3|213109|PHD finger protein 3	BC032205|Phf3|213109|PHD finger protein 3	BC137913|Phf3|213109|PHD finger protein 3	NM_001081080|Phf3|213109|PHD finger protein 3
mm9_v1_chr10_+_45297632_45297737	0.26289	SOX2.p2	NM_172473|Hace1|209462|HECT domain and ankyrin repeat containing, E3 ubiquitin protein ligase 1	AK156958|Hace1|209462|HECT domain and ankyrin repeat containing, E3 ubiquitin protein ligase 1	AK042879|Hace1|209462|HECT domain and ankyrin repeat containing, E3 ubiquitin protein ligase 1	BC120695|Hace1|209462|HECT domain and ankyrin repeat containing, E3 ubiquitin protein ligase 1	BC120697|Hace1|209462|HECT domain and ankyrin repeat containing, E3 ubiquitin protein ligase 1
mm9_v1_chr18_+_56722222_56722222	0.262767	SOX2.p2	AK016958|Phax|56698|phosphorylated adaptor for RNA export	NM_001162989|Phax|56698|phosphorylated adaptor for RNA export
mm9_v1_chr11_+_68939734_68939879	0.262374	SOX2.p2	NM_011786|Aloxe3|23801|arachidonate lipoxygenase 3	Y14695|Aloxe3|23801|arachidonate lipoxygenase 3	BC116258|Aloxe3|23801|arachidonate lipoxygenase 3	BC116259|Aloxe3|23801|arachidonate lipoxygenase 3
mm9_v1_chrX_+_99044723_99044723	0.261915	SOX2.p2	AK142977|Nhsl2|100042480|NHS-like 2	NM_001163610|Nhsl2|100042480|NHS-like 2
mm9_v1_chr17_+_72022808_72022818	0.261288	SOX2.p2	AK158647|Fam179a|320159|family with sequence similarity 179, member A
mm9_v1_chr7_+_51471844_51471850	0.261268	SOX2.p2	BC094281|Klk1b5|16622|kallikrein 1-related peptidase b5	NM_008456|Klk1b5|16622|kallikrein 1-related peptidase b5	BC013659|Klk1b5|16622|kallikrein 1-related peptidase b5
mm9_v1_chr13_+_8202111_8202186	0.260896	SOX2.p2	AK134964|Adarb2|94191|adenosine deaminase, RNA-specific, B2	AK051460|Adarb2|94191|adenosine deaminase, RNA-specific, B2	AK043249|Adarb2|94191|adenosine deaminase, RNA-specific, B2	AK139079|Adarb2|94191|adenosine deaminase, RNA-specific, B2	AK139273|Adarb2|94191|adenosine deaminase, RNA-specific, B2	NM_052977|Adarb2|94191|adenosine deaminase, RNA-specific, B2	BC059822|Adarb2|94191|adenosine deaminase, RNA-specific, B2	AK046083|Adarb2|94191|adenosine deaminase, RNA-specific, B2	AK033916|Adarb2|94191|adenosine deaminase, RNA-specific, B2	AK045538|Adarb2|94191|adenosine deaminase, RNA-specific, B2	BC052426|Adarb2|94191|adenosine deaminase, RNA-specific, B2
mm9_v1_chr7_-_128125714_128125825	0.260402	SOX2.p2	BC117530|Cdr2|12585|cerebellar degeneration-related 2	BC118511|Cdr2|12585|cerebellar degeneration-related 2	AK171706|Cdr2|12585|cerebellar degeneration-related 2	U88588|Cdr2|12585|cerebellar degeneration-related 2	AK157902|Cdr2|12585|cerebellar degeneration-related 2	AK148057|Cdr2|12585|cerebellar degeneration-related 2	NM_007672|Cdr2|12585|cerebellar degeneration-related 2
mm9_v1_chr9_-_114549148_114549229	0.259759	SOX2.p2	AK149944|Cnot10|78893|CCR4-NOT transcription complex, subunit 10	AK167288|Cnot10|78893|CCR4-NOT transcription complex, subunit 10	BC025554|Cnot10|78893|CCR4-NOT transcription complex, subunit 10	AK029103|Cnot10|78893|CCR4-NOT transcription complex, subunit 10	NM_153585|Cnot10|78893|CCR4-NOT transcription complex, subunit 10	AK080503|Cnot10|78893|CCR4-NOT transcription complex, subunit 10	AK157824|Cnot10|78893|CCR4-NOT transcription complex, subunit 10
mm9_v1_chr6_+_29997972_29998071	0.259331	SOX2.p2	AK082580|Nrf1|18181|nuclear respiratory factor 1	NM_001164226|Nrf1|18181|nuclear respiratory factor 1	NM_001164227|Nrf1|18181|nuclear respiratory factor 1	NM_001164228|Nrf1|18181|nuclear respiratory factor 1	NM_001164230|Nrf1|18181|nuclear respiratory factor 1	NM_010938|Nrf1|18181|nuclear respiratory factor 1	AK029034|Nrf1|18181|nuclear respiratory factor 1	AK014494|Nrf1|18181|nuclear respiratory factor 1	AK036604|Nrf1|18181|nuclear respiratory factor 1	AK037697|Nrf1|18181|nuclear respiratory factor 1	AF098077|Nrf1|18181|nuclear respiratory factor 1	AF064728|Nrf1|18181|nuclear respiratory factor 1	AK050861|Nrf1|18181|nuclear respiratory factor 1	AK134483|Nrf1|18181|nuclear respiratory factor 1
mm9_v1_chr10_+_93610663_93610767	0.259285	SOX2.p2	AK146891|Nr2c1|22025|nuclear receptor subfamily 2, group C, member 1	NM_011629|Nr2c1|22025|nuclear receptor subfamily 2, group C, member 1	AK053907|Nr2c1|22025|nuclear receptor subfamily 2, group C, member 1	BC090662|Nr2c1|22025|nuclear receptor subfamily 2, group C, member 1	BC094580|Nr2c1|22025|nuclear receptor subfamily 2, group C, member 1	AK149374|Nr2c1|22025|nuclear receptor subfamily 2, group C, member 1
mm9_v1_chr17_+_87506971_87507037	0.258913	SOX2.p2	BC053015|Socs5|56468|suppressor of cytokine signaling 5	NM_019654|Socs5|56468|suppressor of cytokine signaling 5	AK135099|Socs5|56468|suppressor of cytokine signaling 5
mm9_v1_chr4_+_143780619_143780632	0.258439	SOX2.p2	AK139660|Oog2|381570|oogenesin 2	NM_198661|Oog2|381570|oogenesin 2	AY573562|Oog2|381570|oogenesin 2	BC052839|Oog2|381570|oogenesin 2
mm9_v1_chr4_+_24423561_24423690	0.257822	SOX2.p2	AK166072|Mms22l|212377|MMS22-like, DNA repair protein	AK164069|Mms22l|212377|MMS22-like, DNA repair protein	NM_199467|Mms22l|212377|MMS22-like, DNA repair protein	AK144799|Mms22l|212377|MMS22-like, DNA repair protein
mm9_v1_chr2_-_129525512_129525673	0.257137	SOX2.p2	BC137571|Pdyn|18610|prodynorphin	BC137572|Pdyn|18610|prodynorphin	AF026537|Pdyn|18610|prodynorphin	AK133597|Pdyn|18610|prodynorphin
mm9_v1_chr7_-_26539753_26539832	0.25676	SOX2.p2	BC078642|Hnrnpul1|232989|heterogeneous nuclear ribonucleoprotein U-like 1	AK143666|Hnrnpul1|232989|heterogeneous nuclear ribonucleoprotein U-like 1
mm9_v1_chr7_-_99889932_99889979	0.25584	SOX2.p2	AK014157|4632427E13Rik|666737|RIKEN cDNA 4632427E13 gene	AK051992|4632427E13Rik|666737|RIKEN cDNA 4632427E13 gene	AK018467|4632427E13Rik|666737|RIKEN cDNA 4632427E13 gene	AK019505|4632427E13Rik|666737|RIKEN cDNA 4632427E13 gene	AK084903|4632427E13Rik|666737|RIKEN cDNA 4632427E13 gene	AK084084|4632427E13Rik|666737|RIKEN cDNA 4632427E13 gene	AK145781|4632427E13Rik|666737|RIKEN cDNA 4632427E13 gene
mm9_v1_chr17_-_71339826_71339901	0.255827	SOX2.p2	BC099425|Myl12b|67938|myosin, light chain 12B, regulatory	BC131925|Myl12b|67938|myosin, light chain 12B, regulatory	BC131927|Myl12b|67938|myosin, light chain 12B, regulatory	BC028878|Myl12b|67938|myosin, light chain 12B, regulatory	AK002885|Myl12b|67938|myosin, light chain 12B, regulatory	AK168316|Myl12b|67938|myosin, light chain 12B, regulatory	NM_023402|Myl12b|67938|myosin, light chain 12B, regulatory	AK146115|Myl12b|67938|myosin, light chain 12B, regulatory	AK005133|Myl12b|67938|myosin, light chain 12B, regulatory	AK160123|Myl12b|67938|myosin, light chain 12B, regulatory
mm9_v1_chr2_-_25316553_25316613	0.255754	SOX2.p2	BC029214|BC029214|227622|cDNA sequence BC029214	NM_153557|BC029214|227622|cDNA sequence BC029214
mm9_v1_chr14_+_69647294_69647485	0.254967	SOX2.p2	AF099098|Stc1|20855|stanniocalcin 1	BC021425|Stc1|20855|stanniocalcin 1	AK134260|Stc1|20855|stanniocalcin 1	NM_009285|Stc1|20855|stanniocalcin 1	AK142220|Stc1|20855|stanniocalcin 1	AK149293|Stc1|20855|stanniocalcin 1	AK149351|Stc1|20855|stanniocalcin 1	AK161960|Stc1|20855|stanniocalcin 1
mm9_v1_chr12_+_85981968_85981968	0.254685	SOX2.p2	NM_001168589|Vrtn|432677|vertebrae development homolog (pig)
mm9_v1_chr14_-_48037815_48037862	0.253764	SOX2.p2	BC058087|Dlgap5|218977|discs, large (Drosophila) homolog-associated protein 5	BC027273|Dlgap5|218977|discs, large (Drosophila) homolog-associated protein 5	AK129032|Dlgap5|218977|discs, large (Drosophila) homolog-associated protein 5	AK147955|Dlgap5|218977|discs, large (Drosophila) homolog-associated protein 5	AK048470|Dlgap5|218977|discs, large (Drosophila) homolog-associated protein 5	AK085882|Dlgap5|218977|discs, large (Drosophila) homolog-associated protein 5
mm9_v1_chr2_-_120676125_120676339	0.252864	SOX2.p2	AK046978|Ttbk2|140810|tau tubulin kinase 2	AK053820|Ttbk2|140810|tau tubulin kinase 2	AK137024|Ttbk2|140810|tau tubulin kinase 2	AK148269|Ttbk2|140810|tau tubulin kinase 2	NM_001024856|Ttbk2|140810|tau tubulin kinase 2	NM_001024857|Ttbk2|140810|tau tubulin kinase 2	NM_080788|Ttbk2|140810|tau tubulin kinase 2	AK077011|Ttbk2|140810|tau tubulin kinase 2
mm9_v1_chr6_+_123974775_123974775	0.252667	SOX2.p2	AF053985|Vmn2r26|56552|vomeronasal 2, receptor 26	AY426342|Vmn2r26|56552|vomeronasal 2, receptor 26	NM_019917|Vmn2r26|56552|vomeronasal 2, receptor 26
mm9_v1_chr5_-_72049058_72049225	0.252091	SOX2.p2	AK079551|Gabra4|14397|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 4	AK043806|Gabra4|14397|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 4	AK137354|Gabra4|14397|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 4	AK162893|Gabra4|14397|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 4	BC094603|Gabra4|14397|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 4	AK139970|Gabra4|14397|gamma-aminobutyric acid (GABA) A receptor, subunit alpha 4
mm9_v1_chr10_-_80499974_80500080	0.251489	SOX2.p2	BC085175|Slc39a3|106947|solute carrier family 39 (zinc transporter), member 3	AK087519|Slc39a3|106947|solute carrier family 39 (zinc transporter), member 3
mm9_v1_chr4_+_33397279_33397404	0.251477	SOX2.p2	AK151463|Rngtt|24018|RNA guanylyltransferase and 5'-phosphatase	NM_011884|Rngtt|24018|RNA guanylyltransferase and 5'-phosphatase	AK150497|Rngtt|24018|RNA guanylyltransferase and 5'-phosphatase	AK160007|Rngtt|24018|RNA guanylyltransferase and 5'-phosphatase	AK002922|Rngtt|24018|RNA guanylyltransferase and 5'-phosphatase	AK079488|Rngtt|24018|RNA guanylyltransferase and 5'-phosphatase	AK142016|Rngtt|24018|RNA guanylyltransferase and 5'-phosphatase	AK160706|Rngtt|24018|RNA guanylyltransferase and 5'-phosphatase	BC043657|Rngtt|24018|RNA guanylyltransferase and 5'-phosphatase	AK169305|Rngtt|24018|RNA guanylyltransferase and 5'-phosphatase	AF034568|Rngtt|24018|RNA guanylyltransferase and 5'-phosphatase	AF025653|Rngtt|24018|RNA guanylyltransferase and 5'-phosphatase
mm9_v1_chr6_+_142723841_142723893	0.251471	SOX2.p2	AK213220|Cmas|12764|cytidine monophospho-N-acetylneuraminic acid synthetase
mm9_v1_chr1_+_65357830_65357830	0.251371	SOX2.p2	AK045576|Pth2r|213527|parathyroid hormone 2 receptor	NM_139270|Pth2r|213527|parathyroid hormone 2 receptor
mm9_v1_chr10_-_79076744_79076769	0.251217	SOX2.p2	BC089008|C2cd4c|237397|C2 calcium-dependent domain containing 4C	NM_198614|C2cd4c|237397|C2 calcium-dependent domain containing 4C	AK029946|C2cd4c|237397|C2 calcium-dependent domain containing 4C	NM_001168624|C2cd4c|237397|C2 calcium-dependent domain containing 4C
mm9_v1_chr2_+_71050002_71050098	0.2506	SOX2.p2	NM_001198877|Dync1i2|13427|dynein cytoplasmic 1 intermediate chain 2	NM_001198878|Dync1i2|13427|dynein cytoplasmic 1 intermediate chain 2	NM_010064|Dync1i2|13427|dynein cytoplasmic 1 intermediate chain 2	AK168730|Dync1i2|13427|dynein cytoplasmic 1 intermediate chain 2	AK088015|Dync1i2|13427|dynein cytoplasmic 1 intermediate chain 2	AK135477|Dync1i2|13427|dynein cytoplasmic 1 intermediate chain 2	GU992211|Dync1i2|13427|dynein cytoplasmic 1 intermediate chain 2	GU992212|Dync1i2|13427|dynein cytoplasmic 1 intermediate chain 2	AF063231|Dync1i2|13427|dynein cytoplasmic 1 intermediate chain 2
mm9_v1_chr2_-_101637773_101637865	0.249458	SOX2.p2	BC048394|Prr5l|72446|proline rich 5 like	AK030499|Prr5l|72446|proline rich 5 like	NM_001083810|Prr5l|72446|proline rich 5 like	NM_175181|Prr5l|72446|proline rich 5 like	AK145981|Prr5l|72446|proline rich 5 like
mm9_v1_chr11_-_102226475_102226594	0.248978	SOX2.p2	AK172456|Slc4a1|20533|solute carrier family 4 (anion exchanger), member 1	AK171662|Slc4a1|20533|solute carrier family 4 (anion exchanger), member 1	AK137542|Slc4a1|20533|solute carrier family 4 (anion exchanger), member 1	AK171845|Slc4a1|20533|solute carrier family 4 (anion exchanger), member 1	AK172395|Slc4a1|20533|solute carrier family 4 (anion exchanger), member 1	AK158184|Slc4a1|20533|solute carrier family 4 (anion exchanger), member 1	AK157181|Slc4a1|20533|solute carrier family 4 (anion exchanger), member 1	AK158143|Slc4a1|20533|solute carrier family 4 (anion exchanger), member 1	NM_011403|Slc4a1|20533|solute carrier family 4 (anion exchanger), member 1
mm9_v1_chr5_+_29761203_29761262	0.248893	SOX2.p2	AK148406|Nom1|433864|nucleolar protein with MIF4G domain 1	NM_001033457|Nom1|433864|nucleolar protein with MIF4G domain 1
mm9_v1_chr7_+_15974199_15974319	0.248754	SOX2.p2	NM_145708|Obox2|246792|oocyte specific homeobox 2	BC094912|Obox2|246792|oocyte specific homeobox 2
mm9_v1_chr3_-_94937886_94937954	0.248687	SOX2.p2	BC028867|Scnm1|69269|sodium channel modifier 1	AK013948|Scnm1|69269|sodium channel modifier 1	NM_001163573|Scnm1|69269|sodium channel modifier 1	NM_027013|Scnm1|69269|sodium channel modifier 1
mm9_v1_chr13_+_89680393_89680435	0.248582	SOX2.p2	BC066853|Hapln1|12950|hyaluronan and proteoglycan link protein 1
mm9_v1_chr8_+_47637408_47637440	0.248089	SOX2.p2	BC094675|Mlf1ip|71876|myeloid leukemia factor 1 interacting protein	AK006479|Mlf1ip|71876|myeloid leukemia factor 1 interacting protein	AK050386|Mlf1ip|71876|myeloid leukemia factor 1 interacting protein	BC117784|Mlf1ip|71876|myeloid leukemia factor 1 interacting protein	BC117785|Mlf1ip|71876|myeloid leukemia factor 1 interacting protein	NM_027973|Mlf1ip|71876|myeloid leukemia factor 1 interacting protein	AK081703|Mlf1ip|71876|myeloid leukemia factor 1 interacting protein	AY366362|Mlf1ip|71876|myeloid leukemia factor 1 interacting protein
mm9_v1_chr11_-_60988490_60988572	0.247712	SOX2.p2	AK220368|Usp22|216825|ubiquitin specific peptidase 22	AK040187|Usp22|216825|ubiquitin specific peptidase 22	AK034492|Usp22|216825|ubiquitin specific peptidase 22	AK155071|Usp22|216825|ubiquitin specific peptidase 22	NM_001004143|Usp22|216825|ubiquitin specific peptidase 22
mm9_v1_chr2_-_27331122_27331221	0.247538	SOX2.p2	AK076472|Brd3|67382|bromodomain containing 3	AK136429|Brd3|67382|bromodomain containing 3	BC004832|Brd3|67382|bromodomain containing 3	AF269193|Brd3|67382|bromodomain containing 3	AK161164|Brd3|67382|bromodomain containing 3	AK167573|Brd3|67382|bromodomain containing 3	AK136007|Brd3|67382|bromodomain containing 3	AK160752|Brd3|67382|bromodomain containing 3	AK081471|Brd3|67382|bromodomain containing 3	AK037435|Brd3|67382|bromodomain containing 3	AK159827|Brd3|67382|bromodomain containing 3	NM_001113573|Brd3|67382|bromodomain containing 3	NM_001113574|Brd3|67382|bromodomain containing 3
mm9_v1_chr19_+_45122281_45122364	0.247307	SOX2.p2	AK154274|Sfxn3|94280|sideroflexin 3	AF325262|Sfxn3|94280|sideroflexin 3	AK089985|Sfxn3|94280|sideroflexin 3	AK184595|Sfxn3|94280|sideroflexin 3	AK206211|Sfxn3|94280|sideroflexin 3	AK034514|Sfxn3|94280|sideroflexin 3
mm9_v1_chr10_+_59569052_59569061	0.246934	SOX2.p2	BC060210|Spock2|94214|sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2
mm9_v1_chr18_+_34919205_34919226	0.246857	SOX2.p2	AK044469|Fam53c|66306|family with sequence similarity 53, member C	AK135712|Fam53c|66306|family with sequence similarity 53, member C	AK154214|Fam53c|66306|family with sequence similarity 53, member C	AK166841|Fam53c|66306|family with sequence similarity 53, member C	BC044896|Fam53c|66306|family with sequence similarity 53, member C
mm9_v1_chr15_-_65743815_65743958	0.246835	SOX2.p2	BC048716|Oc90|18256|otoconin 90	AK012981|Oc90|18256|otoconin 90	NM_010953|Oc90|18256|otoconin 90	AF093591|Oc90|18256|otoconin 90
mm9_v1_chr9_+_119311561_119311618	0.246179	SOX2.p2	BC106189|Acvr2b|11481|activin receptor IIB	M84120|Acvr2b|11481|activin receptor IIB	NM_007397|Acvr2b|11481|activin receptor IIB
mm9_v1_chr13_+_60703261_60703571	0.245981	SOX2.p2	NM_029653|Dapk1|69635|death associated protein kinase 1	AY245540|Dapk1|69635|death associated protein kinase 1	AY245541|Dapk1|69635|death associated protein kinase 1	BC057317|Dapk1|69635|death associated protein kinase 1	BC060161|Dapk1|69635|death associated protein kinase 1	AK009701|Dapk1|69635|death associated protein kinase 1	AK145922|Dapk1|69635|death associated protein kinase 1	NM_134062|Dapk1|69635|death associated protein kinase 1
mm9_v1_chr16_+_31948631_31948724	0.245668	SOX2.p2	NM_026554|Ncbp2|68092|nuclear cap binding protein subunit 2	AK008980|Ncbp2|68092|nuclear cap binding protein subunit 2	AK078181|Ncbp2|68092|nuclear cap binding protein subunit 2	AK147027|Ncbp2|68092|nuclear cap binding protein subunit 2	AK012659|Ncbp2|68092|nuclear cap binding protein subunit 2	AK014016|Ncbp2|68092|nuclear cap binding protein subunit 2	AK135597|Ncbp2|68092|nuclear cap binding protein subunit 2	AK077841|Ncbp2|68092|nuclear cap binding protein subunit 2	BC118926|Ncbp2|68092|nuclear cap binding protein subunit 2
mm9_v1_chr7_-_5077551_5077557	0.245575	SOX2.p2	AK006350|Rasl2-9-ps|19428|RAS-like, family 2, locus 9, pseudogene	BC061180|Rasl2-9-ps|19428|RAS-like, family 2, locus 9, pseudogene	BC099553|Rasl2-9-ps|19428|RAS-like, family 2, locus 9, pseudogene	NM_009028|Rasl2-9-ps|19428|RAS-like, family 2, locus 9, pseudogene	BC138995|Rasl2-9-ps|19428|RAS-like, family 2, locus 9, pseudogene	BC145722|Rasl2-9-ps|19428|RAS-like, family 2, locus 9, pseudogene	BC049619|Rasl2-9-ps|19428|RAS-like, family 2, locus 9, pseudogene	L32752|Rasl2-9-ps|19428|RAS-like, family 2, locus 9, pseudogene
mm9_v1_chr11_-_100068823_100068834	0.245184	SOX2.p2	BC011074|Krt14|16664|keratin 14	NM_016958|Krt14|16664|keratin 14
mm9_v1_chr8_+_35217685_35217743	0.244802	SOX2.p2	AK007787|Tmem66|67887|transmembrane protein 66	AK075744|Tmem66|67887|transmembrane protein 66	AK088728|Tmem66|67887|transmembrane protein 66
mm9_v1_chr5_+_114581164_114581232	0.244047	SOX2.p2	NM_011677|Ung|22256|uracil DNA glycosylase	X99018|Ung|22256|uracil DNA glycosylase	U55041|Ung|22256|uracil DNA glycosylase	AK168709|Ung|22256|uracil DNA glycosylase	AK168785|Ung|22256|uracil DNA glycosylase	BC052853|Ung|22256|uracil DNA glycosylase
mm9_v1_chr7_+_14209315_14209343	0.24356	SOX2.p2	NM_001184980|Sult2a5|434264|sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 5
mm9_v1_chr5_+_150242274_150242293	0.243086	SOX2.p2	AK087319|4930588N13Rik|75860|RIKEN cDNA 4930588N13 gene	BC120819|4930588N13Rik|75860|RIKEN cDNA 4930588N13 gene	BC144997|4930588N13Rik|75860|RIKEN cDNA 4930588N13 gene	BC144998|4930588N13Rik|75860|RIKEN cDNA 4930588N13 gene	BC144999|4930588N13Rik|75860|RIKEN cDNA 4930588N13 gene	NM_029464|4930588N13Rik|75860|RIKEN cDNA 4930588N13 gene	AK161244|4930588N13Rik|75860|RIKEN cDNA 4930588N13 gene	AK016369|4930588N13Rik|75860|RIKEN cDNA 4930588N13 gene
mm9_v1_chr3_-_90313339_90313430	0.240289	SOX2.p2	AK004558|2500003M10Rik|66511|RIKEN cDNA 2500003M10 gene	NM_023215|2500003M10Rik|66511|RIKEN cDNA 2500003M10 gene	AB041654|2500003M10Rik|66511|RIKEN cDNA 2500003M10 gene	AK152492|2500003M10Rik|66511|RIKEN cDNA 2500003M10 gene	BC066837|2500003M10Rik|66511|RIKEN cDNA 2500003M10 gene	BC051939|2500003M10Rik|66511|RIKEN cDNA 2500003M10 gene	AK005377|2500003M10Rik|66511|RIKEN cDNA 2500003M10 gene	AK047914|2500003M10Rik|66511|RIKEN cDNA 2500003M10 gene	AK132769|2500003M10Rik|66511|RIKEN cDNA 2500003M10 gene	AK135914|2500003M10Rik|66511|RIKEN cDNA 2500003M10 gene	AK010866|2500003M10Rik|66511|RIKEN cDNA 2500003M10 gene	AK077960|2500003M10Rik|66511|RIKEN cDNA 2500003M10 gene
mm9_v1_chr13_+_8952108_8952122	0.239896	SOX2.p2	AK029364|Idi2|320581|isopentenyl-diphosphate delta isomerase 2	AK081319|Idi2|320581|isopentenyl-diphosphate delta isomerase 2	AY263178|Idi2|320581|isopentenyl-diphosphate delta isomerase 2	NM_177197|Idi2|320581|isopentenyl-diphosphate delta isomerase 2	BC099586|Idi2|320581|isopentenyl-diphosphate delta isomerase 2	BC125310|Idi2|320581|isopentenyl-diphosphate delta isomerase 2	BC138100|Idi2|320581|isopentenyl-diphosphate delta isomerase 2
mm9_v1_chr4_-_136158570_136158663	0.239466	SOX2.p2	AK129170|Kdm1a|99982|lysine (K)-specific demethylase 1A	BC059885|Kdm1a|99982|lysine (K)-specific demethylase 1A	NM_133872|Kdm1a|99982|lysine (K)-specific demethylase 1A
mm9_v1_chr11_+_6315729_6315787	0.238998	SOX2.p2	AK151583|Ppia|268373|peptidylprolyl isomerase A
mm9_v1_chr13_-_47138563_47138585	0.238905	SOX2.p2	AF046887|Tpmt|22017|thiopurine methyltransferase	NM_016785|Tpmt|22017|thiopurine methyltransferase
mm9_v1_chr4_+_34497840_34497946	0.238463	SOX2.p2	NM_001007589|Akirin2|433693|akirin 2	BC082305|Akirin2|433693|akirin 2
mm9_v1_chr17_-_57199207_57199302	0.238321	SOX2.p2	BC072660|Slc25a23|66972|solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23	NM_025877|Slc25a23|66972|solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23
mm9_v1_chr7_+_50718533_50718608	0.237689	SOX2.p2	BC112410|Vsig10l|75690|ZV-set and immunoglobulin domain containing 10 like
mm9_v1_chr8_-_48373564_48373676	0.237022	SOX2.p2	BC099949|Stox2|71069|storkhead box 2
mm9_v1_chr8_-_107813357_107813427	0.237015	SOX2.p2	BC059045|4931428F04Rik|74356|RIKEN cDNA 4931428F04 gene	AK049007|4931428F04Rik|74356|RIKEN cDNA 4931428F04 gene	NM_001166394|4931428F04Rik|74356|RIKEN cDNA 4931428F04 gene	NM_028888|4931428F04Rik|74356|RIKEN cDNA 4931428F04 gene
mm9_v1_chr11_-_99665759_99665763	0.236558	SOX2.p2	AK009035|Krtap4-13|69464|keratin associated protein 4-13	NM_001099312|Gm11569|670472|predicted gene 11569	NM_001099313|Gm11554|670482|predicted gene 11554	NM_027087|Krtap4-13|69464|keratin associated protein 4-13
mm9_v1_chr8_-_69010394_69010447	0.236346	SOX2.p2	BC016246|1810029B16Rik|66282|RIKEN cDNA 1810029B16 gene	BC034844|1810029B16Rik|66282|RIKEN cDNA 1810029B16 gene	AK007637|1810029B16Rik|66282|RIKEN cDNA 1810029B16 gene	NM_025465|1810029B16Rik|66282|RIKEN cDNA 1810029B16 gene	AK009167|1810029B16Rik|66282|RIKEN cDNA 1810029B16 gene	AK011532|1810029B16Rik|66282|RIKEN cDNA 1810029B16 gene	AK051835|1810029B16Rik|66282|RIKEN cDNA 1810029B16 gene	AK031875|1810029B16Rik|66282|RIKEN cDNA 1810029B16 gene
mm9_v1_chr7_-_27981077_27981289	0.236125	SOX2.p2	L15447|Snrpa|53607|small nuclear ribonucleoprotein polypeptide A	BC096648|Snrpa|53607|small nuclear ribonucleoprotein polypeptide A	AK088550|Snrpa|53607|small nuclear ribonucleoprotein polypeptide A	BC094006|Snrpa|53607|small nuclear ribonucleoprotein polypeptide A	AK049541|Snrpa|53607|small nuclear ribonucleoprotein polypeptide A	BC003229|Snrpa|53607|small nuclear ribonucleoprotein polypeptide A	AK013886|Snrpa|53607|small nuclear ribonucleoprotein polypeptide A	NM_015782|Snrpa|53607|small nuclear ribonucleoprotein polypeptide A
mm9_v1_chr4_-_108506131_108506262	0.235745	SOX2.p2	BC024920|Btf3l4|70533|basic transcription factor 3-like 4	BC058282|Btf3l4|70533|basic transcription factor 3-like 4	AK011367|Btf3l4|70533|basic transcription factor 3-like 4	AK167256|Btf3l4|70533|basic transcription factor 3-like 4	BC138215|Btf3l4|70533|basic transcription factor 3-like 4	BC138216|Btf3l4|70533|basic transcription factor 3-like 4	BC024612|Btf3l4|70533|basic transcription factor 3-like 4	AK013120|Btf3l4|70533|basic transcription factor 3-like 4	AK076283|Btf3l4|70533|basic transcription factor 3-like 4	NM_027453|Btf3l4|70533|basic transcription factor 3-like 4	AK004239|Btf3l4|70533|basic transcription factor 3-like 4
mm9_v1_chr9_-_39764653_39764653	0.234713	SOX2.p2	BC119350|Olfr976|258364|olfactory receptor 976	BC120621|Olfr976|258364|olfactory receptor 976	NM_146367|Olfr976|258364|olfactory receptor 976
mm9_v1_chr3_+_153507205_153507229	0.233822	SOX2.p2	BC049572|Asb17|66772|ankyrin repeat and SOCS box-containing 17	AF425641|Asb17|66772|ankyrin repeat and SOCS box-containing 17	AK016273|Asb17|66772|ankyrin repeat and SOCS box-containing 17	NM_025758|Asb17|66772|ankyrin repeat and SOCS box-containing 17	AK017090|Asb17|66772|ankyrin repeat and SOCS box-containing 17
mm9_v1_chr11_+_46337752_46337752	0.233355	SOX2.p2	NM_001163357|Gm12169|210535|predicted gene 12169
mm9_v1_chr9_+_72961223_72961298	0.23302	SOX2.p2	AK153492|Rsl24d1|225215|ribosomal L24 domain containing 1	AK160194|Rsl24d1|225215|ribosomal L24 domain containing 1	BC003885|Rsl24d1|225215|ribosomal L24 domain containing 1	NM_198609|Rsl24d1|225215|ribosomal L24 domain containing 1	BC089481|Rsl24d1|225215|ribosomal L24 domain containing 1	AK164856|Rsl24d1|225215|ribosomal L24 domain containing 1
mm9_v1_chr6_+_64992861_64992872	0.232954	SOX2.p2	AK147884|Smarcad1|13990|SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1
mm9_v1_chr3_+_87924435_87924571	0.232192	SOX2.p2	BC022774|Iqgap3|404710|IQ motif containing GTPase activating protein 3
mm9_v1_chr3_-_26052228_26052228	0.231992	SOX2.p2	BC098461|Nlgn1|192167|neuroligin 1	NM_001163387|Nlgn1|192167|neuroligin 1
mm9_v1_chr17_-_25482323_25482506	0.231583	SOX2.p2	U42405|Tpsab1|17230|tryptase alpha/beta 1	L00653|Tpsab1|17230|tryptase alpha/beta 1	BC011328|Tpsab1|17230|tryptase alpha/beta 1	AK040500|Tpsab1|17230|tryptase alpha/beta 1	NM_031187|Tpsab1|17230|tryptase alpha/beta 1
mm9_v1_chr6_+_41304103_41304177	0.231266	SOX2.p2	BC138698|Try10|436522|trypsin 10	BC146017|Try10|436522|trypsin 10	NM_001038996|Try10|436522|trypsin 10	AK133516|Try10|436522|trypsin 10
mm9_v1_chr4_+_21703416_21703444	0.230878	SOX2.p2	AK040660|Usp45|77593|ubiquitin specific petidase 45	AK162825|Usp45|77593|ubiquitin specific petidase 45	NM_152825|Usp45|77593|ubiquitin specific petidase 45	AK088073|Usp45|77593|ubiquitin specific petidase 45	BC027768|Usp45|77593|ubiquitin specific petidase 45
mm9_v1_chr3_+_96433850_96433878	0.230593	SOX2.p2	NM_001102407|Rbm8a|60365|RNA binding motif protein 8a	NM_025875|Rbm8a|60365|RNA binding motif protein 8a	AK009953|Rbm8a|60365|RNA binding motif protein 8a	AK010284|Rbm8a|60365|RNA binding motif protein 8a	AK011215|Rbm8a|60365|RNA binding motif protein 8a	AK082925|Rbm8a|60365|RNA binding motif protein 8a	BC020086|Rbm8a|60365|RNA binding motif protein 8a	BC058376|Rbm8a|60365|RNA binding motif protein 8a
mm9_v1_chr4_-_32689356_32689356	0.230129	SOX2.p2	NM_010289|Gja10|14610|gap junction protein, alpha 10
mm9_v1_chr15_-_36723995_36724005	0.229656	SOX2.p2	BC050891|Ywhaz|22631|tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide
mm9_v1_chr2_-_125971986_125971986	0.22904	SOX2.p2	NM_029455|4930525F21Rik|75823|RIKEN cDNA 4930525F21 gene
mm9_v1_chr18_-_43952520_43952536	0.229033	SOX2.p2	BC147098|Gm94|225443|predicted gene 94	BC147099|Gm94|225443|predicted gene 94	BC171995|Gm94|225443|predicted gene 94	AK131908|Gm94|225443|predicted gene 94	AK131907|Gm94|225443|predicted gene 94	NM_001033280|Gm94|225443|predicted gene 94
mm9_v1_chr12_-_70298068_70298133	0.22901	SOX2.p2	AK075648|1110034A24Rik|109065|RIKEN cDNA 1110034A24 gene	AK172494|1110034A24Rik|109065|RIKEN cDNA 1110034A24 gene	EU599049|1110034A24Rik|109065|RIKEN cDNA 1110034A24 gene	AK012767|1110034A24Rik|109065|RIKEN cDNA 1110034A24 gene	BC058344|1110034A24Rik|109065|RIKEN cDNA 1110034A24 gene	AK154254|1110034A24Rik|109065|RIKEN cDNA 1110034A24 gene
mm9_v1_chrX_+_7305654_7305720	0.22897	SOX2.p2	BC064757|Praf2|54637|PRA1 domain family 2	AK003344|Praf2|54637|PRA1 domain family 2	AK224918|Praf2|54637|PRA1 domain family 2	NM_138602|Praf2|54637|PRA1 domain family 2	AF229636|Praf2|54637|PRA1 domain family 2
mm9_v1_chrX_-_93152223_93152253	0.228773	SOX2.p2	BC032218|Las1l|76130|LAS1-like (S. cerevisiae)	AK018059|Las1l|76130|LAS1-like (S. cerevisiae)	BC141155|Las1l|76130|LAS1-like (S. cerevisiae)
mm9_v1_chr11_-_115560691_115560842	0.228687	SOX2.p2	AK077750|Grb2|14784|growth factor receptor bound protein 2	AK079087|Grb2|14784|growth factor receptor bound protein 2	AK153557|Grb2|14784|growth factor receptor bound protein 2
mm9_v1_chr9_-_106691395_106691543	0.228515	SOX2.p2	BC133714|Rad54l2|81000|RAD54 like 2 (S. cerevisiae)	AK155151|Rad54l2|81000|RAD54 like 2 (S. cerevisiae)	AK090250|Rad54l2|81000|RAD54 like 2 (S. cerevisiae)	AK083903|Rad54l2|81000|RAD54 like 2 (S. cerevisiae)	NM_030730|Rad54l2|81000|RAD54 like 2 (S. cerevisiae)
mm9_v1_chr7_-_25331020_25331089	0.228107	SOX2.p2	AK009589|2310033E01Rik|641361|RIKEN cDNA 2310033E01 gene	AK009778|2310033E01Rik|641361|RIKEN cDNA 2310033E01 gene	NM_001037143|2310033E01Rik|641361|RIKEN cDNA 2310033E01 gene	AK009604|2310033E01Rik|641361|RIKEN cDNA 2310033E01 gene	AK009924|2310033E01Rik|641361|RIKEN cDNA 2310033E01 gene	BC139039|2310033E01Rik|641361|RIKEN cDNA 2310033E01 gene	BC145686|2310033E01Rik|641361|RIKEN cDNA 2310033E01 gene
mm9_v1_chr11_-_74710562_74710581	0.227997	SOX2.p2	BC058414|Sgsm2|97761|small G protein signaling modulator 2	BC060163|Sgsm2|97761|small G protein signaling modulator 2	NM_197943|Sgsm2|97761|small G protein signaling modulator 2
mm9_v1_chr6_+_134346344_134346362	0.227483	SOX2.p2	AK160247|Bcl2l14|66813|BCL2-like 14 (apoptosis facilitator)	AK016670|Bcl2l14|66813|BCL2-like 14 (apoptosis facilitator)	NM_025778|Bcl2l14|66813|BCL2-like 14 (apoptosis facilitator)	AK016997|Bcl2l14|66813|BCL2-like 14 (apoptosis facilitator)	AK015447|Bcl2l14|66813|BCL2-like 14 (apoptosis facilitator)
mm9_v1_chr11_-_99459418_99459419	0.227459	SOX2.p2	AK009730|Krtap9-3|75586|keratin associated protein 9-3	AK131927|Krtap9-3|75586|keratin associated protein 9-3	NM_029351|Krtap9-3|75586|keratin associated protein 9-3
mm9_v1_chr7_-_52381898_52381900	0.227235	SOX2.p2	AK213140|Rpl13a|22121|ribosomal protein L13A
mm9_v1_chr9_-_20447047_20447249	0.227173	SOX2.p2	AF176525|Fbxl12|30843|F-box and leucine-rich repeat protein 12	BC054471|Fbxl12|30843|F-box and leucine-rich repeat protein 12	NM_013911|Fbxl12|30843|F-box and leucine-rich repeat protein 12
mm9_v1_chr4_+_42965965_42965965	0.22715	SOX2.p2	BC057087|Dnajb5|56323|DnaJ (Hsp40) homolog, subfamily B, member 5	NM_019874|Dnajb5|56323|DnaJ (Hsp40) homolog, subfamily B, member 5
mm9_v1_chr19_+_53674862_53674958	0.226917	SOX2.p2	AK165878|Smc3|13006|structural maintenace of chromosomes 3	NM_007790|Smc3|13006|structural maintenace of chromosomes 3	AK164387|Smc3|13006|structural maintenace of chromosomes 3	AK143996|Smc3|13006|structural maintenace of chromosomes 3	AK140705|Smc3|13006|structural maintenace of chromosomes 3	BC062935|Smc3|13006|structural maintenace of chromosomes 3	AF141294|Smc3|13006|structural maintenace of chromosomes 3	AF047601|Smc3|13006|structural maintenace of chromosomes 3
mm9_v1_chr7_+_22296798_22296798	0.226679	SOX2.p2	NM_001166753|Vmn1r155|667530|vomeronasal 1 receptor 155	NM_001166759|Vmn1r107|673977|vomeronasal 1 receptor 107	NM_001166846|Vmn1r110|100043561|vomeronasal 1 receptor 110	NM_001166848|Vmn1r130|100043596|vomeronasal 1 receptor 130	NM_001166849|Vmn1r137|100043614|vomeronasal 1 receptor 137	NM_001166850|Vmn1r165|100043667|vomeronasal 1 receptor 165
mm9_v1_chr2_+_129926129_129926206	0.226523	SOX2.p2	AK139778|AU015228|99169|expressed sequence AU015228	AK163392|AU015228|99169|expressed sequence AU015228	NM_001033197|AU015228|99169|expressed sequence AU015228	BC150906|AU015228|99169|expressed sequence AU015228
mm9_v1_chr17_+_4995073_4995073	0.226431	SOX2.p2	NM_001085355|Arid1b|239985|AT rich interactive domain 1B (SWI-like)
mm9_v1_chr5_-_123974130_123974185	0.226044	SOX2.p2	AF203914|Diablo|66593|diablo homolog (Drosophila)	AK002887|Diablo|66593|diablo homolog (Drosophila)	AK082903|Diablo|66593|diablo homolog (Drosophila)	AK169573|Diablo|66593|diablo homolog (Drosophila)	BC024780|Diablo|66593|diablo homolog (Drosophila)	AK077198|Diablo|66593|diablo homolog (Drosophila)	AK133194|Diablo|66593|diablo homolog (Drosophila)	BC054109|Diablo|66593|diablo homolog (Drosophila)	AK012760|Diablo|66593|diablo homolog (Drosophila)	NM_023232|Diablo|66593|diablo homolog (Drosophila)
mm9_v1_chr8_-_85966340_85966438	0.225804	SOX2.p2	AK076085|Scoc|56367|short coiled-coil protein	BC092071|Scoc|56367|short coiled-coil protein	BC085265|Scoc|56367|short coiled-coil protein	BC108407|Scoc|56367|short coiled-coil protein	AF115778|Scoc|56367|short coiled-coil protein	BC017629|Scoc|56367|short coiled-coil protein	AK088272|Scoc|56367|short coiled-coil protein	AK003095|Scoc|56367|short coiled-coil protein	AK167488|Scoc|56367|short coiled-coil protein
mm9_v1_chr11_+_115761444_115761621	0.225422	SOX2.p2	NM_183259|2210020M01Rik|66528|RIKEN cDNA 2210020M01 gene	AK020450|2210020M01Rik|66528|RIKEN cDNA 2210020M01 gene	AK004370|2210020M01Rik|66528|RIKEN cDNA 2210020M01 gene	BC065414|2210020M01Rik|66528|RIKEN cDNA 2210020M01 gene
mm9_v1_chr4_+_42231042_42231117	0.225181	SOX2.p2	NM_001193667|Gm1987|100504362|predicted gene 1987	AK144258|Ccl21a|18829|chemokine (C-C motif) ligand 21A (serine)	NM_011124|Ccl21a|18829|chemokine (C-C motif) ligand 21A (serine)	AK155924|Ccl21a|18829|chemokine (C-C motif) ligand 21A (serine)	BC025974|Ccl21a|18829|chemokine (C-C motif) ligand 21A (serine)	BC028747|Ccl21a|18829|chemokine (C-C motif) ligand 21A (serine)	BC038120|Ccl21a|18829|chemokine (C-C motif) ligand 21A (serine)	AF001980|Ccl21a|18829|chemokine (C-C motif) ligand 21A (serine)
mm9_v1_chr2_-_156817751_156817861	0.224905	SOX2.p2	AK002272|Ndrg3|29812|N-myc downstream regulated gene 3	AB033922|Ndrg3|29812|N-myc downstream regulated gene 3	BC018504|Ndrg3|29812|N-myc downstream regulated gene 3	AK036277|Ndrg3|29812|N-myc downstream regulated gene 3	AK037487|Ndrg3|29812|N-myc downstream regulated gene 3	AK029378|Ndrg3|29812|N-myc downstream regulated gene 3	AK004689|Ndrg3|29812|N-myc downstream regulated gene 3	AK154927|Ndrg3|29812|N-myc downstream regulated gene 3	NM_013865|Ndrg3|29812|N-myc downstream regulated gene 3	NM_180956|Ndrg3|29812|N-myc downstream regulated gene 3
mm9_v1_chr7_-_31373735_31373744	0.224869	SOX2.p2	AB182318|Wbp7|75410|WW domain binding protein 7	NM_029274|Wbp7|75410|WW domain binding protein 7
mm9_v1_chr4_+_155484072_155484109	0.22434	SOX2.p2	AK029276|9430015G10Rik|230996|RIKEN cDNA 9430015G10 gene	BC004010|9430015G10Rik|230996|RIKEN cDNA 9430015G10 gene	NM_145557|9430015G10Rik|230996|RIKEN cDNA 9430015G10 gene	NM_177205|9430015G10Rik|230996|RIKEN cDNA 9430015G10 gene	AK034620|9430015G10Rik|230996|RIKEN cDNA 9430015G10 gene
mm9_v1_chr2_+_71049762_71049900	0.224025	SOX2.p2	NM_001198872|Dync1i2|13427|dynein cytoplasmic 1 intermediate chain 2	NM_001198873|Dync1i2|13427|dynein cytoplasmic 1 intermediate chain 2	NM_001198874|Dync1i2|13427|dynein cytoplasmic 1 intermediate chain 2	NM_001198875|Dync1i2|13427|dynein cytoplasmic 1 intermediate chain 2	NM_001198876|Dync1i2|13427|dynein cytoplasmic 1 intermediate chain 2	AK019441|Dync1i2|13427|dynein cytoplasmic 1 intermediate chain 2	AK141837|Dync1i2|13427|dynein cytoplasmic 1 intermediate chain 2	AK150173|Dync1i2|13427|dynein cytoplasmic 1 intermediate chain 2	AK164322|Dync1i2|13427|dynein cytoplasmic 1 intermediate chain 2	AK164437|Dync1i2|13427|dynein cytoplasmic 1 intermediate chain 2	GU992208|Dync1i2|13427|dynein cytoplasmic 1 intermediate chain 2	GU992209|Dync1i2|13427|dynein cytoplasmic 1 intermediate chain 2	GU992210|Dync1i2|13427|dynein cytoplasmic 1 intermediate chain 2
mm9_v1_chr14_-_56778401_56778415	0.223351	SOX2.p2	J02872|Gzmg|14944|granzyme G	BC099473|Gzmg|14944|granzyme G	NM_010375|Gzmg|14944|granzyme G
mm9_v1_chr5_-_138066184_138066305	0.223322	SOX2.p2	AK016870|Fbxo24|71176|F-box protein 24	NM_027708|Fbxo24|71176|F-box protein 24
mm9_v1_chr1_-_52874276_52874420	0.223032	SOX2.p2	BC025072|Inpp1|16329|inositol polyphosphate-1-phosphatase	U27295|Inpp1|16329|inositol polyphosphate-1-phosphatase	AK078382|Inpp1|16329|inositol polyphosphate-1-phosphatase
mm9_v1_chr1_-_59820157_59820193	0.222918	SOX2.p2	AK049886|B430105G09Rik|320907|RIKEN cDNA B430105G09 gene
mm9_v1_chr3_-_122686809_122686855	0.222873	SOX2.p2	AK134835|Usp53|99526|ubiquitin specific peptidase 53
mm9_v1_chr5_+_35292092_35292155	0.222811	SOX2.p2	AK053804|Rgs12|71729|regulator of G-protein signaling 12	NM_173402|Rgs12|71729|regulator of G-protein signaling 12	BC040396|Rgs12|71729|regulator of G-protein signaling 12	AK144822|Rgs12|71729|regulator of G-protein signaling 12	AK145890|Rgs12|71729|regulator of G-protein signaling 12
mm9_v1_chr10_-_120748244_120748244	0.222264	SOX2.p2	NM_029057|Tbc1d30|74694|TBC1 domain family, member 30
mm9_v1_chr7_+_97357406_97357492	0.221767	SOX2.p2	AK163129|Picalm|233489|phosphatidylinositol binding clathrin assembly protein
mm9_v1_chr1_-_31006461_31006538	0.221563	SOX2.p2	BC094447|Ptp4a1|19243|protein tyrosine phosphatase 4a1	BC003761|Ptp4a1|19243|protein tyrosine phosphatase 4a1	BC031734|Ptp4a1|19243|protein tyrosine phosphatase 4a1
mm9_v1_chr13_-_74199688_74199784	0.220173	SOX2.p2	BC080681|Cep72|74470|centrosomal protein 72	BC060686|Cep72|74470|centrosomal protein 72	AK017134|Cep72|74470|centrosomal protein 72	AK034892|Cep72|74470|centrosomal protein 72	NM_028959|Cep72|74470|centrosomal protein 72
mm9_v1_chr2_-_20889276_20889347	0.219688	SOX2.p2	BC150741|Arhgap21|71435|Rho GTPase activating protein 21	BC076629|Arhgap21|71435|Rho GTPase activating protein 21	NM_001081364|Arhgap21|71435|Rho GTPase activating protein 21	NM_001128084|Arhgap21|71435|Rho GTPase activating protein 21
mm9_v1_chr5_-_138713960_138713994	0.219617	SOX2.p2	AK132558|Gal3st4|330217|galactose-3-O-sulfotransferase 4	NM_001033416|Gal3st4|330217|galactose-3-O-sulfotransferase 4	AK138993|Gal3st4|330217|galactose-3-O-sulfotransferase 4
mm9_v1_chr4_-_144376485_144376485	0.219583	SOX2.p2	NM_001126316|Gm438|329993|predicted gene 438
mm9_v1_chr7_-_106987766_106987861	0.218887	SOX2.p2	AK180141|Spcs2|66624|signal peptidase complex subunit 2 homolog (S. cerevisiae)
mm9_v1_chr15_+_57747523_57747567	0.218836	SOX2.p2	AK084542|Wdr67|210544|WD repeat domain 67
mm9_v1_chr5_+_122804377_122804463	0.218366	SOX2.p2	AK150330|Vps29|56433|vacuolar protein sorting 29 (S. pombe)	AK008248|Vps29|56433|vacuolar protein sorting 29 (S. pombe)	AK004103|Vps29|56433|vacuolar protein sorting 29 (S. pombe)	AF193794|Vps29|56433|vacuolar protein sorting 29 (S. pombe)	NM_019780|Vps29|56433|vacuolar protein sorting 29 (S. pombe)	BC005663|Vps29|56433|vacuolar protein sorting 29 (S. pombe)	AK036426|Vps29|56433|vacuolar protein sorting 29 (S. pombe)
mm9_v1_chr5_+_87233514_87233581	0.218351	SOX2.p2	NM_177680|Ythdc1|231386|YTH domain containing 1
mm9_v1_chr4_-_143405981_143405995	0.218018	SOX2.p2	BC080785|Gm13084|381569|predicted gene 13084	AK145369|Gm13084|381569|predicted gene 13084	NM_001005371|Gm13084|381569|predicted gene 13084
mm9_v1_chr1_-_171461510_171461594	0.218011	SOX2.p2	AK010351|Nuf2|66977|NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)	AK012011|Nuf2|66977|NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)	BC020026|Nuf2|66977|NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)	AK089939|Nuf2|66977|NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)	AF326732|Nuf2|66977|NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)	AK044882|Nuf2|66977|NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)	AK162249|Nuf2|66977|NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)	AK132467|Nuf2|66977|NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)	NM_023284|Nuf2|66977|NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)
mm9_v1_chrX_+_35542969_35543017	0.217532	SOX2.p2	NM_001079513|Zbtb33|56805|zinc finger and BTB domain containing 33	NM_020256|Zbtb33|56805|zinc finger and BTB domain containing 33	AK087417|Zbtb33|56805|zinc finger and BTB domain containing 33	AK089423|Zbtb33|56805|zinc finger and BTB domain containing 33	AF097416|Zbtb33|56805|zinc finger and BTB domain containing 33
mm9_v1_chr1_-_153317422_153317565	0.217523	SOX2.p2	AK211660|Rnf2|19821|ring finger protein 2
mm9_v1_chr1_-_162142846_162143024	0.21749	SOX2.p2	U97327|Cacybp|12301|calcyclin binding protein	AK089043|Cacybp|12301|calcyclin binding protein	AK177869|Cacybp|12301|calcyclin binding protein	BC025948|Cacybp|12301|calcyclin binding protein	NM_009786|Cacybp|12301|calcyclin binding protein	AK013924|Cacybp|12301|calcyclin binding protein	AK145013|Cacybp|12301|calcyclin binding protein
mm9_v1_chr7_-_137663474_137663533	0.216811	SOX2.p2	DQ093639|Ate1|11907|arginyltransferase 1	DQ093640|Ate1|11907|arginyltransferase 1	NM_001029895|Ate1|11907|arginyltransferase 1	AK138277|Ate1|11907|arginyltransferase 1
mm9_v1_chr9_+_106073265_106073336	0.216761	SOX2.p2	BC094419|Wdr82|77305|WD repeat domain containing 82	BC157945|Wdr82|77305|WD repeat domain containing 82	BC158054|Wdr82|77305|WD repeat domain containing 82	BC157943|Wdr82|77305|WD repeat domain containing 82
mm9_v1_chr11_-_115884712_115884736	0.216324	SOX2.p2	AK213191|H3f3b|15081|H3 histone, family 3B
mm9_v1_chr12_+_85291557_85291603	0.216287	SOX2.p2	BC138094|2410016O06Rik|71952|RIKEN cDNA 2410016O06 gene	NM_023633|2410016O06Rik|71952|RIKEN cDNA 2410016O06 gene
mm9_v1_chr2_-_167124096_167124195	0.216147	SOX2.p2	
mm9_v1_chr1_-_183950050_183950110	0.214851	SOX2.p2	NM_001083120|Enah|13800|enabled homolog (Drosophila)	NM_001083121|Enah|13800|enabled homolog (Drosophila)	NM_008680|Enah|13800|enabled homolog (Drosophila)	NM_010135|Enah|13800|enabled homolog (Drosophila)
mm9_v1_chr7_+_52810297_52810297	0.214741	SOX2.p2	NM_025330|Hsd17b14|66065|hydroxysteroid (17-beta) dehydrogenase 14
mm9_v1_chr7_-_49128039_49128039	0.214721	SOX2.p2	NM_001105055|Vmn2r58|628422|vomeronasal 2, receptor 58
mm9_v1_chr1_+_183081058_183081062	0.214393	SOX2.p2	NM_030131|Cnih4|98417|cornichon homolog 4 (Drosophila)
mm9_v1_chr2_-_4933760_4933836	0.214262	SOX2.p2	AK021211|Mcm10|70024|minichromosome maintenance deficient 10 (S. cerevisiae)	AK041406|Mcm10|70024|minichromosome maintenance deficient 10 (S. cerevisiae)	AK030780|Mcm10|70024|minichromosome maintenance deficient 10 (S. cerevisiae)	BC094576|Mcm10|70024|minichromosome maintenance deficient 10 (S. cerevisiae)	NM_027290|Mcm10|70024|minichromosome maintenance deficient 10 (S. cerevisiae)
mm9_v1_chr19_+_4878667_4878752	0.213717	SOX2.p2	NM_001168516|Zdhhc24|70605|zinc finger, DHHC domain containing 24	NM_027476|Zdhhc24|70605|zinc finger, DHHC domain containing 24	AK171568|Zdhhc24|70605|zinc finger, DHHC domain containing 24	AK170706|Zdhhc24|70605|zinc finger, DHHC domain containing 24	AK170233|Zdhhc24|70605|zinc finger, DHHC domain containing 24	AK172151|Zdhhc24|70605|zinc finger, DHHC domain containing 24	NM_001168517|Zdhhc24|70605|zinc finger, DHHC domain containing 24	AK047235|Zdhhc24|70605|zinc finger, DHHC domain containing 24	AK017737|Zdhhc24|70605|zinc finger, DHHC domain containing 24	AK028164|Zdhhc24|70605|zinc finger, DHHC domain containing 24	AK169337|Zdhhc24|70605|zinc finger, DHHC domain containing 24	AK043923|Zdhhc24|70605|zinc finger, DHHC domain containing 24	BC056621|Zdhhc24|70605|zinc finger, DHHC domain containing 24	BC071194|Zdhhc24|70605|zinc finger, DHHC domain containing 24
mm9_v1_chr17_-_45705198_45705339	0.213302	SOX2.p2	AK192311|Hsp90ab1|15516|heat shock protein 90 alpha (cytosolic), class B member 1
mm9_v1_chr9_-_53012444_53012529	0.212956	SOX2.p2	AK166787|Ddx10|77591|DEAD (Asp-Glu-Ala-Asp) box polypeptide 10
mm9_v1_chr7_-_26539732_26539751	0.212932	SOX2.p2	NM_144922|Hnrnpul1|232989|heterogeneous nuclear ribonucleoprotein U-like 1	BC021506|Hnrnpul1|232989|heterogeneous nuclear ribonucleoprotein U-like 1	AK155604|Hnrnpul1|232989|heterogeneous nuclear ribonucleoprotein U-like 1
mm9_v1_chr7_-_134281327_134281330	0.212269	SOX2.p2	AK041480|Spn|20737|sialophorin	AK041712|Spn|20737|sialophorin	AK077764|Spn|20737|sialophorin	AK134098|Spn|20737|sialophorin	NM_001037810|Spn|20737|sialophorin	NM_009259|Spn|20737|sialophorin
mm9_v1_chr5_-_86626849_86626920	0.212231	SOX2.p2	L28757|Gnrhr|14715|gonadotropin releasing hormone receptor	L28758|Gnrhr|14715|gonadotropin releasing hormone receptor	BC061250|Gnrhr|14715|gonadotropin releasing hormone receptor	M93108|Gnrhr|14715|gonadotropin releasing hormone receptor	L01119|Gnrhr|14715|gonadotropin releasing hormone receptor	NM_010323|Gnrhr|14715|gonadotropin releasing hormone receptor	L28756|Gnrhr|14715|gonadotropin releasing hormone receptor
mm9_v1_chr9_+_44412931_44412987	0.212073	SOX2.p2	NM_001110826|Ddx6|13209|DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	NM_007841|Ddx6|13209|DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	NM_181324|Ddx6|13209|DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	AK148483|Ddx6|13209|DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	AK036648|Ddx6|13209|DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	AK054144|Ddx6|13209|DEAD (Asp-Glu-Ala-Asp) box polypeptide 6
mm9_v1_chr18_+_76219111_76219147	0.211815	SOX2.p2	BC018187|Zbtb7c|207259|zinc finger and BTB domain containing 7C	AK156372|Zbtb7c|207259|zinc finger and BTB domain containing 7C
mm9_v1_chr11_-_99997241_99997264	0.211773	SOX2.p2	BC057934|Krt15|16665|keratin 15	NM_008469|Krt15|16665|keratin 15
mm9_v1_chr4_+_118293403_118293498	0.2112	SOX2.p2	NM_026932|Ebna1bp2|69072|EBNA1 binding protein 2	BC054723|Ebna1bp2|69072|EBNA1 binding protein 2	AK007491|Ebna1bp2|69072|EBNA1 binding protein 2	AK134732|Ebna1bp2|69072|EBNA1 binding protein 2	AK167070|Ebna1bp2|69072|EBNA1 binding protein 2	BC062876|Ebna1bp2|69072|EBNA1 binding protein 2	AK168269|Ebna1bp2|69072|EBNA1 binding protein 2
mm9_v1_chr16_+_13265171_13265171	0.210729	SOX2.p2	BC028459|Mkl2|239719|MKL/myocardin-like 2	NM_181860|Mkl2|239719|MKL/myocardin-like 2
mm9_v1_chr15_-_72926936_72926959	0.210551	SOX2.p2	AK003962|1110029L17Rik|68722|RIKEN cDNA 1110029L17 gene
mm9_v1_chr18_-_21810868_21810868	0.210325	SOX2.p2	NM_001081403|Klhl14|225266|kelch-like 14 (Drosophila)
mm9_v1_chrX_+_70884742_70884779	0.210002	SOX2.p2	AK141667|Dusp9|75590|dual specificity phosphatase 9	AY316312|Dusp9|75590|dual specificity phosphatase 9	BC100309|Dusp9|75590|dual specificity phosphatase 9	NM_029352|Dusp9|75590|dual specificity phosphatase 9
mm9_v1_chr6_+_55027608_55027621	0.209494	SOX2.p2	AK191772|Gars|353172|glycyl-tRNA synthetase
mm9_v1_chr3_+_55586431_55586482	0.208915	SOX2.p2	NM_010750|Mab21l1|17116|mab-21-like 1 (C. elegans)	AK043552|Mab21l1|17116|mab-21-like 1 (C. elegans)	AF040945|Mab21l1|17116|mab-21-like 1 (C. elegans)	AF228913|Mab21l1|17116|mab-21-like 1 (C. elegans)	AK032114|Mab21l1|17116|mab-21-like 1 (C. elegans)	BC014750|Mab21l1|17116|mab-21-like 1 (C. elegans)
mm9_v1_chr12_-_105251851_105251861	0.208531	SOX2.p2	BC132287|Serpina9|71907|serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	BC144769|Serpina9|71907|serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	AK009343|Serpina9|71907|serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	NM_027997|Serpina9|71907|serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9
mm9_v1_chr7_-_126666995_126666995	0.20823	SOX2.p2	AK005692|Pdilt|71830|protein disulfide isomerase-like, testis expressed	NM_027943|Pdilt|71830|protein disulfide isomerase-like, testis expressed
mm9_v1_chr8_+_32260775_32260840	0.207571	SOX2.p2	AK045392|BC019943|234138|cDNA sequence BC019943	NM_001112729|BC019943|234138|cDNA sequence BC019943	NM_144927|BC019943|234138|cDNA sequence BC019943	AK084242|BC019943|234138|cDNA sequence BC019943	AK046031|BC019943|234138|cDNA sequence BC019943	AK139425|BC019943|234138|cDNA sequence BC019943
mm9_v1_chr11_+_75300278_75300323	0.207335	SOX2.p2	NM_138659|Prpf8|192159|pre-mRNA processing factor 8	AK041017|Prpf8|192159|pre-mRNA processing factor 8
mm9_v1_chr7_-_20819176_20819176	0.207092	SOX2.p2	NM_001166742|Vmn1r118|667259|vomeronasal 1 receptor 118	NM_001167150|Gm8453|667094|predicted gene 8453	NM_001167151|Gm4498|100043523|predicted gene 4498
mm9_v1_chr16_-_17911283_17911450	0.20663	SOX2.p2	AK088520|Dgcr14|27886|DiGeorge syndrome critical region gene 14	AK142684|Dgcr14|27886|DiGeorge syndrome critical region gene 14	AK148404|Dgcr14|27886|DiGeorge syndrome critical region gene 14	BC013711|Dgcr14|27886|DiGeorge syndrome critical region gene 14	AF037256|Dgcr14|27886|DiGeorge syndrome critical region gene 14	NM_001081633|Dgcr14|27886|DiGeorge syndrome critical region gene 14	NM_022408|Dgcr14|27886|DiGeorge syndrome critical region gene 14
mm9_v1_chr2_+_34965011_34965138	0.206429	SOX2.p2	AK041715|Cep110|26920|centrosomal protein 110	NM_012018|Cep110|26920|centrosomal protein 110	AK031338|Cep110|26920|centrosomal protein 110	AK020148|Cep110|26920|centrosomal protein 110	BC038386|Cep110|26920|centrosomal protein 110	BC158010|Cep110|26920|centrosomal protein 110
mm9_v1_chr9_-_108984865_108984900	0.206362	SOX2.p2	BC106104|Ccdc72|66167|coiled-coil domain containing 72	BC054363|Ccdc72|66167|coiled-coil domain containing 72	BC090400|Ccdc72|66167|coiled-coil domain containing 72	BC034602|Ccdc72|66167|coiled-coil domain containing 72	AK169860|Ccdc72|66167|coiled-coil domain containing 72	BC116987|Ccdc72|66167|coiled-coil domain containing 72	BC116989|Ccdc72|66167|coiled-coil domain containing 72	AK160705|Ccdc72|66167|coiled-coil domain containing 72	AK002863|Ccdc72|66167|coiled-coil domain containing 72	AK003762|Ccdc72|66167|coiled-coil domain containing 72	NM_183250|Ccdc72|66167|coiled-coil domain containing 72
mm9_v1_chr9_-_36954842_36954852	0.206138	SOX2.p2	AK144270|Pknox2|208076|Pbx/knotted 1 homeobox 2	AK084178|Pknox2|208076|Pbx/knotted 1 homeobox 2	AK082952|Pknox2|208076|Pbx/knotted 1 homeobox 2	NM_001029838|Pknox2|208076|Pbx/knotted 1 homeobox 2
mm9_v1_chr13_-_27734332_27734361	0.205884	SOX2.p2	AF020525|Prl7a1|19113|prolactin family 7, subfamily a, member 1	AF011381|Prl7a1|19113|prolactin family 7, subfamily a, member 1	BC051671|Prl7a1|19113|prolactin family 7, subfamily a, member 1	AK028371|Prl7a1|19113|prolactin family 7, subfamily a, member 1	AK141309|Prl7a1|19113|prolactin family 7, subfamily a, member 1	AK146050|Prl7a1|19113|prolactin family 7, subfamily a, member 1	NM_001164058|Prl7a1|19113|prolactin family 7, subfamily a, member 1	NM_008930|Prl7a1|19113|prolactin family 7, subfamily a, member 1
mm9_v1_chr8_+_11556062_11556065	0.205626	SOX2.p2	AK145553|Ing1|26356|inhibitor of growth family, member 1	AK076482|Ing1|26356|inhibitor of growth family, member 1	AK141466|Ing1|26356|inhibitor of growth family, member 1	AF177757|Ing1|26356|inhibitor of growth family, member 1	NM_011919|Ing1|26356|inhibitor of growth family, member 1
mm9_v1_chr2_+_31805751_31805822	0.205366	SOX2.p2	AK045539|Aif1l|108897|allograft inflammatory factor 1-like	BC024599|Aif1l|108897|allograft inflammatory factor 1-like	NM_145144|Aif1l|108897|allograft inflammatory factor 1-like
mm9_v1_chr7_-_53152003_53152080	0.203975	SOX2.p2	AJ011734|Syngr4|58867|synaptogyrin 4	AK006050|Syngr4|58867|synaptogyrin 4	BC048469|Syngr4|58867|synaptogyrin 4	NM_021482|Syngr4|58867|synaptogyrin 4
mm9_v1_chr17_-_25891264_25891327	0.203958	SOX2.p2	BC023753|Msln|56047|mesothelin	D86370|Msln|56047|mesothelin	NM_018857|Msln|56047|mesothelin	AK146799|Msln|56047|mesothelin	AK144391|Msln|56047|mesothelin
mm9_v1_chr14_+_36908102_36908154	0.203396	SOX2.p2	BC096580|4930474N05Rik|218921|RIKEN cDNA 4930474N05 gene	AK076810|4930474N05Rik|218921|RIKEN cDNA 4930474N05 gene	NM_175008|4930474N05Rik|218921|RIKEN cDNA 4930474N05 gene	AK133002|4930474N05Rik|218921|RIKEN cDNA 4930474N05 gene	AK132960|4930474N05Rik|218921|RIKEN cDNA 4930474N05 gene	BC132442|4930474N05Rik|218921|RIKEN cDNA 4930474N05 gene	BC132446|4930474N05Rik|218921|RIKEN cDNA 4930474N05 gene
mm9_v1_chr17_-_81464406_81464435	0.203304	SOX2.p2	AK012806|Thumpd2|72167|THUMP domain containing 2	NM_028138|Thumpd2|72167|THUMP domain containing 2
mm9_v1_chr15_-_13103346_13103429	0.203229	SOX2.p2	NM_007666|Cdh6|12563|cadherin 6	AK134611|Cdh6|12563|cadherin 6
mm9_v1_chr10_+_40069255_40069363	0.203087	SOX2.p2	AK052818|Cdk19|78334|cyclin-dependent kinase 19	AK147340|Cdk19|78334|cyclin-dependent kinase 19	BC062100|Cdk19|78334|cyclin-dependent kinase 19	BC048908|Cdk19|78334|cyclin-dependent kinase 19
mm9_v1_chr1_-_65149923_65149948	0.203022	SOX2.p2	BC056430|Cryga|12964|crystallin, gamma A	NM_007774|Cryga|12964|crystallin, gamma A
mm9_v1_chr7_-_21883531_21883531	0.20273	SOX2.p2	NM_001166741|Vmn1r121|667240|vomeronasal 1 receptor 121
mm9_v1_chr6_-_94650118_94650173	0.202717	SOX2.p2	D78572|Lrig1|16206|leucine-rich repeats and immunoglobulin-like domains 1	NM_008377|Lrig1|16206|leucine-rich repeats and immunoglobulin-like domains 1
mm9_v1_chr6_-_8728094_8728149	0.202573	SOX2.p2	BC002030|Ica1|15893|islet cell autoantigen 1	AK192988|Ica1|15893|islet cell autoantigen 1	U26459|Ica1|15893|islet cell autoantigen 1
mm9_v1_chr17_-_55851857_55851925	0.20252	SOX2.p2	AK045286|Pot1b|72836|protection of telomeres 1B	AK165040|Pot1b|72836|protection of telomeres 1B	AK050727|Pot1b|72836|protection of telomeres 1B	AK013364|Pot1b|72836|protection of telomeres 1B	NM_028370|Pot1b|72836|protection of telomeres 1B
mm9_v1_chr18_+_32416881_32416904	0.202483	SOX2.p2	BC024446|Ercc3|13872|excision repair cross-complementing rodent repair deficiency, complementation group 3
mm9_v1_chr4_+_59048027_59048124	0.202263	SOX2.p2	NM_025277|Gng10|14700|guanine nucleotide binding protein (G protein), gamma 10	AK014158|Gng10|14700|guanine nucleotide binding protein (G protein), gamma 10	BC023670|Gng10|14700|guanine nucleotide binding protein (G protein), gamma 10	AK003187|Gng10|14700|guanine nucleotide binding protein (G protein), gamma 10	BC055434|Gng10|14700|guanine nucleotide binding protein (G protein), gamma 10	BC061090|Gng10|14700|guanine nucleotide binding protein (G protein), gamma 10
mm9_v1_chr7_-_126622690_126622768	0.201927	SOX2.p2	AK144065|Umod|22242|uromodulin	AK164688|Umod|22242|uromodulin	L33406|Umod|22242|uromodulin	AK165507|Umod|22242|uromodulin	AK085460|Umod|22242|uromodulin	NM_009470|Umod|22242|uromodulin
mm9_v1_chr19_+_9028319_9028429	0.201201	SOX2.p2	AK044659|Tut1|70044|terminal uridylyl transferase 1, U6 snRNA-specific	BC025499|Tut1|70044|terminal uridylyl transferase 1, U6 snRNA-specific	NM_197993|Tut1|70044|terminal uridylyl transferase 1, U6 snRNA-specific	BC023900|Tut1|70044|terminal uridylyl transferase 1, U6 snRNA-specific	AK138418|Tut1|70044|terminal uridylyl transferase 1, U6 snRNA-specific
mm9_v1_chr14_-_48038081_48038081	0.20119	SOX2.p2	AB076696|Dlgap5|218977|discs, large (Drosophila) homolog-associated protein 5	NM_001145949|Dlgap5|218977|discs, large (Drosophila) homolog-associated protein 5	NM_144553|Dlgap5|218977|discs, large (Drosophila) homolog-associated protein 5
mm9_v1_chr5_+_100408033_100408079	0.200531	SOX2.p2	AK015886|4930524J08Rik|75129|RIKEN cDNA 4930524J08 gene
mm9_v1_chr14_+_70132570_70132619	0.200278	SOX2.p2	AK133329|4930480K23Rik|75016|RIKEN cDNA 4930480K23 gene
mm9_v1_chr5_-_138613028_138613124	0.199428	SOX2.p2	BC066024|Mcm7|17220|minichromosome maintenance deficient 7 (S. cerevisiae)	BC023232|Mcm7|17220|minichromosome maintenance deficient 7 (S. cerevisiae)	BC065164|Mcm7|17220|minichromosome maintenance deficient 7 (S. cerevisiae)	AK150059|Mcm7|17220|minichromosome maintenance deficient 7 (S. cerevisiae)	AK150066|Mcm7|17220|minichromosome maintenance deficient 7 (S. cerevisiae)	AK154052|Mcm7|17220|minichromosome maintenance deficient 7 (S. cerevisiae)	AK133091|Mcm7|17220|minichromosome maintenance deficient 7 (S. cerevisiae)	AK149913|Mcm7|17220|minichromosome maintenance deficient 7 (S. cerevisiae)	D26091|Mcm7|17220|minichromosome maintenance deficient 7 (S. cerevisiae)	NM_008568|Mcm7|17220|minichromosome maintenance deficient 7 (S. cerevisiae)	AK144980|Mcm7|17220|minichromosome maintenance deficient 7 (S. cerevisiae)
mm9_v1_chr7_-_109643286_109643286	0.198968	SOX2.p2	BC106987|Olfr545|258837|olfactory receptor 545	BC128265|Olfr545|258837|olfactory receptor 545	BC128266|Olfr545|258837|olfactory receptor 545	NM_146840|Olfr545|258837|olfactory receptor 545
mm9_v1_chr7_-_21697365_21697365	0.198604	SOX2.p2	NM_001166742|Vmn1r118|667259|vomeronasal 1 receptor 118	NM_001167150|Gm8453|667094|predicted gene 8453	NM_001167151|Gm4498|100043523|predicted gene 4498
mm9_v1_chr10_-_88289526_88289560	0.198494	SOX2.p2	AK145554|Utp20|70683|UTP20, small subunit (SSU) processome component, homolog (yeast)	BC084586|Utp20|70683|UTP20, small subunit (SSU) processome component, homolog (yeast)	NM_175158|Utp20|70683|UTP20, small subunit (SSU) processome component, homolog (yeast)
mm9_v1_chr4_+_73659506_73659598	0.19762	SOX2.p2	AK079349|Frmd3|242506|FERM domain containing 3	NM_001163732|Frmd3|242506|FERM domain containing 3	NM_172869|Frmd3|242506|FERM domain containing 3	AK034956|Frmd3|242506|FERM domain containing 3	AK048561|Frmd3|242506|FERM domain containing 3	BC118964|Frmd3|242506|FERM domain containing 3	BC112419|Frmd3|242506|FERM domain containing 3	BC113795|Frmd3|242506|FERM domain containing 3
mm9_v1_chr7_-_27179256_27179261	0.197495	SOX2.p2	AY360472|Nlrp9c|330490|NLR family, pyrin domain containing 9C	AY596203|Nlrp9c|330490|NLR family, pyrin domain containing 9C	NM_001042612|Nlrp9c|330490|NLR family, pyrin domain containing 9C
mm9_v1_chr19_+_26679649_26679686	0.197412	SOX2.p2	BC075641|Smarca2|67155|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	NM_011416|Smarca2|67155|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	AK020092|Smarca2|67155|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2
mm9_v1_chr9_+_108393006_108393101	0.197068	SOX2.p2	NM_001168371|Usp19|71472|ubiquitin specific peptidase 19	NM_001168372|Usp19|71472|ubiquitin specific peptidase 19	NM_001168373|Usp19|71472|ubiquitin specific peptidase 19	NM_027804|Usp19|71472|ubiquitin specific peptidase 19	NM_145407|Usp19|71472|ubiquitin specific peptidase 19	BC060613|Usp19|71472|ubiquitin specific peptidase 19
mm9_v1_chr1_-_30930715_30930760	0.196129	SOX2.p2	AK133490|Phf3|213109|PHD finger protein 3
mm9_v1_chr7_+_51453560_51453599	0.195189	SOX2.p2	BC132657|Klk1b3|18050|kallikrein 1-related peptidase b3	BC132659|Klk1b3|18050|kallikrein 1-related peptidase b3	NM_008693|Klk1b3|18050|kallikrein 1-related peptidase b3	X01389|Klk1b3|18050|kallikrein 1-related peptidase b3
mm9_v1_chr2_+_179759610_179759731	0.194774	SOX2.p2	BC040823|Lsm14b|241846|LSM14 homolog B (SCD6, S. cerevisiae)	NM_177727|Lsm14b|241846|LSM14 homolog B (SCD6, S. cerevisiae)
mm9_v1_chr16_-_85056592_85056771	0.193869	SOX2.p2	M24397|App|11820|amyloid beta (A4) precursor protein	AK161854|App|11820|amyloid beta (A4) precursor protein
mm9_v1_chr7_+_15245056_15245056	0.193567	SOX2.p2	BC099488|Gm4745|194588|predicted gene 4745	NM_001038676|Gm4745|194588|predicted gene 4745
mm9_v1_chr18_+_75169426_75169445	0.193485	SOX2.p2	
mm9_v1_chr3_-_68930721_68930780	0.193271	SOX2.p2	AF020771|Kpna4|16649|karyopherin (importin) alpha 4	CT010281|Kpna4|16649|karyopherin (importin) alpha 4
mm9_v1_chr10_+_36694535_36694557	0.192966	SOX2.p2	AB221663|Hdac2|15182|histone deacetylase 2
mm9_v1_chr7_-_14574936_14574936	0.192886	SOX2.p2	NM_001101534|Sult2a4|434121|sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 4
mm9_v1_chr8_-_114434098_114434098	0.192741	SOX2.p2	AF176840|Chst5|56773|carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5	NM_019950|Chst5|56773|carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5
mm9_v1_chr6_-_66509701_66509701	0.192382	SOX2.p2	AK029205|Vmn1r32|171188|vomeronasal 1 receptor 32	NM_134170|Vmn1r32|171188|vomeronasal 1 receptor 32
mm9_v1_chr17_-_24210402_24210430	0.19223	SOX2.p2	BC021777|Kctd5|69259|potassium channel tetramerisation domain containing 5	AK129077|Kctd5|69259|potassium channel tetramerisation domain containing 5	AK143644|Kctd5|69259|potassium channel tetramerisation domain containing 5
mm9_v1_chr6_-_136730254_136730285	0.192188	SOX2.p2	BC099968|Gucy2c|14917|guanylate cyclase 2c	NM_001127318|Gucy2c|14917|guanylate cyclase 2c	NM_145067|Gucy2c|14917|guanylate cyclase 2c	AK136496|Gucy2c|14917|guanylate cyclase 2c
mm9_v1_chr10_+_62562532_62562550	0.191781	SOX2.p2	BC092234|Atoh7|53404|atonal homolog 7 (Drosophila)
mm9_v1_chr4_-_25726753_25727001	0.191558	SOX2.p2	AB015426|Fut9|14348|fucosyltransferase 9	BC116874|Fut9|14348|fucosyltransferase 9	BC116876|Fut9|14348|fucosyltransferase 9	AK047650|Fut9|14348|fucosyltransferase 9	AK163871|Fut9|14348|fucosyltransferase 9	AK036183|Fut9|14348|fucosyltransferase 9	AK043410|Fut9|14348|fucosyltransferase 9	AK049167|Fut9|14348|fucosyltransferase 9
mm9_v1_chr2_-_168427037_168427156	0.191044	SOX2.p2	EU887581|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	EU887587|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	EU887593|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	EU887599|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	AK083119|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	EU887583|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	EU887585|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	EU887589|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	EU887591|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	EU887595|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	EU887597|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	EU887601|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	EU887603|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	NM_001037178|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	AK044489|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2
mm9_v1_chr3_-_144761960_144762069	0.190538	SOX2.p2	AY161007|Clca5|229933|chloride channel calcium activated 5	AK048276|Clca5|229933|chloride channel calcium activated 5	AK028704|Clca5|229933|chloride channel calcium activated 5	NM_178697|Clca5|229933|chloride channel calcium activated 5	BC096379|Clca5|229933|chloride channel calcium activated 5	AK035512|Clca5|229933|chloride channel calcium activated 5
mm9_v1_chr4_-_42787449_42787524	0.190457	SOX2.p2	AF001980|Ccl21a|18829|chemokine (C-C motif) ligand 21A (serine)	BC038120|Ccl21a|18829|chemokine (C-C motif) ligand 21A (serine)	BC025974|Ccl21a|18829|chemokine (C-C motif) ligand 21A (serine)	BC028747|Ccl21a|18829|chemokine (C-C motif) ligand 21A (serine)	AK155924|Ccl21a|18829|chemokine (C-C motif) ligand 21A (serine)	NM_011124|Ccl21a|18829|chemokine (C-C motif) ligand 21A (serine)	AK144258|Ccl21a|18829|chemokine (C-C motif) ligand 21A (serine)	NM_001193667|Gm1987|100504362|predicted gene 1987
mm9_v1_chr9_+_20447739_20447785	0.190351	SOX2.p2	AK051149|Ubl5|66177|ubiquitin-like 5	NM_025401|Ubl5|66177|ubiquitin-like 5	AK040449|Ubl5|66177|ubiquitin-like 5
mm9_v1_chr19_+_43686803_43686990	0.189967	SOX2.p2	BC072614|Nkx2-3|18089|NK2 transcription factor related, locus 3 (Drosophila)	NM_008699|Nkx2-3|18089|NK2 transcription factor related, locus 3 (Drosophila)	AK044871|Nkx2-3|18089|NK2 transcription factor related, locus 3 (Drosophila)	AF202036|Nkx2-3|18089|NK2 transcription factor related, locus 3 (Drosophila)	Y11117|Nkx2-3|18089|NK2 transcription factor related, locus 3 (Drosophila)
mm9_v1_chr9_-_24578197_24578288	0.189754	SOX2.p2	AJ277486|Tbx20|57246|T-box 20
mm9_v1_chr12_-_72237590_72237690	0.188925	SOX2.p2	AK012712|Timm9|30056|translocase of inner mitochondrial membrane 9 homolog (yeast)	AK171071|Timm9|30056|translocase of inner mitochondrial membrane 9 homolog (yeast)	AF150101|Timm9|30056|translocase of inner mitochondrial membrane 9 homolog (yeast)	BC028435|Timm9|30056|translocase of inner mitochondrial membrane 9 homolog (yeast)	BC024370|Timm9|30056|translocase of inner mitochondrial membrane 9 homolog (yeast)	AK018764|Timm9|30056|translocase of inner mitochondrial membrane 9 homolog (yeast)	AK165848|Timm9|30056|translocase of inner mitochondrial membrane 9 homolog (yeast)	NM_001024853|Timm9|30056|translocase of inner mitochondrial membrane 9 homolog (yeast)	NM_001024854|Timm9|30056|translocase of inner mitochondrial membrane 9 homolog (yeast)	NM_013896|Timm9|30056|translocase of inner mitochondrial membrane 9 homolog (yeast)	AK172179|Timm9|30056|translocase of inner mitochondrial membrane 9 homolog (yeast)
mm9_v1_chr16_+_43619057_43619100	0.188731	SOX2.p2	AK178854|Zbtb20|56490|zinc finger and BTB domain containing 20	AK013698|Zbtb20|56490|zinc finger and BTB domain containing 20	AK036125|Zbtb20|56490|zinc finger and BTB domain containing 20
mm9_v1_chr10_-_120748007_120748075	0.188701	SOX2.p2	AK173079|Tbc1d30|74694|TBC1 domain family, member 30	AK044521|Tbc1d30|74694|TBC1 domain family, member 30	BC072607|Tbc1d30|74694|TBC1 domain family, member 30	AK049989|Tbc1d30|74694|TBC1 domain family, member 30
mm9_v1_chr13_+_49748707_49748855	0.188582	SOX2.p2	AK147172|Nol8|70930|nucleolar protein 8	NM_001081350|Nol8|70930|nucleolar protein 8	BC125575|Nol8|70930|nucleolar protein 8	BC125579|Nol8|70930|nucleolar protein 8	AK029961|Nol8|70930|nucleolar protein 8	BC049166|Nol8|70930|nucleolar protein 8
mm9_v1_chr11_-_86621130_86621161	0.18849	SOX2.p2	AK029935|Dhx40|67487|DEAH (Asp-Glu-Ala-His) box polypeptide 40	AK010512|Dhx40|67487|DEAH (Asp-Glu-Ala-His) box polypeptide 40	NM_026191|Dhx40|67487|DEAH (Asp-Glu-Ala-His) box polypeptide 40
mm9_v1_chr6_+_113573980_113574047	0.188367	SOX2.p2	AK159238|Vhl|22346|von Hippel-Lindau tumor suppressor	U12570|Vhl|22346|von Hippel-Lindau tumor suppressor	AK171604|Vhl|22346|von Hippel-Lindau tumor suppressor	AK171264|Vhl|22346|von Hippel-Lindau tumor suppressor	NM_009507|Vhl|22346|von Hippel-Lindau tumor suppressor	S76748|Vhl|22346|von Hippel-Lindau tumor suppressor	BC052417|Vhl|22346|von Hippel-Lindau tumor suppressor	AK161408|Vhl|22346|von Hippel-Lindau tumor suppressor
mm9_v1_chr11_+_79391766_79391883	0.188121	SOX2.p2	AK053047|Nf1|18015|neurofibromatosis 1
mm9_v1_chr2_-_121781725_121781827	0.18798	SOX2.p2	BC141002|Mageb3|17147|melanoma antigen, family B, 3	AK019658|Mageb3|17147|melanoma antigen, family B, 3	NM_008545|Mageb3|17147|melanoma antigen, family B, 3
mm9_v1_chr16_-_36562219_36562219	0.18757	SOX2.p2	AF110178|Casr|12374|calcium-sensing receptor	AF110179|Casr|12374|calcium-sensing receptor	NM_013803|Casr|12374|calcium-sensing receptor
mm9_v1_chr12_-_70458152_70458166	0.187419	SOX2.p2	AK017826|Nemf|66244|nuclear export mediator factor	NM_025441|Nemf|66244|nuclear export mediator factor
mm9_v1_chr17_+_26852581_26852657	0.187023	SOX2.p2	AK030092|A930001N09Rik|77128|RIKEN cDNA A930001N09 gene	NM_029870|A930001N09Rik|77128|RIKEN cDNA A930001N09 gene	AK044760|A930001N09Rik|77128|RIKEN cDNA A930001N09 gene	AK020796|A930001N09Rik|77128|RIKEN cDNA A930001N09 gene	AK132423|A930001N09Rik|77128|RIKEN cDNA A930001N09 gene	AK132454|A930001N09Rik|77128|RIKEN cDNA A930001N09 gene
mm9_v1_chr13_-_33997576_33997576	0.186714	SOX2.p2	BC062169|Serpinb6c|97848|serine (or cysteine) peptidase inhibitor, clade B, member 6c	NM_148942|Serpinb6c|97848|serine (or cysteine) peptidase inhibitor, clade B, member 6c
mm9_v1_chr18_-_21458623_21458645	0.186415	SOX2.p2	AK220564|Fam59a|381126|family with sequence similarity 59, member A	AK148318|Fam59a|381126|family with sequence similarity 59, member A	NM_001033445|Fam59a|381126|family with sequence similarity 59, member A
mm9_v1_chr18_+_34784589_34784686	0.186242	SOX2.p2	NM_009004|Kif20a|19348|kinesin family member 20A	AK083412|Kif20a|19348|kinesin family member 20A	AK051995|Kif20a|19348|kinesin family member 20A	AK084732|Kif20a|19348|kinesin family member 20A	AK142764|Kif20a|19348|kinesin family member 20A	AK083697|Kif20a|19348|kinesin family member 20A	AK051201|Kif20a|19348|kinesin family member 20A	AK053280|Kif20a|19348|kinesin family member 20A	AK144844|Kif20a|19348|kinesin family member 20A	BC060608|Kif20a|19348|kinesin family member 20A	NM_001166406|Kif20a|19348|kinesin family member 20A
mm9_v1_chr5_+_115777413_115777475	0.186232	SOX2.p2	AK020084|Srsf9|108014|serine/arginine-rich splicing factor 9
mm9_v1_chr16_-_96303958_96304070	0.185564	SOX2.p2	BC095940|Brwd1|93871|bromodomain and WD repeat domain containing 1	BC145265|Brwd1|93871|bromodomain and WD repeat domain containing 1	AJ292467|Brwd1|93871|bromodomain and WD repeat domain containing 1	AJ292468|Brwd1|93871|bromodomain and WD repeat domain containing 1	AK030493|Brwd1|93871|bromodomain and WD repeat domain containing 1	NM_001103179|Brwd1|93871|bromodomain and WD repeat domain containing 1	NM_145125|Brwd1|93871|bromodomain and WD repeat domain containing 1	NM_176928|Brwd1|93871|bromodomain and WD repeat domain containing 1	AK051870|Brwd1|93871|bromodomain and WD repeat domain containing 1
mm9_v1_chr8_-_113551591_113551618	0.185257	SOX2.p2	BC025594|Ddx19b|234733|DEAD (Asp-Glu-Ala-Asp) box polypeptide 19b
mm9_v1_chr8_+_35217674_35217675	0.185137	SOX2.p2	BC013497|Tmem66|67887|transmembrane protein 66
mm9_v1_chr11_+_95122842_95123008	0.184862	SOX2.p2	AF235035|Tac4|93670|tachykinin 4	NM_053093|Tac4|93670|tachykinin 4	BC119426|Tac4|93670|tachykinin 4	AF515827|Tac4|93670|tachykinin 4
mm9_v1_chr2_+_131763454_131763725	0.184757	SOX2.p2	AK215651|Prnp|19122|prion protein	AK205534|Prnp|19122|prion protein	AK213884|Prnp|19122|prion protein	AK206219|Prnp|19122|prion protein
mm9_v1_chr14_+_27081743_27081743	0.184606	SOX2.p2	BC055782|Duxbl|278672|double homeobox B-like	NM_001177538|Gm10394|100039227|predicted gene 10394	NM_001177539|Gm10391|100039293|predicted gene 10391	NM_183389|Duxbl|278672|double homeobox B-like
mm9_v1_chr13_+_27334298_27334313	0.183986	SOX2.p2	AK005542|Prl3b1|18776|prolactin family 3, subfamily b, member 1	AK005543|Prl3b1|18776|prolactin family 3, subfamily b, member 1	AK131667|Prl3b1|18776|prolactin family 3, subfamily b, member 1	M14647|Prl3b1|18776|prolactin family 3, subfamily b, member 1	NM_008865|Prl3b1|18776|prolactin family 3, subfamily b, member 1	AK167483|Prl3b1|18776|prolactin family 3, subfamily b, member 1	BC099386|Prl3b1|18776|prolactin family 3, subfamily b, member 1
mm9_v1_chr7_+_25655075_25655144	0.183736	SOX2.p2	BC100434|Dmrtc2|71241|doublesex and mab-3 related transcription factor like family C2	NM_027732|Dmrtc2|71241|doublesex and mab-3 related transcription factor like family C2	AF542046|Dmrtc2|71241|doublesex and mab-3 related transcription factor like family C2	AK017020|Dmrtc2|71241|doublesex and mab-3 related transcription factor like family C2	BC138203|Dmrtc2|71241|doublesex and mab-3 related transcription factor like family C2	BC145988|Dmrtc2|71241|doublesex and mab-3 related transcription factor like family C2
mm9_v1_chr3_+_51299153_51299205	0.183512	SOX2.p2	
mm9_v1_chr12_+_83717883_83718024	0.182838	SOX2.p2	AK139323|Rgs6|50779|regulator of G-protein signaling 6	AK052527|Rgs6|50779|regulator of G-protein signaling 6	NM_015812|Rgs6|50779|regulator of G-protein signaling 6
mm9_v1_chr18_+_33098914_33099011	0.182396	SOX2.p2	AK043114|Camk4|12326|calcium/calmodulin-dependent protein kinase IV	X58995|Camk4|12326|calcium/calmodulin-dependent protein kinase IV
mm9_v1_chr9_-_64062342_64062398	0.181846	SOX2.p2	AK165664|Map2k1|26395|mitogen-activated protein kinase kinase 1
mm9_v1_chr14_-_58353136_58353256	0.181818	SOX2.p2	AY015061|Lats2|50523|large tumor suppressor 2	AY015062|Lats2|50523|large tumor suppressor 2	AB023958|Lats2|50523|large tumor suppressor 2	BC040025|Lats2|50523|large tumor suppressor 2	NM_153382|Lats2|50523|large tumor suppressor 2
mm9_v1_chr7_+_63049505_63049618	0.18156	SOX2.p2	NM_146190|Tubgcp5|233276|tubulin, gamma complex associated protein 5	AK051326|Tubgcp5|233276|tubulin, gamma complex associated protein 5	AK044887|Tubgcp5|233276|tubulin, gamma complex associated protein 5	AK160939|Tubgcp5|233276|tubulin, gamma complex associated protein 5	AK032031|Tubgcp5|233276|tubulin, gamma complex associated protein 5	AK086158|Tubgcp5|233276|tubulin, gamma complex associated protein 5	AK152033|Tubgcp5|233276|tubulin, gamma complex associated protein 5	AK153331|Tubgcp5|233276|tubulin, gamma complex associated protein 5	AK161681|Tubgcp5|233276|tubulin, gamma complex associated protein 5	AK151454|Tubgcp5|233276|tubulin, gamma complex associated protein 5	AK153357|Tubgcp5|233276|tubulin, gamma complex associated protein 5	AK044444|Tubgcp5|233276|tubulin, gamma complex associated protein 5
mm9_v1_chr18_+_7869414_7869561	0.180833	SOX2.p2	AF320996|Wac|225131|WW domain containing adaptor with coiled-coil	AK173274|Wac|225131|WW domain containing adaptor with coiled-coil	BC057178|Wac|225131|WW domain containing adaptor with coiled-coil
mm9_v1_chr3_+_94938009_94938098	0.18058	SOX2.p2	AK154180|Lysmd1|217779|LysM, putative peptidoglycan-binding, domain containing 1	NM_153121|Lysmd1|217779|LysM, putative peptidoglycan-binding, domain containing 1	BC024838|Lysmd1|217779|LysM, putative peptidoglycan-binding, domain containing 1	AK054348|Lysmd1|217779|LysM, putative peptidoglycan-binding, domain containing 1	AK011517|Lysmd1|217779|LysM, putative peptidoglycan-binding, domain containing 1
mm9_v1_chr12_-_46175433_46175475	0.179246	SOX2.p2	NM_144552|Stxbp6|217517|syntaxin binding protein 6 (amisyn)
mm9_v1_chr14_-_52640348_52640407	0.179234	SOX2.p2	BC096486|Zfp219|69890|zinc finger protein 219	AB063578|Zfp219|69890|zinc finger protein 219	NM_027248|Zfp219|69890|zinc finger protein 219
mm9_v1_chr4_+_24900565_24900565	0.178736	SOX2.p2	AK036257|Gpr63|81006|G protein-coupled receptor 63	NM_030733|Gpr63|81006|G protein-coupled receptor 63
mm9_v1_chr19_+_27397077_27397240	0.178579	SOX2.p2	BC046490|Kcnv2|240595|potassium channel, subfamily V, member 2	BC039042|Kcnv2|240595|potassium channel, subfamily V, member 2	NM_183179|Kcnv2|240595|potassium channel, subfamily V, member 2	AY238939|Kcnv2|240595|potassium channel, subfamily V, member 2
mm9_v1_chr4_-_129167980_129168013	0.178412	SOX2.p2	AF201734|Tssk3|58864|testis-specific serine kinase 3	AF298901|Tssk3|58864|testis-specific serine kinase 3	AK005983|Tssk3|58864|testis-specific serine kinase 3	BC048470|Tssk3|58864|testis-specific serine kinase 3	AK019840|Tssk3|58864|testis-specific serine kinase 3	NM_080442|Tssk3|58864|testis-specific serine kinase 3
mm9_v1_chr12_+_120085663_120085788	0.176786	SOX2.p2	BC082582|Sp8|320145|trans-acting transcription factor 8
mm9_v1_chr8_-_108467275_108467292	0.17646	SOX2.p2	AK004914|Lcat|16816|lecithin cholesterol acyltransferase	J05154|Lcat|16816|lecithin cholesterol acyltransferase	BC028861|Lcat|16816|lecithin cholesterol acyltransferase
mm9_v1_chr17_-_46462714_46462714	0.176235	SOX2.p2	AF406642|Abcc10|224814|ATP-binding cassette, sub-family C (CFTR/MRP), member 10	NM_145140|Abcc10|224814|ATP-binding cassette, sub-family C (CFTR/MRP), member 10
mm9_v1_chr13_-_61356684_61356712	0.176147	SOX2.p2	BC068241|Cts8|56094|cathepsin 8	AY014780|Cts8|56094|cathepsin 8	AK049474|Cts8|56094|cathepsin 8	NM_019541|Cts8|56094|cathepsin 8	AF250840|Cts8|56094|cathepsin 8
mm9_v1_chr11_+_87912709_87912809	0.175686	SOX2.p2	BC025434|Cuedc1|103841|CUE domain containing 1	BC024476|Cuedc1|103841|CUE domain containing 1
mm9_v1_chr17_+_70911084_70911126	0.175642	SOX2.p2	NM_001128181|Dlgap1|224997|discs, large (Drosophila) homolog-associated protein 1	AK136926|Dlgap1|224997|discs, large (Drosophila) homolog-associated protein 1
mm9_v1_chr1_+_129999868_129999934	0.174656	SOX2.p2	AK144098|R3hdm1|226412|R3H domain 1 (binds single-stranded nucleic acids)	NM_181750|R3hdm1|226412|R3H domain 1 (binds single-stranded nucleic acids)	AK141150|R3hdm1|226412|R3H domain 1 (binds single-stranded nucleic acids)	BC049181|R3hdm1|226412|R3H domain 1 (binds single-stranded nucleic acids)	AK051765|R3hdm1|226412|R3H domain 1 (binds single-stranded nucleic acids)
mm9_v1_chr3_+_96474053_96474053	0.174608	SOX2.p2	NM_001081139|Ankrd35|213121|ankyrin repeat domain 35
mm9_v1_chr16_-_19884312_19884367	0.174324	SOX2.p2	BC053981|A930003A15Rik|68162|RIKEN cDNA A930003A15 gene	AK153879|A930003A15Rik|68162|RIKEN cDNA A930003A15 gene	AK086168|A930003A15Rik|68162|RIKEN cDNA A930003A15 gene
mm9_v1_chr5_-_147032932_147033023	0.174001	SOX2.p2	AY039004|Rnf6|74132|ring finger protein (C3H2C3 type) 6	AK049503|Rnf6|74132|ring finger protein (C3H2C3 type) 6	BC138545|Rnf6|74132|ring finger protein (C3H2C3 type) 6	AK004745|Rnf6|74132|ring finger protein (C3H2C3 type) 6	NM_028774|Rnf6|74132|ring finger protein (C3H2C3 type) 6
mm9_v1_chr3_+_87600872_87601015	0.173981	SOX2.p2	AK142578|Insrr|23920|insulin receptor-related receptor	NM_011832|Insrr|23920|insulin receptor-related receptor	AK081512|Insrr|23920|insulin receptor-related receptor	AB007135|Insrr|23920|insulin receptor-related receptor	BC137855|Insrr|23920|insulin receptor-related receptor
mm9_v1_chr13_+_55736365_55736414	0.173778	SOX2.p2	AK008639|Ddx46|212880|DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	AK137835|Ddx46|212880|DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	BC019403|Ddx46|212880|DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	NM_145975|Ddx46|212880|DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	AK088950|Ddx46|212880|DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	BC092240|Ddx46|212880|DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	BC028552|Ddx46|212880|DEAD (Asp-Glu-Ala-Asp) box polypeptide 46
mm9_v1_chr9_+_44143931_44144022	0.173533	SOX2.p2	
mm9_v1_chr8_-_127275549_127275749	0.173417	SOX2.p2	BC023460|Fam89a|69627|family with sequence similarity 89, member A	BC115734|Fam89a|69627|family with sequence similarity 89, member A	BC115819|Fam89a|69627|family with sequence similarity 89, member A	NM_001081120|Fam89a|69627|family with sequence similarity 89, member A
mm9_v1_chr17_+_25024425_25024425	0.173133	SOX2.p2	AF403038|Spsb3|79043|splA/ryanodine receptor domain and SOCS box containing 3	AK009325|Spsb3|79043|splA/ryanodine receptor domain and SOCS box containing 3	NM_027141|Spsb3|79043|splA/ryanodine receptor domain and SOCS box containing 3
mm9_v1_chr16_-_88885333_88885333	0.173128	SOX2.p2	AF345294|Krtap16-4|170654|keratin associated protein 16-4	BC116200|Krtap16-4|170654|keratin associated protein 16-4	BC116201|Krtap16-4|170654|keratin associated protein 16-4	NM_130873|Krtap16-4|170654|keratin associated protein 16-4
mm9_v1_chr8_+_22969372_22969372	0.17284	SOX2.p2	AJ437645|Defb10|246085|defensin beta 10	NM_139225|Defb10|246085|defensin beta 10
mm9_v1_chr9_-_76171352_76171416	0.172836	SOX2.p2	AY336084|Hcrtr2|387285|hypocretin (orexin) receptor 2	AY336085|Hcrtr2|387285|hypocretin (orexin) receptor 2	BC140957|Hcrtr2|387285|hypocretin (orexin) receptor 2	AK038551|Hcrtr2|387285|hypocretin (orexin) receptor 2	AK048781|Hcrtr2|387285|hypocretin (orexin) receptor 2	NM_198962|Hcrtr2|387285|hypocretin (orexin) receptor 2	AK079572|Hcrtr2|387285|hypocretin (orexin) receptor 2
mm9_v1_chr2_-_71384748_71384810	0.172041	SOX2.p2	M80540|Dlx2|13392|distal-less homeobox 2	AK144652|Dlx2|13392|distal-less homeobox 2	NM_010054|Dlx2|13392|distal-less homeobox 2
mm9_v1_chr8_-_123181945_123181993	0.171361	SOX2.p2	AK185099|Cox4nb|18117|COX4 neighbor
mm9_v1_chr6_-_87300891_87300908	0.171288	SOX2.p2	BC099446|Gkn1|66283|gastrokine 1	BC132540|Gkn1|66283|gastrokine 1	BC132542|Gkn1|66283|gastrokine 1	AK008640|Gkn1|66283|gastrokine 1	AK008647|Gkn1|66283|gastrokine 1	AK008722|Gkn1|66283|gastrokine 1	AK008956|Gkn1|66283|gastrokine 1	AK009145|Gkn1|66283|gastrokine 1	AK028136|Gkn1|66283|gastrokine 1	AK008622|Gkn1|66283|gastrokine 1	AK008641|Gkn1|66283|gastrokine 1	AK008745|Gkn1|66283|gastrokine 1	AK008933|Gkn1|66283|gastrokine 1	AK008990|Gkn1|66283|gastrokine 1	AK019050|Gkn1|66283|gastrokine 1	AY456960|Gkn1|66283|gastrokine 1	NM_025466|Gkn1|66283|gastrokine 1
mm9_v1_chr19_-_47993687_47993788	0.170322	SOX2.p2	AK171522|Itprip|414801|inositol 1,4,5-triphosphate receptor interacting protein	AK171539|Itprip|414801|inositol 1,4,5-triphosphate receptor interacting protein	AK014762|Itprip|414801|inositol 1,4,5-triphosphate receptor interacting protein	AK220222|Itprip|414801|inositol 1,4,5-triphosphate receptor interacting protein	AK165192|Itprip|414801|inositol 1,4,5-triphosphate receptor interacting protein	AK171911|Itprip|414801|inositol 1,4,5-triphosphate receptor interacting protein	BC063749|Itprip|414801|inositol 1,4,5-triphosphate receptor interacting protein	AK014581|Wdr96|70806|WD repeat domain 96	AK160686|Itprip|414801|inositol 1,4,5-triphosphate receptor interacting protein	NM_001001738|Itprip|414801|inositol 1,4,5-triphosphate receptor interacting protein
mm9_v1_chr18_+_30432499_30432592	0.169678	SOX2.p2	AK030578|Pik3c3|225326|phosphoinositide-3-kinase, class 3	BC024675|Pik3c3|225326|phosphoinositide-3-kinase, class 3	NM_181414|Pik3c3|225326|phosphoinositide-3-kinase, class 3	AK044997|Pik3c3|225326|phosphoinositide-3-kinase, class 3	BC057678|Pik3c3|225326|phosphoinositide-3-kinase, class 3	BC027029|Pik3c3|225326|phosphoinositide-3-kinase, class 3
mm9_v1_chr19_+_5041341_5041422	0.16884	SOX2.p2	AF233580|Brms1|107392|breast cancer metastasis-suppressor 1	AK076729|Brms1|107392|breast cancer metastasis-suppressor 1	BC016108|Brms1|107392|breast cancer metastasis-suppressor 1	NM_134155|Brms1|107392|breast cancer metastasis-suppressor 1	BC003485|Brms1|107392|breast cancer metastasis-suppressor 1
mm9_v1_chr11_-_90252228_90252237	0.168815	SOX2.p2	NM_172563|Hlf|217082|hepatic leukemia factor
mm9_v1_chrX_-_70905384_70905478	0.167581	SOX2.p2	BC055891|Pnck|93843|pregnancy upregulated non-ubiquitously expressed CaM kinase	BC051996|Pnck|93843|pregnancy upregulated non-ubiquitously expressed CaM kinase	AK158755|Pnck|93843|pregnancy upregulated non-ubiquitously expressed CaM kinase
mm9_v1_chr7_+_25184715_25184739	0.16755	SOX2.p2	AK169651|1500002O20Rik|71997|RIKEN cDNA 1500002O20 gene	BC034211|1500002O20Rik|71997|RIKEN cDNA 1500002O20 gene
mm9_v1_chr3_-_68930786_68930811	0.167304	SOX2.p2	BC026821|Kpna4|16649|karyopherin (importin) alpha 4
mm9_v1_chr4_-_83132289_83132381	0.166693	SOX2.p2	BC043079|Psip1|101739|PC4 and SFRS1 interacting protein 1	NM_133948|Psip1|101739|PC4 and SFRS1 interacting protein 1	BC002104|Psip1|101739|PC4 and SFRS1 interacting protein 1	AK161426|Psip1|101739|PC4 and SFRS1 interacting protein 1	AK011572|Psip1|101739|PC4 and SFRS1 interacting protein 1	BC052177|Psip1|101739|PC4 and SFRS1 interacting protein 1
mm9_v1_chr13_-_69672440_69672453	0.166581	SOX2.p2	AK152550|Papd7|210106|PAP associated domain containing 7
mm9_v1_chr18_-_20904585_20904945	0.165522	SOX2.p2	AK144997|B4galt6|56386|UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	AK138247|B4galt6|56386|UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	AK163956|B4galt6|56386|UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	AK164262|B4galt6|56386|UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	AK164724|B4galt6|56386|UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	AK137385|B4galt6|56386|UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	AK138610|B4galt6|56386|UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	AF097158|B4galt6|56386|UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	NM_019737|B4galt6|56386|UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6
mm9_v1_chr16_+_20548675_20548742	0.165489	SOX2.p2	NM_013852|Abcf3|27406|ATP-binding cassette, sub-family F (GCN20), member 3	AK030626|Abcf3|27406|ATP-binding cassette, sub-family F (GCN20), member 3	BC032923|Abcf3|27406|ATP-binding cassette, sub-family F (GCN20), member 3
mm9_v1_chr15_-_81560257_81560281	0.165463	SOX2.p2	BC052862|Rangap1|19387|RAN GTPase activating protein 1	AK088768|Rangap1|19387|RAN GTPase activating protein 1	AK145459|Rangap1|19387|RAN GTPase activating protein 1	AK129452|Rangap1|19387|RAN GTPase activating protein 1
mm9_v1_chr2_+_90780646_90780662	0.165452	SOX2.p2	AK143698|Celf1|13046|CUGBP, Elav-like family member 1
mm9_v1_chr10_+_50312445_50312544	0.164508	SOX2.p2	AK144867|Ascc3|77987|activating signal cointegrator 1 complex subunit 3	NM_001146089|Ascc3|77987|activating signal cointegrator 1 complex subunit 3	NM_198007|Ascc3|77987|activating signal cointegrator 1 complex subunit 3	AK052745|Ascc3|77987|activating signal cointegrator 1 complex subunit 3
mm9_v1_chr4_-_40650194_40650231	0.164443	SOX2.p2	AK017522|Aptx|66408|aprataxin	AK088928|Aptx|66408|aprataxin	BC071213|Aptx|66408|aprataxin	AK010516|Aptx|66408|aprataxin	BC021872|Aptx|66408|aprataxin	NM_001025444|Aptx|66408|aprataxin
mm9_v1_chr10_-_8238569_8238650	0.164165	SOX2.p2	AK086181|Ust|338362|uronyl-2-sulfotransferase	AK147850|Ust|338362|uronyl-2-sulfotransferase	NM_177387|Ust|338362|uronyl-2-sulfotransferase
mm9_v1_chr9_+_53213390_53213402	0.164042	SOX2.p2	AK016083|4930550C14Rik|75311|RIKEN cDNA 4930550C14 gene	NM_029247|4930550C14Rik|75311|RIKEN cDNA 4930550C14 gene	BC115638|4930550C14Rik|75311|RIKEN cDNA 4930550C14 gene	BC115639|4930550C14Rik|75311|RIKEN cDNA 4930550C14 gene
mm9_v1_chr12_+_70397667_70397700	0.164009	SOX2.p2	AK078408|Klhdc2|69554|kelch domain containing 2	NM_027117|Klhdc2|69554|kelch domain containing 2
mm9_v1_chr19_-_45857958_45858012	0.162876	SOX2.p2	AK129188|Mgea5|76055|meningioma expressed antigen 5 (hyaluronidase)
mm9_v1_chr2_+_113839219_113839495	0.162834	SOX2.p2	AK082668|A530058N18Rik|320846|RIKEN cDNA A530058N18 gene	AK045761|A530058N18Rik|320846|RIKEN cDNA A530058N18 gene	AK043120|A530058N18Rik|320846|RIKEN cDNA A530058N18 gene	AK044743|A530058N18Rik|320846|RIKEN cDNA A530058N18 gene	AK046235|A530058N18Rik|320846|RIKEN cDNA A530058N18 gene	AK045885|A530058N18Rik|320846|RIKEN cDNA A530058N18 gene
mm9_v1_chr9_-_79825502_79825688	0.162497	SOX2.p2	AK017709|Filip1|70598|filamin A interacting protein 1	BC125581|Filip1|70598|filamin A interacting protein 1	BC131965|Filip1|70598|filamin A interacting protein 1	NM_001081243|Filip1|70598|filamin A interacting protein 1
mm9_v1_chr6_-_55631039_55631067	0.161448	SOX2.p2	AK144303|Neurod6|11922|neurogenic differentiation 6	BC087831|Neurod6|11922|neurogenic differentiation 6	U29086|Neurod6|11922|neurogenic differentiation 6
mm9_v1_chr16_-_94008999_94009081	0.161301	SOX2.p2	BC132183|Cldn14|56173|claudin 14	BC138497|Cldn14|56173|claudin 14	AF314089|Cldn14|56173|claudin 14	NM_019500|Cldn14|56173|claudin 14
mm9_v1_chr2_+_121782185_121782265	0.16124	SOX2.p2	AK033382|Ctdspl2|329506|CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2	NM_212450|Ctdspl2|329506|CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2	AK169248|Ctdspl2|329506|CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2	AK044805|Ctdspl2|329506|CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2	AK053513|Ctdspl2|329506|CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2	BC066219|Ctdspl2|329506|CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2	AK030085|Ctdspl2|329506|CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2	AK041422|Ctdspl2|329506|CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2	AK049463|Ctdspl2|329506|CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2	AK160431|Ctdspl2|329506|CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2	BC052660|Ctdspl2|329506|CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2
mm9_v1_chr8_-_37312569_37312569	0.161064	SOX2.p2	NM_001081150|Lonrf1|244421|LON peptidase N-terminal domain and ring finger 1
mm9_v1_chr2_+_181599126_181599193	0.160449	SOX2.p2	AK010875|Polr3k|67005|polymerase (RNA) III (DNA directed) polypeptide K	AK021353|Polr3k|67005|polymerase (RNA) III (DNA directed) polypeptide K	AK031110|Polr3k|67005|polymerase (RNA) III (DNA directed) polypeptide K	AK005152|Polr3k|67005|polymerase (RNA) III (DNA directed) polypeptide K	AK088206|Polr3k|67005|polymerase (RNA) III (DNA directed) polypeptide K	AK008637|Polr3k|67005|polymerase (RNA) III (DNA directed) polypeptide K
mm9_v1_chr18_+_25224729_25224737	0.160071	SOX2.p2	BC060607|Fhod3|225288|formin homology 2 domain containing 3
mm9_v1_chr19_+_10257363_10257524	0.160049	SOX2.p2	NM_146094|Fads1|76267|fatty acid desaturase 1	BC026831|Fads1|76267|fatty acid desaturase 1	AK154367|Fads1|76267|fatty acid desaturase 1	BC022139|Fads1|76267|fatty acid desaturase 1	BC026848|Fads1|76267|fatty acid desaturase 1	AB072976|Fads1|76267|fatty acid desaturase 1	AK080706|Fads1|76267|fatty acid desaturase 1	AF061504|Fads1|76267|fatty acid desaturase 1	AK083959|Fads1|76267|fatty acid desaturase 1	BC063053|Fads1|76267|fatty acid desaturase 1
mm9_v1_chr19_-_7280741_7280794	0.159489	SOX2.p2	BC054410|Otub1|107260|OTU domain, ubiquitin aldehyde binding 1	AK027996|Otub1|107260|OTU domain, ubiquitin aldehyde binding 1	AK087195|Otub1|107260|OTU domain, ubiquitin aldehyde binding 1	AK140070|Otub1|107260|OTU domain, ubiquitin aldehyde binding 1	AK145273|Otub1|107260|OTU domain, ubiquitin aldehyde binding 1	AK145970|Otub1|107260|OTU domain, ubiquitin aldehyde binding 1	BC022575|Otub1|107260|OTU domain, ubiquitin aldehyde binding 1	NM_134150|Otub1|107260|OTU domain, ubiquitin aldehyde binding 1
mm9_v1_chr18_-_37803782_37803859	0.158344	SOX2.p2	BC029673|Taf7|24074|TAF7 RNA polymerase II, TATA box binding protein (TBP)-associated factor	AF144562|Taf7|24074|TAF7 RNA polymerase II, TATA box binding protein (TBP)-associated factor	AK075700|Taf7|24074|TAF7 RNA polymerase II, TATA box binding protein (TBP)-associated factor	AK029380|Taf7|24074|TAF7 RNA polymerase II, TATA box binding protein (TBP)-associated factor	AK076362|Taf7|24074|TAF7 RNA polymerase II, TATA box binding protein (TBP)-associated factor	AK089054|Taf7|24074|TAF7 RNA polymerase II, TATA box binding protein (TBP)-associated factor	NM_175770|Taf7|24074|TAF7 RNA polymerase II, TATA box binding protein (TBP)-associated factor
mm9_v1_chr6_-_24477665_24477717	0.158127	SOX2.p2	AK019324|Ndufa5|68202|NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5	AK019301|Ndufa5|68202|NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5	NM_026614|Ndufa5|68202|NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5
mm9_v1_chr11_-_68825972_68825998	0.158093	SOX2.p2	
mm9_v1_chr19_+_10969734_10969805	0.157483	SOX2.p2	AK088769|Prpf19|28000|PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae)	AF251503|Prpf19|28000|PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae)	BC004070|Prpf19|28000|PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae)	NM_134129|Prpf19|28000|PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae)
mm9_v1_chr3_-_94910641_94910756	0.157393	SOX2.p2	D86177|Pip5k1a|18720|phosphatidylinositol-4-phosphate 5-kinase, type 1 alpha	AK167816|Pip5k1a|18720|phosphatidylinositol-4-phosphate 5-kinase, type 1 alpha
mm9_v1_chr1_-_52874501_52874576	0.157095	SOX2.p2	NM_008384|Inpp1|16329|inositol polyphosphate-1-phosphatase
mm9_v1_chr10_-_62041134_62041209	0.156018	SOX2.p2	AK149629|2510003E04Rik|72320|RIKEN cDNA 2510003E04 gene	AK003009|2510003E04Rik|72320|RIKEN cDNA 2510003E04 gene	AK158730|2510003E04Rik|72320|RIKEN cDNA 2510003E04 gene	BC055307|2510003E04Rik|72320|RIKEN cDNA 2510003E04 gene	BC090974|2510003E04Rik|72320|RIKEN cDNA 2510003E04 gene	BC046485|2510003E04Rik|72320|RIKEN cDNA 2510003E04 gene	AK161007|2510003E04Rik|72320|RIKEN cDNA 2510003E04 gene	AK129320|2510003E04Rik|72320|RIKEN cDNA 2510003E04 gene	AK035659|2510003E04Rik|72320|RIKEN cDNA 2510003E04 gene	AK141324|2510003E04Rik|72320|RIKEN cDNA 2510003E04 gene	NM_028197|2510003E04Rik|72320|RIKEN cDNA 2510003E04 gene
mm9_v1_chr3_-_137806320_137806370	0.15526	SOX2.p2	AK171129|C230076A16Rik|320496|RIKEN cDNA C230076A16 gene	AK039300|C230076A16Rik|320496|RIKEN cDNA C230076A16 gene	AK136278|Mttp|17777|microsomal triglyceride transfer protein	NM_001163457|Mttp|17777|microsomal triglyceride transfer protein
mm9_v1_chr17_-_46817717_46817797	0.155141	SOX2.p2	AJ278127|Klhdc3|71765|kelch domain containing 3	AK170623|Klhdc3|71765|kelch domain containing 3	AB053465|Klhdc3|71765|kelch domain containing 3	AK079082|Klhdc3|71765|kelch domain containing 3
mm9_v1_chr8_-_114516147_114516201	0.155103	SOX2.p2	BC019976|Adat1|30947|adenosine deaminase, tRNA-specific 1	AK039699|Adat1|30947|adenosine deaminase, tRNA-specific 1	AK161044|Adat1|30947|adenosine deaminase, tRNA-specific 1	AK035614|Adat1|30947|adenosine deaminase, tRNA-specific 1	AK082399|Adat1|30947|adenosine deaminase, tRNA-specific 1	NM_013925|Adat1|30947|adenosine deaminase, tRNA-specific 1
mm9_v1_chr4_+_147374850_147374855	0.154812	SOX2.p2	AK147180|Nppa|230899|natriuretic peptide type A	BC089615|Nppa|230899|natriuretic peptide type A	NM_008725|Nppa|230899|natriuretic peptide type A
mm9_v1_chr13_-_34222209_34222227	0.15434	SOX2.p2	BC138935|Tubb2b|73710|tubulin, beta 2B	BC138936|Tubb2b|73710|tubulin, beta 2B	AK168908|Tubb2b|73710|tubulin, beta 2B	AK010786|Tubb2b|73710|tubulin, beta 2B	NM_023716|Tubb2b|73710|tubulin, beta 2B
mm9_v1_chr3_+_45182311_45182350	0.153931	SOX2.p2	BC037259|Pcdh10|18526|protocadherin 10	NM_001098170|Pcdh10|18526|protocadherin 10	NM_001098171|Pcdh10|18526|protocadherin 10	NM_001098172|Pcdh10|18526|protocadherin 10	NM_011043|Pcdh10|18526|protocadherin 10	AK081621|Pcdh10|18526|protocadherin 10	AK081977|Pcdh10|18526|protocadherin 10	BC026712|Pcdh10|18526|protocadherin 10	AK122503|Pcdh10|18526|protocadherin 10
mm9_v1_chr17_-_56702631_56702768	0.153753	SOX2.p2	AK214865|Safb2|224902|scaffold attachment factor B2
mm9_v1_chr9_+_108295164_108295164	0.153432	SOX2.p2	AK007115|1700102P08Rik|112418|RIKEN cDNA 1700102P08 gene	BC061048|1700102P08Rik|112418|RIKEN cDNA 1700102P08 gene	NM_053216|1700102P08Rik|112418|RIKEN cDNA 1700102P08 gene
mm9_v1_chr1_+_157005804_157006022	0.152124	SOX2.p2	NM_021433|Stx6|58244|syntaxin 6	AK018167|Stx6|58244|syntaxin 6	AK031673|Stx6|58244|syntaxin 6	AK159392|Stx6|58244|syntaxin 6	AK019106|Stx6|58244|syntaxin 6	AK044905|Stx6|58244|syntaxin 6	AK049124|Stx6|58244|syntaxin 6	AK009690|Stx6|58244|syntaxin 6	AK151549|Stx6|58244|syntaxin 6	BC029205|Stx6|58244|syntaxin 6	AF237814|Stx6|58244|syntaxin 6
mm9_v1_chr4_+_135728188_135728308	0.150171	SOX2.p2	AK087452|E2f2|242705|E2F transcription factor 2	NM_177733|E2f2|242705|E2F transcription factor 2
mm9_v1_chr11_-_90252208_90252214	0.150108	SOX2.p2	BC058705|Hlf|217082|hepatic leukemia factor
mm9_v1_chr19_-_5295389_5295474	0.149954	SOX2.p2	BC029745|Sf3b2|319322|splicing factor 3b, subunit 2	AK151354|Sf3b2|319322|splicing factor 3b, subunit 2	AK019282|Sf3b2|319322|splicing factor 3b, subunit 2	AK152965|Sf3b2|319322|splicing factor 3b, subunit 2	AK012009|Sf3b2|319322|splicing factor 3b, subunit 2	AK150961|Sf3b2|319322|splicing factor 3b, subunit 2	AK159893|Sf3b2|319322|splicing factor 3b, subunit 2	AK011613|Sf3b2|319322|splicing factor 3b, subunit 2	BC045207|Sf3b2|319322|splicing factor 3b, subunit 2	AK146540|Sf3b2|319322|splicing factor 3b, subunit 2	AK152327|Sf3b2|319322|splicing factor 3b, subunit 2	AK146864|Sf3b2|319322|splicing factor 3b, subunit 2	AK147687|Sf3b2|319322|splicing factor 3b, subunit 2	AK149776|Sf3b2|319322|splicing factor 3b, subunit 2	AK012643|Sf3b2|319322|splicing factor 3b, subunit 2	AK142136|Sf3b2|319322|splicing factor 3b, subunit 2	AK146063|Sf3b2|319322|splicing factor 3b, subunit 2	BC049118|Sf3b2|319322|splicing factor 3b, subunit 2	NM_030109|Sf3b2|319322|splicing factor 3b, subunit 2
mm9_v1_chr5_+_120881778_120882006	0.149807	SOX2.p2	U61155|Lhx5|16873|LIM homeobox protein 5	AK140208|Lhx5|16873|LIM homeobox protein 5	NM_008499|Lhx5|16873|LIM homeobox protein 5	AK048778|Lhx5|16873|LIM homeobox protein 5	AK033927|Lhx5|16873|LIM homeobox protein 5	BC057585|Lhx5|16873|LIM homeobox protein 5
mm9_v1_chr5_+_147644465_147644491	0.149715	SOX2.p2	NM_019647|Rpl21|19933|ribosomal protein L21
mm9_v1_chr10_-_41529396_41529437	0.149659	SOX2.p2	AF397908|Cep57l1|103268|centrosomal protein 57-like 1	AK012710|Cep57l1|103268|centrosomal protein 57-like 1	AK010530|Cep57l1|103268|centrosomal protein 57-like 1	AK041460|Cep57l1|103268|centrosomal protein 57-like 1	NM_026643|Cep57l1|103268|centrosomal protein 57-like 1	NM_029132|Cep57l1|103268|centrosomal protein 57-like 1
mm9_v1_chr10_-_30562434_30562625	0.149248	SOX2.p2	AK031506|Hey2|15214|hairy/enhancer-of-split related with YRPW motif 2	AB093589|Hey2|15214|hairy/enhancer-of-split related with YRPW motif 2	BC103575|Hey2|15214|hairy/enhancer-of-split related with YRPW motif 2	BC105651|Hey2|15214|hairy/enhancer-of-split related with YRPW motif 2	BC103576|Hey2|15214|hairy/enhancer-of-split related with YRPW motif 2	BC105652|Hey2|15214|hairy/enhancer-of-split related with YRPW motif 2	AF173902|Hey2|15214|hairy/enhancer-of-split related with YRPW motif 2	AF232240|Hey2|15214|hairy/enhancer-of-split related with YRPW motif 2	AK158000|Hey2|15214|hairy/enhancer-of-split related with YRPW motif 2	AF172287|Hey2|15214|hairy/enhancer-of-split related with YRPW motif 2	AJ271867|Hey2|15214|hairy/enhancer-of-split related with YRPW motif 2	NM_013904|Hey2|15214|hairy/enhancer-of-split related with YRPW motif 2
mm9_v1_chr14_+_117324999_117325104	0.147664	SOX2.p2	AK032866|Gpc6|23888|glypican 6	BC023448|Gpc6|23888|glypican 6
mm9_v1_chr2_-_130110142_130110202	0.147629	SOX2.p2	BC009022|Idh3b|170718|isocitrate dehydrogenase 3 (NAD+) beta	AY035212|Idh3b|170718|isocitrate dehydrogenase 3 (NAD+) beta	AK046059|Idh3b|170718|isocitrate dehydrogenase 3 (NAD+) beta	NM_130884|Idh3b|170718|isocitrate dehydrogenase 3 (NAD+) beta
mm9_v1_chr5_+_54200858_54200899	0.146915	SOX2.p2	NM_144517|Tbc1d19|67249|TBC1 domain family, member 19	AK083084|Tbc1d19|67249|TBC1 domain family, member 19
mm9_v1_chr6_-_83781704_83781750	0.146864	SOX2.p2	AK140686|Paip2b|232164|poly(A) binding protein interacting protein 2B	AK159287|Paip2b|232164|poly(A) binding protein interacting protein 2B	NM_146169|Paip2b|232164|poly(A) binding protein interacting protein 2B
mm9_v1_chr2_+_164159054_164159070	0.146623	SOX2.p2	S60687|Svs5|20944|seminal vesicle secretory protein 5
mm9_v1_chr4_-_143247148_143247148	0.146511	SOX2.p2	NM_001126325|Gm13088|277668|predicted gene 13088
mm9_v1_chr17_-_23701091_23701154	0.146413	SOX2.p2	AK147992|Zfp213|449521|zinc finger protein 213	BC038178|Zfp213|449521|zinc finger protein 213	AK039822|6330415G19Rik|320020|RIKEN cDNA 6330415G19 gene
mm9_v1_chr14_+_112074336_112074336	0.146114	SOX2.p2	NM_198865|Slitrk5|75409|SLIT and NTRK-like family, member 5
mm9_v1_chr1_-_21069242_21069313	0.145792	SOX2.p2	AY029530|Tram2|170829|translocating chain-associating membrane protein 2	BC018212|Tram2|170829|translocating chain-associating membrane protein 2	NM_133252|Tram2|170829|translocating chain-associating membrane protein 2	AK082751|Tram2|170829|translocating chain-associating membrane protein 2	NM_177409|Tram2|170829|translocating chain-associating membrane protein 2
mm9_v1_chr5_+_91456489_91456542	0.145086	SOX2.p2	BC119291|Epgn|71920|epithelial mitogen	BC119293|Epgn|71920|epithelial mitogen	BC145041|Epgn|71920|epithelial mitogen	AJ291391|Epgn|71920|epithelial mitogen	NM_053087|Epgn|71920|epithelial mitogen
mm9_v1_chr7_-_22086485_22086485	0.144329	SOX2.p2	NM_001166838|Vmn1r126|100043013|vomeronasal 1 receptor 126	NM_001167164|Gm4214|100043079|predicted gene 4214	NM_001167165|Gm4175|100043019|predicted gene 4175
mm9_v1_chr1_+_91476810_91476856	0.144313	SOX2.p2	AK147521|Agap1|347722|ArfGAP with GTPase domain, ankyrin repeat and PH domain 1
mm9_v1_chr15_+_73578771_73578842	0.144021	SOX2.p2	AK143702|Ptp4a3|19245|protein tyrosine phosphatase 4a3	AK172192|Ptp4a3|19245|protein tyrosine phosphatase 4a3	AK014601|Ptp4a3|19245|protein tyrosine phosphatase 4a3
mm9_v1_chr9_+_79914751_79914905	0.143952	SOX2.p2	AK129219|Senp6|215351|SUMO/sentrin specific peptidase 6	BC061480|Senp6|215351|SUMO/sentrin specific peptidase 6	BC052718|Senp6|215351|SUMO/sentrin specific peptidase 6
mm9_v1_chr3_+_36451511_36451588	0.142843	SOX2.p2	NM_019393|Exosc9|50911|exosome component 9	AK169568|Exosc9|50911|exosome component 9	AK076096|Exosc9|50911|exosome component 9	BC005622|Exosc9|50911|exosome component 9	AK010253|Exosc9|50911|exosome component 9	AF152841|Exosc9|50911|exosome component 9	BC052156|Exosc9|50911|exosome component 9	AK083794|Exosc9|50911|exosome component 9	BC158075|Exosc9|50911|exosome component 9	AK011636|Exosc9|50911|exosome component 9
mm9_v1_chr6_-_83781657_83781701	0.14284	SOX2.p2	BC017133|Paip2b|232164|poly(A) binding protein interacting protein 2B	BC034096|Paip2b|232164|poly(A) binding protein interacting protein 2B	BC039969|Paip2b|232164|poly(A) binding protein interacting protein 2B	AK173114|Paip2b|232164|poly(A) binding protein interacting protein 2B	AK168804|Paip2b|232164|poly(A) binding protein interacting protein 2B	AK045922|Paip2b|232164|poly(A) binding protein interacting protein 2B
mm9_v1_chr8_+_108939222_108939238	0.142769	SOX2.p2	AK032286|Zfp90|22751|zinc finger protein 90	AK154205|Zfp90|22751|zinc finger protein 90	NM_011764|Zfp90|22751|zinc finger protein 90
mm9_v1_chr4_+_57580989_57581153	0.142631	SOX2.p2	AK045344|Palm2|242481|paralemmin 2	NM_172868|Palm2|242481|paralemmin 2	BC113156|Palm2|242481|paralemmin 2
mm9_v1_chr10_+_59568976_59569004	0.142406	SOX2.p2	AJ278999|Spock2|94214|sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2	BC057324|Spock2|94214|sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2	NM_052994|Spock2|94214|sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2
mm9_v1_chr14_-_52533039_52533074	0.14155	SOX2.p2	AK158900|Ndrg2|29811|N-myc downstream regulated gene 2
mm9_v1_chr10_+_36694322_36694389	0.141364	SOX2.p2	AK165734|Hdac2|15182|histone deacetylase 2	NM_008229|Hdac2|15182|histone deacetylase 2	AK051753|Hdac2|15182|histone deacetylase 2	BC138517|Hdac2|15182|histone deacetylase 2	U31758|Hdac2|15182|histone deacetylase 2
mm9_v1_chr15_-_81560283_81560301	0.141307	SOX2.p2	BC071200|Rangap1|19387|RAN GTPase activating protein 1	AK159009|Rangap1|19387|RAN GTPase activating protein 1
mm9_v1_chr10_+_82448326_82448493	0.141281	SOX2.p2	BC137629|Chst11|58250|carbohydrate sulfotransferase 11	BC144793|Chst11|58250|carbohydrate sulfotransferase 11
mm9_v1_chr11_-_69431369_69431406	0.140951	SOX2.p2	U85644|Shbg|20415|sex hormone binding globulin	BC120785|Shbg|20415|sex hormone binding globulin	BC120787|Shbg|20415|sex hormone binding globulin	AK010959|Shbg|20415|sex hormone binding globulin	NM_011367|Shbg|20415|sex hormone binding globulin
mm9_v1_chr14_+_51544629_51544699	0.140876	SOX2.p2	BC052401|Apex1|11792|apurinic/apyrimidinic endonuclease 1	AK013296|Apex1|11792|apurinic/apyrimidinic endonuclease 1	D90374|Apex1|11792|apurinic/apyrimidinic endonuclease 1	NM_009687|Apex1|11792|apurinic/apyrimidinic endonuclease 1
mm9_v1_chr5_-_136646451_136646559	0.139348	SOX2.p2	BC115648|Orai2|269717|ORAI calcium release-activated calcium modulator 2	BC115649|Orai2|269717|ORAI calcium release-activated calcium modulator 2	AK195764|Orai2|269717|ORAI calcium release-activated calcium modulator 2	AK215306|Orai2|269717|ORAI calcium release-activated calcium modulator 2	AK079619|Orai2|269717|ORAI calcium release-activated calcium modulator 2	BC066070|Orai2|269717|ORAI calcium release-activated calcium modulator 2	AK087038|Orai2|269717|ORAI calcium release-activated calcium modulator 2	AK036013|Orai2|269717|ORAI calcium release-activated calcium modulator 2	AK042940|Orai2|269717|ORAI calcium release-activated calcium modulator 2	NM_178751|Orai2|269717|ORAI calcium release-activated calcium modulator 2
mm9_v1_chr3_+_121426422_121426632	0.139318	SOX2.p2	BC024886|F3|14066|coagulation factor III	NM_010171|F3|14066|coagulation factor III	BC016397|F3|14066|coagulation factor III	M26071|F3|14066|coagulation factor III	AK137642|F3|14066|coagulation factor III	AK144872|F3|14066|coagulation factor III	M57896|F3|14066|coagulation factor III	CT010367|F3|14066|coagulation factor III
mm9_v1_chr11_+_84984593_84984597	0.139265	SOX2.p2	BC048674|1700125H20Rik|73634|RIKEN cDNA 1700125H20 gene	NM_028589|1700125H20Rik|73634|RIKEN cDNA 1700125H20 gene
mm9_v1_chr7_-_52308243_52308250	0.138812	SOX2.p2	BC075628|Prr12|233210|proline rich 12	NM_175022|Prr12|233210|proline rich 12
mm9_v1_chr8_+_35217677_35217684	0.138685	SOX2.p2	BC024888|Tmem66|67887|transmembrane protein 66	AK163218|Tmem66|67887|transmembrane protein 66
mm9_v1_chr6_-_129401762_129402017	0.138528	SOX2.p2	AK049608|Clec1a|243653|C-type lectin domain family 1, member a	AK031121|Clec1a|243653|C-type lectin domain family 1, member a	BC052840|Clec1a|243653|C-type lectin domain family 1, member a	AK036846|Clec1a|243653|C-type lectin domain family 1, member a	AK165920|Clec1a|243653|C-type lectin domain family 1, member a	NM_175526|Clec1a|243653|C-type lectin domain family 1, member a
mm9_v1_chr2_-_155937623_155937702	0.138365	SOX2.p2	AK220288|Cpne1|266692|copine I	BC052473|Rbm12|75710|RNA binding motif protein 12	BC057554|Cpne1|266692|copine I	AK035014|Rbm12|75710|RNA binding motif protein 12	AK080772|Rbm12|75710|RNA binding motif protein 12	AF393215|Rbm12|75710|RNA binding motif protein 12	AF393216|Rbm12|75710|RNA binding motif protein 12	AK028882|Cpne1|266692|copine I	AK152323|Cpne1|266692|copine I	NM_029397|Rbm12|75710|RNA binding motif protein 12	NM_170588|Cpne1|266692|copine I	NM_170590|Cpne1|266692|copine I	NM_170598|Rbm12|75710|RNA binding motif protein 12
mm9_v1_chr17_+_34701239_34701309	0.138346	SOX2.p2	NM_010929|Notch4|18132|Notch gene homolog 4 (Drosophila)	AK166261|Notch4|18132|Notch gene homolog 4 (Drosophila)	AK166493|Notch4|18132|Notch gene homolog 4 (Drosophila)	M80456|Notch4|18132|Notch gene homolog 4 (Drosophila)	BC138044|Notch4|18132|Notch gene homolog 4 (Drosophila)	BC145114|Notch4|18132|Notch gene homolog 4 (Drosophila)
mm9_v1_chr18_-_33623400_33623430	0.137662	SOX2.p2	NM_001109989|D0H4S114|27528|DNA segment, human D4S114
mm9_v1_chr13_-_94269673_94269706	0.137481	SOX2.p2	BC020052|Jmy|57748|junction-mediating and regulatory protein
mm9_v1_chr7_+_21657274_21657274	0.137363	SOX2.p2	NM_001166744|Vmn1r116|667268|vomeronasal 1 receptor 116
mm9_v1_chr11_-_4999069_4999098	0.136855	SOX2.p2	AK049743|Ewsr1|14030|Ewing sarcoma breakpoint region 1	NM_007968|Ewsr1|14030|Ewing sarcoma breakpoint region 1	X79233|Ewsr1|14030|Ewing sarcoma breakpoint region 1	AK046434|Ewsr1|14030|Ewing sarcoma breakpoint region 1
mm9_v1_chr13_-_49748055_49748114	0.136638	SOX2.p2	AK014919|Cenpp|66336|centromere protein P	BC147207|Cenpp|66336|centromere protein P	BC147208|Cenpp|66336|centromere protein P	AK012863|Cenpp|66336|centromere protein P	NM_025495|Cenpp|66336|centromere protein P	AK006234|Cenpp|66336|centromere protein P
mm9_v1_chr4_+_41774206_41774242	0.13607	SOX2.p2	BC087957|Ccl21c|65956|chemokine (C-C motif) ligand 21C (leucine)	NM_001193666|Gm13304|100504346|predicted gene 13304	NM_001193668|Gm10591|100504239|predicted gene 10591	NM_023052|Ccl21c|65956|chemokine (C-C motif) ligand 21C (leucine)	BC038120|Ccl21a|18829|chemokine (C-C motif) ligand 21A (serine)	NM_011335|Ccl21b|100042493|chemokine (C-C motif) ligand 21B (leucine)	U88322|Ccl21c|65956|chemokine (C-C motif) ligand 21C (leucine)
mm9_v1_chr7_+_52471161_52471287	0.135918	SOX2.p2	AK144857|Tead2|21677|TEA domain family member 2	AK146595|Tead2|21677|TEA domain family member 2	AK132009|Tead2|21677|TEA domain family member 2	Y10026|Tead2|21677|TEA domain family member 2	AK137064|Tead2|21677|TEA domain family member 2	AK143155|Tead2|21677|TEA domain family member 2
mm9_v1_chr7_-_106628533_106628572	0.13582	SOX2.p2	
mm9_v1_chr4_+_42625654_42625690	0.135713	SOX2.p2	BC087957|Ccl21c|65956|chemokine (C-C motif) ligand 21C (leucine)	NM_001193666|Gm13304|100504346|predicted gene 13304	NM_001193668|Gm10591|100504239|predicted gene 10591	NM_023052|Ccl21c|65956|chemokine (C-C motif) ligand 21C (leucine)	BC038120|Ccl21a|18829|chemokine (C-C motif) ligand 21A (serine)	NM_011335|Ccl21b|100042493|chemokine (C-C motif) ligand 21B (leucine)	U88322|Ccl21c|65956|chemokine (C-C motif) ligand 21C (leucine)
mm9_v1_chr11_-_86517662_86517713	0.135666	SOX2.p2	AK167527|Cltc|67300|clathrin, heavy polypeptide (Hc)
mm9_v1_chr4_-_42393043_42393079	0.135512	SOX2.p2	NM_011335|Ccl21b|100042493|chemokine (C-C motif) ligand 21B (leucine)	U88322|Ccl21c|65956|chemokine (C-C motif) ligand 21C (leucine)	BC038120|Ccl21a|18829|chemokine (C-C motif) ligand 21A (serine)	BC087957|Ccl21c|65956|chemokine (C-C motif) ligand 21C (leucine)	NM_001193666|Gm13304|100504346|predicted gene 13304	NM_001193668|Gm10591|100504239|predicted gene 10591	NM_023052|Ccl21c|65956|chemokine (C-C motif) ligand 21C (leucine)
mm9_v1_chr11_-_106021399_106021524	0.135462	SOX2.p2	BC068130|Limd2|67803|LIM domain containing 2	AK049809|Limd2|67803|LIM domain containing 2	AK167349|Limd2|67803|LIM domain containing 2	AK169829|Limd2|67803|LIM domain containing 2	AK012581|Limd2|67803|LIM domain containing 2	AK032430|Limd2|67803|LIM domain containing 2	AK040486|Limd2|67803|LIM domain containing 2	NM_172397|Limd2|67803|LIM domain containing 2
mm9_v1_chr9_+_108393149_108393235	0.135445	SOX2.p2	AK043088|Usp19|71472|ubiquitin specific peptidase 19	AK171942|Usp19|71472|ubiquitin specific peptidase 19	AK146504|Usp19|71472|ubiquitin specific peptidase 19	AK160807|Usp19|71472|ubiquitin specific peptidase 19	AK159473|Usp19|71472|ubiquitin specific peptidase 19
mm9_v1_chr2_+_22751003_22751041	0.135036	SOX2.p2	NM_019501|Pdss1|56075|prenyl (solanesyl) diphosphate synthase, subunit 1
mm9_v1_chr14_-_64162810_64162839	0.134889	SOX2.p2	AK044957|Mtmr9|210376|myotubularin related protein 9
mm9_v1_chr3_-_93858806_93858806	0.134866	SOX2.p2	AK033449|Gm9125|668359|predicted gene 9125	NM_001163730|Gm9125|668359|predicted gene 9125
mm9_v1_chr13_-_27605067_27605083	0.134499	SOX2.p2	AF230921|Prl8a8|74188|prolactin family 8, subfamily a, member 81	AF230922|Prl8a8|74188|prolactin family 8, subfamily a, member 81	AF230923|Prl8a8|74188|prolactin family 8, subfamily a, member 81	BC100326|Prl8a8|74188|prolactin family 8, subfamily a, member 81	AF466150|Prl8a8|74188|prolactin family 8, subfamily a, member 81	NM_023741|Prl8a8|74188|prolactin family 8, subfamily a, member 81	AK167369|Prl8a8|74188|prolactin family 8, subfamily a, member 81	AK005568|Prl8a8|74188|prolactin family 8, subfamily a, member 81
mm9_v1_chr4_-_119211373_119211373	0.134465	SOX2.p2	BC076608|AA415398|433752|expressed sequence AA415398	NM_001004178|AA415398|433752|expressed sequence AA415398
mm9_v1_chr7_+_148317160_148317300	0.134282	SOX2.p2	AK036368|Ptdss2|27388|phosphatidylserine synthase 2	NM_013782|Ptdss2|27388|phosphatidylserine synthase 2	AK031906|Ptdss2|27388|phosphatidylserine synthase 2	AK048026|Ptdss2|27388|phosphatidylserine synthase 2	AK081275|Ptdss2|27388|phosphatidylserine synthase 2	AK021249|Ptdss2|27388|phosphatidylserine synthase 2	AK032686|Ptdss2|27388|phosphatidylserine synthase 2	AK137415|Ptdss2|27388|phosphatidylserine synthase 2	BC053517|Ptdss2|27388|phosphatidylserine synthase 2	AF099053|Ptdss2|27388|phosphatidylserine synthase 2
mm9_v1_chr11_-_100122302_100122344	0.134249	SOX2.p2	AB013608|Krt17|16667|keratin 17	NM_010663|Krt17|16667|keratin 17	BC032161|Krt17|16667|keratin 17	BC132454|Krt17|16667|keratin 17	BC132456|Krt17|16667|keratin 17
mm9_v1_chr14_-_64162744_64162804	0.13416	SOX2.p2	BC046275|Mtmr9|210376|myotubularin related protein 9	NM_177594|Mtmr9|210376|myotubularin related protein 9	AK035026|Mtmr9|210376|myotubularin related protein 9
mm9_v1_chr15_-_39775498_39775574	0.13414	SOX2.p2	BC058345|Lrp12|239393|low density lipoprotein-related protein 12
mm9_v1_chr9_+_79914685_79914721	0.134127	SOX2.p2	AK053904|Senp6|215351|SUMO/sentrin specific peptidase 6	NM_146003|Senp6|215351|SUMO/sentrin specific peptidase 6
mm9_v1_chr7_-_72516109_72516162	0.133843	SOX2.p2	D14340|Tjp1|21872|tight junction protein 1	NM_001163574|Tjp1|21872|tight junction protein 1	NM_009386|Tjp1|21872|tight junction protein 1
mm9_v1_chr4_-_59973470_59973536	0.132828	SOX2.p2	EU882229|Mup4|17843|major urinary protein 4	BC012227|Mup4|17843|major urinary protein 4	M16358|Mup4|17843|major urinary protein 4	NM_008648|Mup4|17843|major urinary protein 4
mm9_v1_chr12_-_77896410_77896435	0.132684	SOX2.p2	BC010823|Gpx2|14776|glutathione peroxidase 2	AK131940|Gpx2|14776|glutathione peroxidase 2
mm9_v1_chr16_-_18248659_18248687	0.132152	SOX2.p2	L25255|Ranbp1|19385|RAN binding protein 1
mm9_v1_chr19_+_3767420_3767525	0.132011	SOX2.p2	AK083227|Suv420h1|225888|suppressor of variegation 4-20 homolog 1 (Drosophila)	NM_001167884|Suv420h1|225888|suppressor of variegation 4-20 homolog 1 (Drosophila)	NM_001167885|Suv420h1|225888|suppressor of variegation 4-20 homolog 1 (Drosophila)	NM_001167886|Suv420h1|225888|suppressor of variegation 4-20 homolog 1 (Drosophila)	NM_001167887|Suv420h1|225888|suppressor of variegation 4-20 homolog 1 (Drosophila)	NM_001167888|Suv420h1|225888|suppressor of variegation 4-20 homolog 1 (Drosophila)	NM_001167889|Suv420h1|225888|suppressor of variegation 4-20 homolog 1 (Drosophila)	NM_144871|Suv420h1|225888|suppressor of variegation 4-20 homolog 1 (Drosophila)	AK087267|Suv420h1|225888|suppressor of variegation 4-20 homolog 1 (Drosophila)
mm9_v1_chr6_-_39369941_39369948	0.131948	SOX2.p2	AK005137|Mkrn1|54484|makorin, ring finger protein, 1
mm9_v1_chr10_-_29920326_29920345	0.131487	SOX2.p2	AK005988|Cenpw|66311|centromere protein W	AK011700|Cenpw|66311|centromere protein W	AK141272|Cenpw|66311|centromere protein W	BC147188|Cenpw|66311|centromere protein W	BC147189|Cenpw|66311|centromere protein W	BC147710|Cenpw|66311|centromere protein W	BC147721|Cenpw|66311|centromere protein W	NM_001109747|Cenpw|66311|centromere protein W
mm9_v1_chr10_-_29082247_29082247	0.131178	SOX2.p2	BC050795|Rnf146|68031|ring finger protein 146	NM_001110196|Rnf146|68031|ring finger protein 146	NM_001110197|Rnf146|68031|ring finger protein 146	NM_001110198|Rnf146|68031|ring finger protein 146	NM_026518|Rnf146|68031|ring finger protein 146
mm9_v1_chr1_-_123424939_123425041	0.130576	SOX2.p2	BC114988|Htr5b|15564|5-hydroxytryptamine (serotonin) receptor 5B	BC115825|Htr5b|15564|5-hydroxytryptamine (serotonin) receptor 5B	NM_010483|Htr5b|15564|5-hydroxytryptamine (serotonin) receptor 5B	X69867|Htr5b|15564|5-hydroxytryptamine (serotonin) receptor 5B
mm9_v1_chr2_-_26264694_26264752	0.13035	SOX2.p2	AK170786|Inpp5e|64436|inositol polyphosphate-5-phosphatase E	AF226683|Inpp5e|64436|inositol polyphosphate-5-phosphatase E	BC057566|Inpp5e|64436|inositol polyphosphate-5-phosphatase E	BC080295|Inpp5e|64436|inositol polyphosphate-5-phosphatase E	BC052717|Inpp5e|64436|inositol polyphosphate-5-phosphatase E	NM_033134|Inpp5e|64436|inositol polyphosphate-5-phosphatase E	AK170812|Inpp5e|64436|inositol polyphosphate-5-phosphatase E	AK080075|Inpp5e|64436|inositol polyphosphate-5-phosphatase E	AK047245|Inpp5e|64436|inositol polyphosphate-5-phosphatase E	AK158135|Inpp5e|64436|inositol polyphosphate-5-phosphatase E	AK154097|Inpp5e|64436|inositol polyphosphate-5-phosphatase E
mm9_v1_chr14_+_26761977_26762068	0.130349	SOX2.p2	DQ224405|Cphx|105594|cytoplasmic polyadenylated homeobox	AK049114|Cphx|105594|cytoplasmic polyadenylated homeobox	NM_175342|Cphx|105594|cytoplasmic polyadenylated homeobox	BC132038|Cphx|105594|cytoplasmic polyadenylated homeobox	BC132040|Cphx|105594|cytoplasmic polyadenylated homeobox	BC095973|Cphx|105594|cytoplasmic polyadenylated homeobox
mm9_v1_chr14_+_26901730_26901821	0.130349	SOX2.p2	DQ224405|Cphx|105594|cytoplasmic polyadenylated homeobox	AK049114|Cphx|105594|cytoplasmic polyadenylated homeobox	NM_175342|Cphx|105594|cytoplasmic polyadenylated homeobox	BC132038|Cphx|105594|cytoplasmic polyadenylated homeobox	BC132040|Cphx|105594|cytoplasmic polyadenylated homeobox	BC095973|Cphx|105594|cytoplasmic polyadenylated homeobox
mm9_v1_chr14_+_27041341_27041432	0.130349	SOX2.p2	DQ224405|Cphx|105594|cytoplasmic polyadenylated homeobox	AK049114|Cphx|105594|cytoplasmic polyadenylated homeobox	NM_175342|Cphx|105594|cytoplasmic polyadenylated homeobox	BC132038|Cphx|105594|cytoplasmic polyadenylated homeobox	BC132040|Cphx|105594|cytoplasmic polyadenylated homeobox	BC095973|Cphx|105594|cytoplasmic polyadenylated homeobox
mm9_v1_chrX_+_69467355_69467355	0.129664	SOX2.p2	BC104088|Magea4|17140|melanoma antigen, family A, 4	BC104089|Magea4|17140|melanoma antigen, family A, 4	NM_020280|Magea4|17140|melanoma antigen, family A, 4
mm9_v1_chr4_+_116393559_116393581	0.129627	SOX2.p2	AK047755|Tesk2|230661|testis-specific kinase 2	NM_146151|Tesk2|230661|testis-specific kinase 2	AK031814|Tesk2|230661|testis-specific kinase 2	AK053368|Tesk2|230661|testis-specific kinase 2	BC029766|Tesk2|230661|testis-specific kinase 2
mm9_v1_chr9_+_107483603_107483637	0.12946	SOX2.p2	BC018457|Hyal3|109685|hyaluronoglucosaminidase 3	NM_178020|Hyal3|109685|hyaluronoglucosaminidase 3	AY048681|Hyal3|109685|hyaluronoglucosaminidase 3
mm9_v1_chr4_-_116494091_116494112	0.129207	SOX2.p2	AK049217|Hpdl|242642|4-hydroxyphenylpyruvate dioxygenase-like	AK043902|Hpdl|242642|4-hydroxyphenylpyruvate dioxygenase-like	AK078929|Hpdl|242642|4-hydroxyphenylpyruvate dioxygenase-like	NM_146256|Hpdl|242642|4-hydroxyphenylpyruvate dioxygenase-like
mm9_v1_chr2_+_153571990_153572007	0.129008	SOX2.p2	BC052405|Mapre1|13589|microtubule-associated protein, RP/EB family, member 1
mm9_v1_chr10_-_78215809_78215811	0.12805	SOX2.p2	AK016452|Ccdc105|70976|coiled-coil domain containing 105	NM_027630|Ccdc105|70976|coiled-coil domain containing 105
mm9_v1_chr12_+_58331420_58331438	0.127997	SOX2.p2	AK168989|Mipol1|73490|mirror-image polydactyly gene 1 homolog (human)	AK085510|Mipol1|73490|mirror-image polydactyly gene 1 homolog (human)	AK050030|Mipol1|73490|mirror-image polydactyly gene 1 homolog (human)	AK077915|Mipol1|73490|mirror-image polydactyly gene 1 homolog (human)	AK163490|Mipol1|73490|mirror-image polydactyly gene 1 homolog (human)
mm9_v1_chr10_-_62255007_62255115	0.127846	SOX2.p2	BC034174|Ccar1|67500|cell division cycle and apoptosis regulator 1	BC051052|Ccar1|67500|cell division cycle and apoptosis regulator 1	NM_026201|Ccar1|67500|cell division cycle and apoptosis regulator 1
mm9_v1_chr9_+_43901941_43901990	0.127434	SOX2.p2	AK047204|Usp2|53376|ubiquitin specific peptidase 2	AK081112|Usp2|53376|ubiquitin specific peptidase 2
mm9_v1_chr11_+_101414168_101414211	0.127401	SOX2.p2	NM_008676|Nbr1|17966|neighbor of Brca1 gene 1	U73039|Nbr1|17966|neighbor of Brca1 gene 1	AK128992|Nbr1|17966|neighbor of Brca1 gene 1	BC052709|Nbr1|17966|neighbor of Brca1 gene 1	AK154081|Nbr1|17966|neighbor of Brca1 gene 1	AK129043|Nbr1|17966|neighbor of Brca1 gene 1
mm9_v1_chrX_-_93152262_93152300	0.127208	SOX2.p2	AK089160|Las1l|76130|LAS1-like (S. cerevisiae)	NM_152822|Las1l|76130|LAS1-like (S. cerevisiae)	AK163919|Las1l|76130|LAS1-like (S. cerevisiae)
mm9_v1_chr9_+_108984968_108985054	0.127182	SOX2.p2	AK137013|Ccdc51|66658|coiled-coil domain containing 51	AK141240|Ccdc51|66658|coiled-coil domain containing 51	NM_025689|Ccdc51|66658|coiled-coil domain containing 51	AK017860|Ccdc51|66658|coiled-coil domain containing 51
mm9_v1_chr2_+_164228640_164228712	0.125866	SOX2.p2	AK052449|Rbpjl|19668|recombination signal binding protein for immunoglobulin kappa J region-like	NM_009036|Rbpjl|19668|recombination signal binding protein for immunoglobulin kappa J region-like	Y10926|Rbpjl|19668|recombination signal binding protein for immunoglobulin kappa J region-like	BC152311|Rbpjl|19668|recombination signal binding protein for immunoglobulin kappa J region-like	AK131832|Rbpjl|19668|recombination signal binding protein for immunoglobulin kappa J region-like	AK131814|Rbpjl|19668|recombination signal binding protein for immunoglobulin kappa J region-like
mm9_v1_chr19_+_10969732_10969733	0.125557	SOX2.p2	AK164681|Prpf19|28000|PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae)
mm9_v1_chr7_+_16132605_16132645	0.125222	SOX2.p2	NM_027802|Obox1|71468|oocyte specific homeobox 1	AK018362|Obox1|71468|oocyte specific homeobox 1	AK136061|Obox1|71468|oocyte specific homeobox 1	BC141323|Obox1|71468|oocyte specific homeobox 1	BC141324|Obox1|71468|oocyte specific homeobox 1
mm9_v1_chr17_+_37139856_37139982	0.125165	SOX2.p2	D21850|Zfp57|22715|zinc finger protein 57
mm9_v1_chr5_-_28793627_28793640	0.125024	SOX2.p2	BC063087|Shh|20423|sonic hedgehog	AK077688|Shh|20423|sonic hedgehog	NM_009170|Shh|20423|sonic hedgehog
mm9_v1_chr7_+_50469408_50469408	0.124896	SOX2.p2	EU599041|EU599041|100170401|expressed sequence EU599041	EU599042|EU599041|100170401|expressed sequence EU599041	NM_001177525|EU599041|100170401|expressed sequence EU599041
mm9_v1_chr4_-_129012546_129012617	0.124868	SOX2.p2	U35141|Rbbp4|19646|retinoblastoma binding protein 4	AK166437|Rbbp4|19646|retinoblastoma binding protein 4	AK082419|Rbbp4|19646|retinoblastoma binding protein 4	BC138568|Rbbp4|19646|retinoblastoma binding protein 4	BC138570|Rbbp4|19646|retinoblastoma binding protein 4	NM_009030|Rbbp4|19646|retinoblastoma binding protein 4
mm9_v1_chr7_-_23350361_23350361	0.12481	SOX2.p2	NM_001167162|Gm4201|100043061|predicted gene 4201	NM_001167163|Gm4141|100042976|predicted gene 4141
mm9_v1_chr10_+_14480024_14480094	0.124803	SOX2.p2	BC144884|Nmbr|18101|neuromedin B receptor	BC144885|Nmbr|18101|neuromedin B receptor	BC119237|Nmbr|18101|neuromedin B receptor	NM_008703|Nmbr|18101|neuromedin B receptor
mm9_v1_chr6_-_136776557_136776669	0.124744	SOX2.p2	AK031678|Wbp11|60321|WW domain binding protein 11	BC021823|Wbp11|60321|WW domain binding protein 11	BC006600|Wbp11|60321|WW domain binding protein 11	AK144968|Wbp11|60321|WW domain binding protein 11	AK153927|Wbp11|60321|WW domain binding protein 11	AK145049|Wbp11|60321|WW domain binding protein 11	AK011001|Wbp11|60321|WW domain binding protein 11
mm9_v1_chr2_+_146838735_146838857	0.124141	SOX2.p2	AK168037|Xrn2|24128|5'-3' exoribonuclease 2	AK031247|Xrn2|24128|5'-3' exoribonuclease 2	AK167019|Xrn2|24128|5'-3' exoribonuclease 2	BC054743|Xrn2|24128|5'-3' exoribonuclease 2	NM_011917|Xrn2|24128|5'-3' exoribonuclease 2	AK011711|Xrn2|24128|5'-3' exoribonuclease 2	AK053643|Xrn2|24128|5'-3' exoribonuclease 2	AK133654|Xrn2|24128|5'-3' exoribonuclease 2	AK163899|Xrn2|24128|5'-3' exoribonuclease 2	BC052395|Xrn2|24128|5'-3' exoribonuclease 2	AK004800|Xrn2|24128|5'-3' exoribonuclease 2	BC052823|Xrn2|24128|5'-3' exoribonuclease 2	D38517|Xrn2|24128|5'-3' exoribonuclease 2
mm9_v1_chr7_+_73834774_73834871	0.124083	SOX2.p2	NM_001191001|Lins|72635|lines homolog (Drosophila)	NM_152815|Lins|72635|lines homolog (Drosophila)	AK156066|Lins|72635|lines homolog (Drosophila)	AK044132|Lins|72635|lines homolog (Drosophila)	AK012554|Lins|72635|lines homolog (Drosophila)	AK171170|Lins|72635|lines homolog (Drosophila)	BC030943|Lins|72635|lines homolog (Drosophila)	BC058648|Lins|72635|lines homolog (Drosophila)
mm9_v1_chrX_-_34708836_34708836	0.123859	SOX2.p2	AK133120|Akap14|434756|A kinase (PRKA) anchor protein 14	BC147265|Akap14|434756|A kinase (PRKA) anchor protein 14	BC147494|Akap14|434756|A kinase (PRKA) anchor protein 14	NM_001033785|Akap14|434756|A kinase (PRKA) anchor protein 14
mm9_v1_chr11_+_99797604_99797636	0.123834	SOX2.p2	AK037252|Krtap31-2|432602|keratin associated protein 31-2	NM_001025244|Krtap31-2|432602|keratin associated protein 31-2	BC147120|Krtap31-2|432602|keratin associated protein 31-2	BC147121|Krtap31-2|432602|keratin associated protein 31-2
mm9_v1_chr13_+_105019467_105019467	0.123051	SOX2.p2	AB043687|Cenpk|60411|centromere protein K	NM_021790|Cenpk|60411|centromere protein K
mm9_v1_chr5_-_144031666_144031702	0.122852	SOX2.p2	NM_017467|Zfp316|54201|zinc finger protein 316
mm9_v1_chr8_-_28266926_28267017	0.121893	SOX2.p2	BC091001|Rab11fip1|75767|RAB11 family interacting protein 1 (class I)
mm9_v1_chr15_+_76077149_76077297	0.121414	SOX2.p2	AK003920|Grina|66168|glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (glutamate binding)	BC019157|Grina|66168|glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (glutamate binding)	BC010802|Grina|66168|glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (glutamate binding)	NM_023168|Grina|66168|glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (glutamate binding)	BC037667|Grina|66168|glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (glutamate binding)	AF182040|Grina|66168|glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (glutamate binding)
mm9_v1_chr16_-_15966723_15966739	0.120978	SOX2.p2	BC085258|2310008H04Rik|224008|RIKEN cDNA 2310008H04 gene
mm9_v1_chr18_-_33623668_33623692	0.120417	SOX2.p2	NM_001109988|D0H4S114|27528|DNA segment, human D4S114
mm9_v1_chr9_-_21875719_21875761	0.120199	SOX2.p2	AK046492|Zfp653|319601|zinc finger protein 653	AK157635|Zfp653|319601|zinc finger protein 653
mm9_v1_chr9_-_43013831_43013943	0.119952	SOX2.p2	Z18537|Pou2f3|18988|POU domain, class 2, transcription factor 3	L14677|Pou2f3|18988|POU domain, class 2, transcription factor 3	NM_011139|Pou2f3|18988|POU domain, class 2, transcription factor 3
mm9_v1_chr16_+_72663393_72663448	0.119912	SOX2.p2	AK138485|Robo1|19876|roundabout homolog 1 (Drosophila)	AK143001|Robo1|19876|roundabout homolog 1 (Drosophila)	NM_019413|Robo1|19876|roundabout homolog 1 (Drosophila)	AK032752|Robo1|19876|roundabout homolog 1 (Drosophila)	AK142047|Robo1|19876|roundabout homolog 1 (Drosophila)
mm9_v1_chr1_+_63223728_63223739	0.119831	SOX2.p2	AF029844|Eef1b2|55949|eukaryotic translation elongation factor 1 beta 2
mm9_v1_chr10_-_80813198_80813232	0.119819	SOX2.p2	AK153816|Hmg20b|15353|high mobility group 20 B	NM_001163166|Hmg20b|15353|high mobility group 20 B
mm9_v1_chr7_+_28964518_28964559	0.119661	SOX2.p2	AK148342|Dyrk1b|13549|dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1b
mm9_v1_chr12_-_106923394_106923487	0.119214	SOX2.p2	AK085790|Atg2b|76559|ATG2 autophagy related 2 homolog B (S. cerevisiae)	AK083213|Atg2b|76559|ATG2 autophagy related 2 homolog B (S. cerevisiae)	BC062182|Atg2b|76559|ATG2 autophagy related 2 homolog B (S. cerevisiae)	AK086802|Atg2b|76559|ATG2 autophagy related 2 homolog B (S. cerevisiae)	NM_029654|Atg2b|76559|ATG2 autophagy related 2 homolog B (S. cerevisiae)
mm9_v1_chr11_+_4157570_4157570	0.119132	SOX2.p2	NM_008501|Lif|16878|leukemia inhibitory factor
mm9_v1_chr5_-_135027949_135028024	0.119102	SOX2.p2	BC121191|Clip2|269713|CAP-GLY domain containing linker protein 2
mm9_v1_chr2_-_165151935_165152001	0.118896	SOX2.p2	AK047040|Elmo2|140579|engulfment and cell motility 2, ced-12 homolog (C. elegans)	AK050823|Elmo2|140579|engulfment and cell motility 2, ced-12 homolog (C. elegans)	AK053574|Elmo2|140579|engulfment and cell motility 2, ced-12 homolog (C. elegans)	AK032033|Elmo2|140579|engulfment and cell motility 2, ced-12 homolog (C. elegans)	BC023954|Elmo2|140579|engulfment and cell motility 2, ced-12 homolog (C. elegans)	AK038097|Elmo2|140579|engulfment and cell motility 2, ced-12 homolog (C. elegans)	AK045428|Elmo2|140579|engulfment and cell motility 2, ced-12 homolog (C. elegans)	AK129023|Elmo2|140579|engulfment and cell motility 2, ced-12 homolog (C. elegans)	NM_080287|Elmo2|140579|engulfment and cell motility 2, ced-12 homolog (C. elegans)	NM_207706|Elmo2|140579|engulfment and cell motility 2, ced-12 homolog (C. elegans)
mm9_v1_chr2_-_131855504_131855666	0.118047	SOX2.p2	BC057402|Rassf2|215653|Ras association (RalGDS/AF-6) domain family member 2	AK028384|Rassf2|215653|Ras association (RalGDS/AF-6) domain family member 2
mm9_v1_chrX_-_45388010_45388030	0.117586	SOX2.p2	BC020015|Apln|30878|apelin	DQ832282|Apln|30878|apelin	NM_013912|Apln|30878|apelin	AK042076|Apln|30878|apelin
mm9_v1_chr2_+_22751081_22751226	0.117354	SOX2.p2	AK012307|Pdss1|56075|prenyl (solanesyl) diphosphate synthase, subunit 1	AB210841|Pdss1|56075|prenyl (solanesyl) diphosphate synthase, subunit 1	BC026820|Pdss1|56075|prenyl (solanesyl) diphosphate synthase, subunit 1	BC107274|Pdss1|56075|prenyl (solanesyl) diphosphate synthase, subunit 1	BC107273|Pdss1|56075|prenyl (solanesyl) diphosphate synthase, subunit 1
mm9_v1_chr4_-_143998305_143998366	0.117203	SOX2.p2	AK167683|Pramef12|77632|PRAME family member 12	BC066168|Pramef12|77632|PRAME family member 12	AK019795|Pramef12|77632|PRAME family member 12	NM_029948|Pramef12|77632|PRAME family member 12
mm9_v1_chr13_+_3477477_3477548	0.116979	SOX2.p2	AK084238|2810429I04Rik|76937|RIKEN cDNA 2810429I04 gene	AK013191|2810429I04Rik|76937|RIKEN cDNA 2810429I04 gene	AK034854|2810429I04Rik|76937|RIKEN cDNA 2810429I04 gene	AK087718|2810429I04Rik|76937|RIKEN cDNA 2810429I04 gene	AK043092|2810429I04Rik|76937|RIKEN cDNA 2810429I04 gene	AK031301|2810429I04Rik|76937|RIKEN cDNA 2810429I04 gene	AK043278|2810429I04Rik|76937|RIKEN cDNA 2810429I04 gene
mm9_v1_chr9_-_49606862_49606915	0.116871	SOX2.p2	BC011310|Ncam1|17967|neural cell adhesion molecule 1
mm9_v1_chr3_+_31801595_31801757	0.116445	SOX2.p2	AK012400|Kcnmb2|72413|potassium large conductance calcium-activated channel, subfamily M, beta member 2	BC046227|Kcnmb2|72413|potassium large conductance calcium-activated channel, subfamily M, beta member 2	BC058957|Kcnmb2|72413|potassium large conductance calcium-activated channel, subfamily M, beta member 2	NM_028231|Kcnmb2|72413|potassium large conductance calcium-activated channel, subfamily M, beta member 2
mm9_v1_chr6_+_113481672_113481700	0.115762	SOX2.p2	NM_001033244|Fancd2|211651|Fanconi anemia, complementation group D2	AK142384|Fancd2|211651|Fanconi anemia, complementation group D2	BC139004|Fancd2|211651|Fanconi anemia, complementation group D2	AK019136|Fancd2|211651|Fanconi anemia, complementation group D2	AK155602|Fancd2|211651|Fanconi anemia, complementation group D2	AK166411|Fancd2|211651|Fanconi anemia, complementation group D2
mm9_v1_chr5_-_121822213_121822316	0.115199	SOX2.p2	AK211451|Trafd1|231712|TRAF type zinc finger domain containing 1	AK212088|Trafd1|231712|TRAF type zinc finger domain containing 1
mm9_v1_chr11_+_74644441_74644466	0.115081	SOX2.p2	AK147933|Mnt|17428|max binding protein
mm9_v1_chr14_-_48037874_48037887	0.115077	SOX2.p2	AK164575|Dlgap5|218977|discs, large (Drosophila) homolog-associated protein 5	AK036384|Dlgap5|218977|discs, large (Drosophila) homolog-associated protein 5	AK135820|Dlgap5|218977|discs, large (Drosophila) homolog-associated protein 5
mm9_v1_chr9_-_24500725_24500736	0.113555	SOX2.p2	AK030128|Dpy19l2|320752|dpy-19-like 2 (C. elegans)	AK029497|Dpy19l2|320752|dpy-19-like 2 (C. elegans)	NM_001166207|Dpy19l2|320752|dpy-19-like 2 (C. elegans)
mm9_v1_chr12_+_59312790_59312790	0.112851	SOX2.p2	AK046464|Sstr1|20605|somatostatin receptor 1	NM_009216|Sstr1|20605|somatostatin receptor 1
mm9_v1_chrX_+_65931715_65931923	0.112725	SOX2.p2	AK053829|Fmr1|14265|fragile X mental retardation syndrome 1 homolog	BC079671|Fmr1|14265|fragile X mental retardation syndrome 1 homolog	NM_008031|Fmr1|14265|fragile X mental retardation syndrome 1 homolog	AK140343|Fmr1|14265|fragile X mental retardation syndrome 1 homolog	AK046605|Fmr1|14265|fragile X mental retardation syndrome 1 homolog	AK053701|Fmr1|14265|fragile X mental retardation syndrome 1 homolog	AK080898|Fmr1|14265|fragile X mental retardation syndrome 1 homolog	AK080948|Fmr1|14265|fragile X mental retardation syndrome 1 homolog	L23971|Fmr1|14265|fragile X mental retardation syndrome 1 homolog
mm9_v1_chr19_-_4201541_4201648	0.111417	SOX2.p2	BC082556|Rad9|19367|RAD9 homolog (S. pombe)	AF045663|Rad9|19367|RAD9 homolog (S. pombe)	NM_011237|Rad9|19367|RAD9 homolog (S. pombe)	AK138973|Rad9|19367|RAD9 homolog (S. pombe)	AK134293|Rad9|19367|RAD9 homolog (S. pombe)	AK165833|Rad9|19367|RAD9 homolog (S. pombe)
mm9_v1_chr18_+_37906739_37906841	0.111307	SOX2.p2	AY013793|Pcdhga10|93722|protocadherin gamma subfamily A, 10	NM_033593|Pcdhga10|93722|protocadherin gamma subfamily A, 10
mm9_v1_chr1_-_135972341_135972341	0.111229	SOX2.p2	
mm9_v1_chr7_-_23249092_23249093	0.11021	SOX2.p2	BC107204|Gm10670|100042971|predicted gene 10670	NM_001167160|Gm10665|100043058|predicted gene 10665	NM_001167161|Gm10670|100042971|predicted gene 10670
mm9_v1_chr2_+_121282841_121282867	0.109662	SOX2.p2	AK168506|2310003F16Rik|67693|RIKEN cDNA 2310003F16 gene	BC021588|2310003F16Rik|67693|RIKEN cDNA 2310003F16 gene
mm9_v1_chr11_-_50700944_50701002	0.109261	SOX2.p2	BC049793|Zfp454|237758|zinc finger protein 454	NM_172794|Zfp454|237758|zinc finger protein 454	AK046117|Zfp454|237758|zinc finger protein 454
mm9_v1_chr11_+_87405628_87405720	0.109246	SOX2.p2	AF262986|Mtmr4|170749|myotubularin related protein 4	NM_133215|Mtmr4|170749|myotubularin related protein 4	BC058091|Mtmr4|170749|myotubularin related protein 4	BC058364|Mtmr4|170749|myotubularin related protein 4
mm9_v1_chr5_+_8660076_8660096	0.109208	SOX2.p2	M30697|Abcb1a|18671|ATP-binding cassette, sub-family B (MDR/TAP), member 1A	AK008292|Abcb1a|18671|ATP-binding cassette, sub-family B (MDR/TAP), member 1A	M33581|Abcb1a|18671|ATP-binding cassette, sub-family B (MDR/TAP), member 1A	NM_011076|Abcb1a|18671|ATP-binding cassette, sub-family B (MDR/TAP), member 1A
mm9_v1_chr19_-_41970627_41970698	0.108786	SOX2.p2	BC062977|Rrp12|107094|ribosomal RNA processing 12 homolog (S. cerevisiae)	NM_199447|Rrp12|107094|ribosomal RNA processing 12 homolog (S. cerevisiae)	AK146550|Rrp12|107094|ribosomal RNA processing 12 homolog (S. cerevisiae)	BC056232|Rrp12|107094|ribosomal RNA processing 12 homolog (S. cerevisiae)
mm9_v1_chrX_-_92391841_92391855	0.108493	SOX2.p2	AK163874|Arhgef9|236915|CDC42 guanine nucleotide exchange factor (GEF) 9
mm9_v1_chr15_+_74551611_74551685	0.108448	SOX2.p2	BC047266|4930572J05Rik|223626|RIKEN cDNA 4930572J05 gene	NM_198607|4930572J05Rik|223626|RIKEN cDNA 4930572J05 gene
mm9_v1_chr8_+_35217633_35217673	0.108093	SOX2.p2	BC022616|Tmem66|67887|transmembrane protein 66	AK093942|Tmem66|67887|transmembrane protein 66
mm9_v1_chr9_+_18208861_18208863	0.10761	SOX2.p2	AK139937|Ubtfl1|546118|upstream binding transcription factor, RNA polymerase I-like 1	NM_001033793|Ubtfl1|546118|upstream binding transcription factor, RNA polymerase I-like 1	AK163257|Ubtfl1|546118|upstream binding transcription factor, RNA polymerase I-like 1
mm9_v1_chr9_+_4376532_4376599	0.107047	SOX2.p2	AK032884|8430410K20Rik|78100|RIKEN cDNA 8430410K20 gene	AK020232|8430410K20Rik|78100|RIKEN cDNA 8430410K20 gene	AK132023|8430410K20Rik|78100|RIKEN cDNA 8430410K20 gene
mm9_v1_chr8_-_85966482_85966569	0.106297	SOX2.p2	NM_019708|Scoc|56367|short coiled-coil protein
mm9_v1_chr4_+_129168433_129168515	0.105805	SOX2.p2	NM_001085491|1700125D06Rik|68233|RIKEN cDNA 1700125D06 gene	AK018987|1700125D06Rik|68233|RIKEN cDNA 1700125D06 gene	AK006760|1700125D06Rik|68233|RIKEN cDNA 1700125D06 gene	AK018964|1700125D06Rik|68233|RIKEN cDNA 1700125D06 gene	AK018907|1700125D06Rik|68233|RIKEN cDNA 1700125D06 gene	BC048660|1700125D06Rik|68233|RIKEN cDNA 1700125D06 gene
mm9_v1_chr12_-_20821426_20821639	0.10573	SOX2.p2	AK006529|1700030C10Rik|69513|RIKEN cDNA 1700030C10 gene	AK041326|1700030C10Rik|69513|RIKEN cDNA 1700030C10 gene	BC050987|1700030C10Rik|69513|RIKEN cDNA 1700030C10 gene	BC100365|1700030C10Rik|69513|RIKEN cDNA 1700030C10 gene
mm9_v1_chr15_-_99305127_99305160	0.10552	SOX2.p2	BC016225|Bcdin3d|75284|BCDIN3 domain containing	BC078455|Bcdin3d|75284|BCDIN3 domain containing	AK016154|Bcdin3d|75284|BCDIN3 domain containing	NM_029236|Bcdin3d|75284|BCDIN3 domain containing
mm9_v1_chr10_-_14425271_14425365	0.105501	SOX2.p2	AK009227|Vta1|66201|Vps20-associated 1 homolog (S. cerevisiae)	BC026752|Vta1|66201|Vps20-associated 1 homolog (S. cerevisiae)	AK002611|Vta1|66201|Vps20-associated 1 homolog (S. cerevisiae)	NM_025418|Vta1|66201|Vps20-associated 1 homolog (S. cerevisiae)	AK003213|Vta1|66201|Vps20-associated 1 homolog (S. cerevisiae)	AK004323|Vta1|66201|Vps20-associated 1 homolog (S. cerevisiae)
mm9_v1_chr17_-_87846158_87846274	0.10516	SOX2.p2	BC021347|Calm2|12314|calmodulin 2	BC051444|Calm2|12314|calmodulin 2	BC100301|Calm2|12314|calmodulin 2	AK013068|Calm2|12314|calmodulin 2	AK012247|Calm2|12314|calmodulin 2	AK168741|Calm2|12314|calmodulin 2	AK005089|Calm2|12314|calmodulin 2	AK012564|Calm2|12314|calmodulin 2	AK161268|Calm2|12314|calmodulin 2	AK161984|Calm2|12314|calmodulin 2	AK152303|Calm2|12314|calmodulin 2	L31642|Calm2|12314|calmodulin 2	AK160636|Calm2|12314|calmodulin 2	NM_007589|Calm2|12314|calmodulin 2
mm9_v1_chr2_-_22751051_22751075	0.103859	SOX2.p2	AK079472|A130006I12Rik|319264|RIKEN cDNA A130006I12 gene
mm9_v1_chr14_-_51544497_51544585	0.103367	SOX2.p2	BC002296|Osgep|66246|O-sialoglycoprotein endopeptidase	AK167893|Osgep|66246|O-sialoglycoprotein endopeptidase	AK049955|Osgep|66246|O-sialoglycoprotein endopeptidase	AK005291|Osgep|66246|O-sialoglycoprotein endopeptidase	AK049480|Osgep|66246|O-sialoglycoprotein endopeptidase	AK157554|Osgep|66246|O-sialoglycoprotein endopeptidase	AK166415|Osgep|66246|O-sialoglycoprotein endopeptidase	AK076246|Osgep|66246|O-sialoglycoprotein endopeptidase	AK088346|Osgep|66246|O-sialoglycoprotein endopeptidase	AK142730|Osgep|66246|O-sialoglycoprotein endopeptidase	NM_133676|Osgep|66246|O-sialoglycoprotein endopeptidase
mm9_v1_chr12_+_85029101_85029215	0.103294	SOX2.p2	BC014744|Psen1|19164|presenilin 1	BC071233|Psen1|19164|presenilin 1	AK134615|Psen1|19164|presenilin 1	AK148101|Psen1|19164|presenilin 1	AK165984|Psen1|19164|presenilin 1	L42177|Psen1|19164|presenilin 1	AK134232|Psen1|19164|presenilin 1	BC030409|Psen1|19164|presenilin 1
mm9_v1_chr11_-_58426971_58426993	0.103251	SOX2.p2	BC019553|2210407C18Rik|78354|RIKEN cDNA 2210407C18 gene	NM_144544|2210407C18Rik|78354|RIKEN cDNA 2210407C18 gene
mm9_v1_chr13_-_23714425_23714427	0.103028	SOX2.p2	BC089600|Hist1h1e|50709|histone cluster 1, H1e	NM_015787|Hist1h1e|50709|histone cluster 1, H1e
mm9_v1_chr4_-_34562138_34562200	0.10293	SOX2.p2	AB190257|Orc3|50793|origin recognition complex, subunit 3	BC061252|Orc3|50793|origin recognition complex, subunit 3	AK145324|Orc3|50793|origin recognition complex, subunit 3	AK045388|Orc3|50793|origin recognition complex, subunit 3	AJ132830|Orc3|50793|origin recognition complex, subunit 3	NM_001159563|Orc3|50793|origin recognition complex, subunit 3	NM_015824|Orc3|50793|origin recognition complex, subunit 3	AK086579|Orc3|50793|origin recognition complex, subunit 3
mm9_v1_chr6_-_71858736_71858760	0.102785	SOX2.p2	AK032831|Ptcd3|69956|pentatricopeptide repeat domain 3	AK011665|Ptcd3|69956|pentatricopeptide repeat domain 3	AK146005|Ptcd3|69956|pentatricopeptide repeat domain 3	AK172480|Ptcd3|69956|pentatricopeptide repeat domain 3	BC115434|Ptcd3|69956|pentatricopeptide repeat domain 3	AK146172|Ptcd3|69956|pentatricopeptide repeat domain 3	NM_027275|Ptcd3|69956|pentatricopeptide repeat domain 3
mm9_v1_chr18_+_77303959_77304054	0.102144	SOX2.p2	AK078813|Pias2|17344|protein inhibitor of activated STAT 2	AK149142|Pias2|17344|protein inhibitor of activated STAT 2	AK086653|Pias2|17344|protein inhibitor of activated STAT 2	AF201391|Pias2|17344|protein inhibitor of activated STAT 2
mm9_v1_chr10_-_57252184_57252250	0.102033	SOX2.p2	BC017148|Serinc1|56442|serine incorporator 1	AK159280|Serinc1|56442|serine incorporator 1
mm9_v1_chr6_-_89986834_89986834	0.101823	SOX2.p2	NM_053218|Vmn1r48|113845|vomeronasal 1 receptor 48
mm9_v1_chr13_-_56236910_56236913	0.101008	SOX2.p2	NM_001159513|H2afy|26914|H2A histone family, member Y	NM_001159514|H2afy|26914|H2A histone family, member Y	NM_001159515|H2afy|26914|H2A histone family, member Y	NM_012015|H2afy|26914|H2A histone family, member Y
mm9_v1_chr5_-_105411580_105411736	0.100807	SOX2.p2	BC029095|Abcg3|27405|ATP-binding cassette, sub-family G (WHITE), member 3	AK037614|Abcg3|27405|ATP-binding cassette, sub-family G (WHITE), member 3	AF324242|Abcg3|27405|ATP-binding cassette, sub-family G (WHITE), member 3	AK051880|Abcg3|27405|ATP-binding cassette, sub-family G (WHITE), member 3	AK156626|Abcg3|27405|ATP-binding cassette, sub-family G (WHITE), member 3	BC138773|Abcg3|27405|ATP-binding cassette, sub-family G (WHITE), member 3	BC138772|Abcg3|27405|ATP-binding cassette, sub-family G (WHITE), member 3	NM_030239|Abcg3|27405|ATP-binding cassette, sub-family G (WHITE), member 3	AK030831|Abcg3|27405|ATP-binding cassette, sub-family G (WHITE), member 3
mm9_v1_chr11_-_86570918_86571097	0.100763	SOX2.p2	AK158438|Cltc|67300|clathrin, heavy polypeptide (Hc)	BC079897|Cltc|67300|clathrin, heavy polypeptide (Hc)	NM_001003908|Cltc|67300|clathrin, heavy polypeptide (Hc)	AK171732|Cltc|67300|clathrin, heavy polypeptide (Hc)	AK156869|Cltc|67300|clathrin, heavy polypeptide (Hc)
mm9_v1_chr7_+_134388553_134388625	0.100652	SOX2.p2	BC052091|Zfp771|244216|zinc finger protein 771	BC062882|Zfp771|244216|zinc finger protein 771
mm9_v1_chr2_-_38640034_38640034	0.100538	SOX2.p2	NM_001159548|Nr6a1|14536|nuclear receptor subfamily 6, group A, member 1	NM_001159549|Nr6a1|14536|nuclear receptor subfamily 6, group A, member 1
mm9_v1_chr14_+_62218348_62218392	0.099664	SOX2.p2	NM_023233|Trim13|66597|tripartite motif-containing 13	AK013959|Trim13|66597|tripartite motif-containing 13	AK017850|Trim13|66597|tripartite motif-containing 13
mm9_v1_chr15_-_76554119_76554177	0.0992265	SOX2.p2	AK186599|C030006K11Rik|223665|RIKEN cDNA C030006K11 gene
mm9_v1_chr8_+_73118329_73118423	0.0990462	SOX2.p2	AF288525|Isyna1|71780|myo-inositol 1-phosphate synthase A1	NM_023627|Isyna1|71780|myo-inositol 1-phosphate synthase A1	AK137089|Isyna1|71780|myo-inositol 1-phosphate synthase A1	BC003458|Isyna1|71780|myo-inositol 1-phosphate synthase A1	AK005029|Isyna1|71780|myo-inositol 1-phosphate synthase A1	AK079323|Isyna1|71780|myo-inositol 1-phosphate synthase A1
mm9_v1_chr13_+_54890763_54890824	0.0989942	SOX2.p2	AK166272|Tspan17|74257|tetraspanin 17	NM_028841|Tspan17|74257|tetraspanin 17	AK171691|Tspan17|74257|tetraspanin 17	BC010346|Tspan17|74257|tetraspanin 17	AK008761|Tspan17|74257|tetraspanin 17
mm9_v1_chr2_-_35972131_35972337	0.0989311	SOX2.p2	AK220096|Rbm18|67889|RNA binding motif protein 18
mm9_v1_chr9_-_24956188_24956257	0.0986154	SOX2.p2	AK164769|Herpud2|80517|HERPUD family member 2	AK019862|Herpud2|80517|HERPUD family member 2
mm9_v1_chr11_+_85639174_85639217	0.0984518	SOX2.p2	
mm9_v1_chr9_-_24578684_24578746	0.0984227	SOX2.p2	AF306667|Tbx20|57246|T-box 20	AK052155|Tbx20|57246|T-box 20	AK052389|Tbx20|57246|T-box 20	NM_020496|Tbx20|57246|T-box 20	NM_194263|Tbx20|57246|T-box 20	AF260557|Tbx20|57246|T-box 20
mm9_v1_chr7_+_22881885_22881885	0.0983454	SOX2.p2	NM_001166748|Vmn1r139|667444|vomeronasal 1 receptor 139
mm9_v1_chr7_+_23546715_23546715	0.0983454	SOX2.p2	NM_001166754|Vmn1r157|667551|vomeronasal 1 receptor 157	NM_001166845|Vmn1r109|100043559|vomeronasal 1 receptor 109
mm9_v1_chr7_+_22399110_22399110	0.0983454	SOX2.p2	NM_001166748|Vmn1r139|667444|vomeronasal 1 receptor 139
mm9_v1_chr7_+_21556203_21556203	0.0983454	SOX2.p2	NM_001166847|Vmn1r112|100043569|vomeronasal 1 receptor 112
mm9_v1_chr11_+_6289339_6289394	0.0977527	SOX2.p2	NM_028601|Zmiz2|52915|zinc finger, MIZ-type containing 2
mm9_v1_chr2_-_148597157_148597232	0.097226	SOX2.p2	BC100526|Cst11|78240|cystatin 11	AF454373|Cst11|78240|cystatin 11	AK020300|Cst11|78240|cystatin 11	NM_030059|Cst11|78240|cystatin 11
mm9_v1_chr15_-_101616888_101616888	0.0963232	SOX2.p2	NM_213728|Krt72-ps|105866|keratin 72, pseudogene
mm9_v1_chr12_+_75028976_75029036	0.0958865	SOX2.p2	AK076395|Hif1a|15251|hypoxia inducible factor 1, alpha subunit
mm9_v1_chrX_+_35669345_35669443	0.0943477	SOX2.p2	BC137923|Atp1b4|67821|ATPase, (Na+)/K+ transporting, beta 4 polypeptide	BC137924|Atp1b4|67821|ATPase, (Na+)/K+ transporting, beta 4 polypeptide	AK053500|Atp1b4|67821|ATPase, (Na+)/K+ transporting, beta 4 polypeptide	AF348324|Atp1b4|67821|ATPase, (Na+)/K+ transporting, beta 4 polypeptide	AF348325|Atp1b4|67821|ATPase, (Na+)/K+ transporting, beta 4 polypeptide	NM_133690|Atp1b4|67821|ATPase, (Na+)/K+ transporting, beta 4 polypeptide
mm9_v1_chr2_+_154439056_154439103	0.0941699	SOX2.p2	AK089176|Zfp341|228807|zinc finger protein 341	BC057098|Zfp341|228807|zinc finger protein 341	NM_199304|Zfp341|228807|zinc finger protein 341
mm9_v1_chr4_-_96220030_96220248	0.093405	SOX2.p2	AK180579|Cyp2j6|13110|cytochrome P450, family 2, subfamily j, polypeptide 6	AK186838|Cyp2j6|13110|cytochrome P450, family 2, subfamily j, polypeptide 6	AK193212|Cyp2j6|13110|cytochrome P450, family 2, subfamily j, polypeptide 6	AK210777|Cyp2j6|13110|cytochrome P450, family 2, subfamily j, polypeptide 6	AK078893|Cyp2j6|13110|cytochrome P450, family 2, subfamily j, polypeptide 6	AK165663|Cyp2j6|13110|cytochrome P450, family 2, subfamily j, polypeptide 6	AK038636|Cyp2j6|13110|cytochrome P450, family 2, subfamily j, polypeptide 6
mm9_v1_chr7_-_134537132_134537134	0.0932997	SOX2.p2	BC010442|E430018J23Rik|101604|RIKEN cDNA E430018J23 gene	AK088474|E430018J23Rik|101604|RIKEN cDNA E430018J23 gene	NM_198011|E430018J23Rik|101604|RIKEN cDNA E430018J23 gene
mm9_v1_chr8_-_72149070_72149075	0.0929372	SOX2.p2	AK139223|Zfp868|234362|zinc finger protein 868	NM_001045553|Zfp868|234362|zinc finger protein 868
mm9_v1_chr9_+_26541302_26541653	0.0928747	SOX2.p2	AK082739|B3gat1|76898|beta-1,3-glucuronyltransferase 1 (glucuronosyltransferase P)	AK220561|B3gat1|76898|beta-1,3-glucuronyltransferase 1 (glucuronosyltransferase P)	AK044599|B3gat1|76898|beta-1,3-glucuronyltransferase 1 (glucuronosyltransferase P)	AK041316|B3gat1|76898|beta-1,3-glucuronyltransferase 1 (glucuronosyltransferase P)	AB055781|B3gat1|76898|beta-1,3-glucuronyltransferase 1 (glucuronosyltransferase P)	AK003020|B3gat1|76898|beta-1,3-glucuronyltransferase 1 (glucuronosyltransferase P)
mm9_v1_chr7_-_21060272_21060273	0.0927313	SOX2.p2	BC107204|Gm10670|100042971|predicted gene 10670	NM_001167160|Gm10665|100043058|predicted gene 10665	NM_001167161|Gm10670|100042971|predicted gene 10670
mm9_v1_chr19_+_18824472_18824480	0.0924786	SOX2.p2	AY135644|Trpm6|225997|transient receptor potential cation channel, subfamily M, member 6	NM_153417|Trpm6|225997|transient receptor potential cation channel, subfamily M, member 6	BC145223|Trpm6|225997|transient receptor potential cation channel, subfamily M, member 6
mm9_v1_chr13_-_98976043_98976393	0.0924009	SOX2.p2	BC138030|Rgnef|110596|Rho-guanine nucleotide exchange factor	BC075734|Rgnef|110596|Rho-guanine nucleotide exchange factor	BC098331|Rgnef|110596|Rho-guanine nucleotide exchange factor	NM_012026|Rgnef|110596|Rho-guanine nucleotide exchange factor	U73199|Rgnef|110596|Rho-guanine nucleotide exchange factor	BC022978|Rgnef|110596|Rho-guanine nucleotide exchange factor	AK173325|Rgnef|110596|Rho-guanine nucleotide exchange factor
mm9_v1_chr1_+_43787442_43787446	0.0918696	SOX2.p2	AK049805|1500015O10Rik|78896|RIKEN cDNA 1500015O10 gene	NM_024283|1500015O10Rik|78896|RIKEN cDNA 1500015O10 gene
mm9_v1_chr2_+_151668662_151668699	0.0915497	SOX2.p2	AK020904|Rspo4|228770|R-spondin family, member 4	AK043484|Rspo4|228770|R-spondin family, member 4	NM_001040689|Rspo4|228770|R-spondin family, member 4	BC048707|Rspo4|228770|R-spondin family, member 4	BC116367|Rspo4|228770|R-spondin family, member 4
mm9_v1_chr4_+_107640938_107641047	0.091369	SOX2.p2	BC030400|Slc1a7|242607|solute carrier family 1 (glutamate transporter), member 7	NM_146255|Slc1a7|242607|solute carrier family 1 (glutamate transporter), member 7	AK044671|Slc1a7|242607|solute carrier family 1 (glutamate transporter), member 7	AK044586|Slc1a7|242607|solute carrier family 1 (glutamate transporter), member 7
mm9_v1_chr12_+_99506844_99506881	0.091353	SOX2.p2	AK134113|Gpr65|14744|G-protein coupled receptor 65	NM_008152|Gpr65|14744|G-protein coupled receptor 65	U39827|Gpr65|14744|G-protein coupled receptor 65	AK142853|Gpr65|14744|G-protein coupled receptor 65
mm9_v1_chr18_+_37649118_37649272	0.0908495	SOX2.p2	AK140341|Pcdhb18|93889|protocadherin beta 18	NM_053143|Pcdhb18|93889|protocadherin beta 18	BC099958|Pcdhb18|93889|protocadherin beta 18	AY013779|Pcdhb18|93889|protocadherin beta 18
mm9_v1_chr12_-_86039703_86039802	0.0900264	SOX2.p2	AY993933|Tmem90a|627191|transmembrane protein 90a	AK140195|Tmem90a|627191|transmembrane protein 90a	NM_001033334|Tmem90a|627191|transmembrane protein 90a	AY993934|Tmem90a|627191|transmembrane protein 90a
mm9_v1_chr6_+_86321479_86321568	0.0900084	SOX2.p2	BC051470|Snrpg|68011|small nuclear ribonucleoprotein polypeptide G	AK013235|Snrpg|68011|small nuclear ribonucleoprotein polypeptide G	NM_026506|Snrpg|68011|small nuclear ribonucleoprotein polypeptide G	AK011129|Snrpg|68011|small nuclear ribonucleoprotein polypeptide G	AK012802|Snrpg|68011|small nuclear ribonucleoprotein polypeptide G	BC094411|Snrpg|68011|small nuclear ribonucleoprotein polypeptide G	BC027499|Snrpg|68011|small nuclear ribonucleoprotein polypeptide G	AK017852|Snrpg|68011|small nuclear ribonucleoprotein polypeptide G
mm9_v1_chr7_-_22546493_22546493	0.089751	SOX2.p2	NM_001167164|Gm4214|100043079|predicted gene 4214	NM_001167165|Gm4175|100043019|predicted gene 4175
mm9_v1_chr7_-_23769691_23769691	0.089751	SOX2.p2	NM_001167164|Gm4214|100043079|predicted gene 4214	NM_001167165|Gm4175|100043019|predicted gene 4175
mm9_v1_chr3_-_54858963_54858976	0.0895501	SOX2.p2	AK077114|Ccna1|12427|cyclin A1	NM_007628|Ccna1|12427|cyclin A1	X84311|Ccna1|12427|cyclin A1
mm9_v1_chr1_-_99873795_99873812	0.089518	SOX2.p2	BC129869|Pam|18484|peptidylglycine alpha-amidating monooxygenase
mm9_v1_chr17_-_13102778_13102865	0.0886624	SOX2.p2	BC158033|Pnldc1|240023|poly(A)-specific ribonuclease (PARN)-like domain containing 1	BC172002|Pnldc1|240023|poly(A)-specific ribonuclease (PARN)-like domain containing 1	NM_001034866|Pnldc1|240023|poly(A)-specific ribonuclease (PARN)-like domain containing 1
mm9_v1_chr4_-_44180323_44180519	0.0884818	SOX2.p2	BC062976|Rnf38|73469|ring finger protein 38	BC060730|Rnf38|73469|ring finger protein 38	NM_175201|Rnf38|73469|ring finger protein 38	AK006888|Rnf38|73469|ring finger protein 38
mm9_v1_chr3_-_92261456_92261538	0.0881275	SOX2.p2	NM_011478|Sprr3|20766|small proline-rich protein 3	BC125629|Sprr3|20766|small proline-rich protein 3
mm9_v1_chr11_-_68787314_68787359	0.0880211	SOX2.p2	BC087921|Rangrf|57785|RAN guanine nucleotide release factor	NM_001101644|Gm4535|100043585|predicted gene 4535	NM_021329|Rangrf|57785|RAN guanine nucleotide release factor	AF243512|Rangrf|57785|RAN guanine nucleotide release factor	BC038470|Rangrf|57785|RAN guanine nucleotide release factor	AK010288|Rangrf|57785|RAN guanine nucleotide release factor
mm9_v1_chr8_-_124102548_124102765	0.0879572	SOX2.p2	AB041586|Fbxo31|76454|F-box protein 31	AK163641|Fbxo31|76454|F-box protein 31	BC026929|Fbxo31|76454|F-box protein 31	AK140412|Fbxo31|76454|F-box protein 31	NM_133765|Fbxo31|76454|F-box protein 31
mm9_v1_chr17_-_57199014_57199114	0.087905	SOX2.p2	AK206310|Slc25a23|66972|solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23	AK158821|Slc25a23|66972|solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23
mm9_v1_chr8_+_3493117_3493286	0.0878302	SOX2.p2	AK155446|Zfp358|140482|zinc finger protein 358	NM_080461|Zfp358|140482|zinc finger protein 358	AF397208|Zfp358|140482|zinc finger protein 358
mm9_v1_chr16_-_96349334_96349335	0.0874668	SOX2.p2	AK010763|Hmgn1|15312|high mobility group nucleosomal binding domain 1
mm9_v1_chr6_+_125046576_125046586	0.0856274	SOX2.p2	AK020564|Chd4|107932|chromodomain helicase DNA binding protein 4
mm9_v1_chr17_-_74715708_74715816	0.0850287	SOX2.p2	NM_001146222|Dpy30|66310|dpy-30 homolog (C. elegans)	BC002240|Dpy30|66310|dpy-30 homolog (C. elegans)	AK013073|Dpy30|66310|dpy-30 homolog (C. elegans)	AK077902|Dpy30|66310|dpy-30 homolog (C. elegans)	NM_001146223|Dpy30|66310|dpy-30 homolog (C. elegans)
mm9_v1_chr11_+_89891661_89891661	0.0850093	SOX2.p2	AK007878|Tmem100|67888|transmembrane protein 100	NM_026433|Tmem100|67888|transmembrane protein 100
mm9_v1_chr6_-_49164469_49164732	0.0849352	SOX2.p2	AB046173|Igf2bp3|140488|insulin-like growth factor 2 mRNA binding protein 3	BC045138|Igf2bp3|140488|insulin-like growth factor 2 mRNA binding protein 3	BC049082|Igf2bp3|140488|insulin-like growth factor 2 mRNA binding protein 3	AK011797|Igf2bp3|140488|insulin-like growth factor 2 mRNA binding protein 3	AK088465|Igf2bp3|140488|insulin-like growth factor 2 mRNA binding protein 3	AK011689|Igf2bp3|140488|insulin-like growth factor 2 mRNA binding protein 3
mm9_v1_chr7_-_26539409_26539730	0.0847514	SOX2.p2	AK087545|Hnrnpul1|232989|heterogeneous nuclear ribonucleoprotein U-like 1	AK042090|Hnrnpul1|232989|heterogeneous nuclear ribonucleoprotein U-like 1	NM_178089|Hnrnpul1|232989|heterogeneous nuclear ribonucleoprotein U-like 1
mm9_v1_chr19_+_45005608_45005655	0.0844028	SOX2.p2	NM_001081225|Fam178a|226151|family with sequence similarity 178, member A	AK031688|Fam178a|226151|family with sequence similarity 178, member A	AK147588|Fam178a|226151|family with sequence similarity 178, member A	AK020064|Fam178a|226151|family with sequence similarity 178, member A	AK045983|Fam178a|226151|family with sequence similarity 178, member A
mm9_v1_chr16_-_18811669_18811731	0.0837952	SOX2.p2	AF081537|Cdc45|12544|cell division cycle 45 homolog (S. cerevisiae)	AF081538|Cdc45|12544|cell division cycle 45 homolog (S. cerevisiae)	AK147013|Cdc45|12544|cell division cycle 45 homolog (S. cerevisiae)	AJ223729|Cdc45|12544|cell division cycle 45 homolog (S. cerevisiae)	BC006856|Cdc45|12544|cell division cycle 45 homolog (S. cerevisiae)	AF098068|Cdc45|12544|cell division cycle 45 homolog (S. cerevisiae)	AK167850|Cdc45|12544|cell division cycle 45 homolog (S. cerevisiae)	BC028635|Cdc45|12544|cell division cycle 45 homolog (S. cerevisiae)	NM_001161623|Cdc45|12544|cell division cycle 45 homolog (S. cerevisiae)
mm9_v1_chr11_-_74710462_74710503	0.0833317	SOX2.p2	AK122273|Sgsm2|97761|small G protein signaling modulator 2
mm9_v1_chrX_+_13044797_13044798	0.0825759	SOX2.p2	BC035244|Nyx|236690|nyctalopin	NM_173415|Nyx|236690|nyctalopin	BC048381|Nyx|236690|nyctalopin
mm9_v1_chr13_-_14615371_14615494	0.081915	SOX2.p2	AK051569|Hecw1|94253|HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	AK084246|Hecw1|94253|HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	AK086170|Hecw1|94253|HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	AK047678|Hecw1|94253|HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	NM_001081348|Hecw1|94253|HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	AK053694|Hecw1|94253|HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1
mm9_v1_chr13_+_89680457_89680462	0.0818389	SOX2.p2	AK048107|Hapln1|12950|hyaluronan and proteoglycan link protein 1	AK003582|Hapln1|12950|hyaluronan and proteoglycan link protein 1
mm9_v1_chr10_+_127896244_127896376	0.0818212	SOX2.p2	NM_001114096|Smarcc2|68094|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	NM_001114097|Smarcc2|68094|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	NM_198160|Smarcc2|68094|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	BC058720|Smarcc2|68094|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	AK089461|Smarcc2|68094|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	AK170530|Smarcc2|68094|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	AK146971|Smarcc2|68094|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	BC040363|Smarcc2|68094|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2
mm9_v1_chr11_-_99671205_99671209	0.0817318	SOX2.p2	AK009035|Krtap4-13|69464|keratin associated protein 4-13	BC104358|Gm11554|670482|predicted gene 11554	BC104359|Gm11554|670482|predicted gene 11554	BC119472|Gm11554|670482|predicted gene 11554	BC119473|Gm11554|670482|predicted gene 11554	NM_001099313|Gm11554|670482|predicted gene 11554	NM_027087|Krtap4-13|69464|keratin associated protein 4-13
mm9_v1_chrX_-_75098856_75098869	0.0817075	SOX2.p2	AK137501|Pbsn|54192|probasin
mm9_v1_chr4_-_40649942_40649948	0.0816482	SOX2.p2	AY040780|Aptx|66408|aprataxin	AY208844|Aptx|66408|aprataxin	AK077351|Aptx|66408|aprataxin	NM_025545|Aptx|66408|aprataxin
mm9_v1_chr15_-_79272424_79272474	0.0815404	SOX2.p2	BC026127|Csnk1e|27373|casein kinase 1, epsilon	AB028241|Csnk1e|27373|casein kinase 1, epsilon	AB028736|Csnk1e|27373|casein kinase 1, epsilon
mm9_v1_chr3_+_17954500_17954591	0.081084	SOX2.p2	AK047201|Bhlhe22|59058|basic helix-loop-helix family, member e22
mm9_v1_chr11_+_100182042_100182059	0.0810351	SOX2.p2	Z50159|Eif1|20918|eukaryotic translation initiation factor 1
mm9_v1_chr5_+_65194784_65194811	0.0808413	SOX2.p2	BC116938|Klf3|16599|Kruppel-like factor 3 (basic)	BC119214|Klf3|16599|Kruppel-like factor 3 (basic)
mm9_v1_chr1_-_154233721_154233811	0.0801314	SOX2.p2	AK169429|Tsen15|66637|tRNA splicing endonuclease 15 homolog (S. cerevisiae)	BC024342|Tsen15|66637|tRNA splicing endonuclease 15 homolog (S. cerevisiae)	AK004261|Tsen15|66637|tRNA splicing endonuclease 15 homolog (S. cerevisiae)	AK053666|Tsen15|66637|tRNA splicing endonuclease 15 homolog (S. cerevisiae)	AK011608|Tsen15|66637|tRNA splicing endonuclease 15 homolog (S. cerevisiae)	BC145701|Tsen15|66637|tRNA splicing endonuclease 15 homolog (S. cerevisiae)	AK017650|Tsen15|66637|tRNA splicing endonuclease 15 homolog (S. cerevisiae)	NM_025677|Tsen15|66637|tRNA splicing endonuclease 15 homolog (S. cerevisiae)
mm9_v1_chr11_+_103053625_103053722	0.080008	SOX2.p2	AK158820|Fmnl1|57778|formin-like 1
mm9_v1_chr3_+_131227808_131227844	0.0798664	SOX2.p2	AK160875|Papss1|23971|3'-phosphoadenosine 5'-phosphosulfate synthase 1
mm9_v1_chr15_-_81560309_81560370	0.0798073	SOX2.p2	AK035571|Rangap1|19387|RAN GTPase activating protein 1	AK042930|Rangap1|19387|RAN GTPase activating protein 1	AK133905|Rangap1|19387|RAN GTPase activating protein 1	AK159525|Rangap1|19387|RAN GTPase activating protein 1	BC066213|Rangap1|19387|RAN GTPase activating protein 1	U08110|Rangap1|19387|RAN GTPase activating protein 1	NM_001146174|Rangap1|19387|RAN GTPase activating protein 1	NM_011241|Rangap1|19387|RAN GTPase activating protein 1
mm9_v1_chr14_-_55305438_55305460	0.0796786	SOX2.p2	AK122342|Acin1|56215|apoptotic chromatin condensation inducer 1	AK012337|Acin1|56215|apoptotic chromatin condensation inducer 1	AK050467|Acin1|56215|apoptotic chromatin condensation inducer 1	BC075691|Acin1|56215|apoptotic chromatin condensation inducer 1	AK030449|Acin1|56215|apoptotic chromatin condensation inducer 1
mm9_v1_chr14_-_64162562_64162594	0.079584	SOX2.p2	AK152320|Mtmr9|210376|myotubularin related protein 9
mm9_v1_chr8_-_13890244_13890296	0.0795592	SOX2.p2	BC029192|2410022L05Rik|66423|RIKEN cDNA 2410022L05 gene	AK010573|2410022L05Rik|66423|RIKEN cDNA 2410022L05 gene	AK008882|2410022L05Rik|66423|RIKEN cDNA 2410022L05 gene	NM_025556|2410022L05Rik|66423|RIKEN cDNA 2410022L05 gene
mm9_v1_chr17_+_25023618_25023724	0.0787581	SOX2.p2	NM_001163750|Spsb3|79043|splA/ryanodine receptor domain and SOCS box containing 3	NM_001163751|Spsb3|79043|splA/ryanodine receptor domain and SOCS box containing 3	BC072556|Spsb3|79043|splA/ryanodine receptor domain and SOCS box containing 3	AK076170|Spsb3|79043|splA/ryanodine receptor domain and SOCS box containing 3	AK082768|Spsb3|79043|splA/ryanodine receptor domain and SOCS box containing 3	AK220234|Spsb3|79043|splA/ryanodine receptor domain and SOCS box containing 3	AK156579|Spsb3|79043|splA/ryanodine receptor domain and SOCS box containing 3	AK167474|Spsb3|79043|splA/ryanodine receptor domain and SOCS box containing 3
mm9_v1_chr6_+_92041408_92041534	0.0785737	SOX2.p2	NM_011630|Nr2c2|22026|nuclear receptor subfamily 2, group C, member 2	AK157305|Nr2c2|22026|nuclear receptor subfamily 2, group C, member 2
mm9_v1_chr19_-_33466561_33466800	0.0783385	SOX2.p2	DQ788834|Rnls|67795|renalase, FAD-dependent amine oxidase	BC052355|Rnls|67795|renalase, FAD-dependent amine oxidase	AK014866|Rnls|67795|renalase, FAD-dependent amine oxidase	AK018322|Rnls|67795|renalase, FAD-dependent amine oxidase	AK170321|Rnls|67795|renalase, FAD-dependent amine oxidase	NM_001146342|Rnls|67795|renalase, FAD-dependent amine oxidase	NM_001167818|Rnls|67795|renalase, FAD-dependent amine oxidase
mm9_v1_chr19_-_41281263_41281324	0.0780625	SOX2.p2	BC132537|Tll2|24087|tolloid-like 2	BC145132|Tll2|24087|tolloid-like 2	NM_011904|Tll2|24087|tolloid-like 2	AF073526|Tll2|24087|tolloid-like 2
mm9_v1_chr2_+_31805852_31805870	0.0779794	SOX2.p2	AK028955|Aif1l|108897|allograft inflammatory factor 1-like	AB035322|Aif1l|108897|allograft inflammatory factor 1-like
mm9_v1_chr11_+_20991293_20991320	0.0775163	SOX2.p2	AK020915|Peli1|67245|pellino 1
mm9_v1_chr2_-_102026486_102026616	0.077234	SOX2.p2	AK032208|Ldlrad3|241576|low density lipoprotein receptor class A domain containing 3	AK029683|Ldlrad3|241576|low density lipoprotein receptor class A domain containing 3	NM_178886|Ldlrad3|241576|low density lipoprotein receptor class A domain containing 3	BC138178|Ldlrad3|241576|low density lipoprotein receptor class A domain containing 3	BC145174|Ldlrad3|241576|low density lipoprotein receptor class A domain containing 3	BC138177|Ldlrad3|241576|low density lipoprotein receptor class A domain containing 3
mm9_v1_chr3_+_102975621_102975695	0.0769754	SOX2.p2	NM_026602|Bcas2|68183|breast carcinoma amplified sequence 2	BC013627|Bcas2|68183|breast carcinoma amplified sequence 2	BC037062|Bcas2|68183|breast carcinoma amplified sequence 2	AK018786|Bcas2|68183|breast carcinoma amplified sequence 2	AK005825|Bcas2|68183|breast carcinoma amplified sequence 2	AK020098|Bcas2|68183|breast carcinoma amplified sequence 2	AK153513|Bcas2|68183|breast carcinoma amplified sequence 2	AK166967|Bcas2|68183|breast carcinoma amplified sequence 2	AY043239|Bcas2|68183|breast carcinoma amplified sequence 2	BC023382|Bcas2|68183|breast carcinoma amplified sequence 2
mm9_v1_chr6_+_54276835_54277005	0.0765621	SOX2.p2	AK136438|Prr15|78004|proline rich 15	BC055838|Prr15|78004|proline rich 15	AK021401|Prr15|78004|proline rich 15	AJ132433|Prr15|78004|proline rich 15	NM_030024|Prr15|78004|proline rich 15
mm9_v1_chr6_+_3944011_3944021	0.0764891	SOX2.p2	AK020863|Gngt1|14699|guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	AK020903|Gngt1|14699|guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	NM_010314|Gngt1|14699|guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	BC023064|Gngt1|14699|guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1
mm9_v1_chr3_+_87885892_87885972	0.0759531	SOX2.p2	BC151102|Iqgap3|404710|IQ motif containing GTPase activating protein 3	AK050913|Iqgap3|404710|IQ motif containing GTPase activating protein 3	AK162700|Iqgap3|404710|IQ motif containing GTPase activating protein 3	BC068159|Iqgap3|404710|IQ motif containing GTPase activating protein 3	NM_001033484|Iqgap3|404710|IQ motif containing GTPase activating protein 3
mm9_v1_chr16_-_15966921_15966936	0.0758176	SOX2.p2	BC069859|2310008H04Rik|224008|RIKEN cDNA 2310008H04 gene
mm9_v1_chr16_+_32877857_32877985	0.0757753	SOX2.p2	NM_001159349|Fyttd1|69823|forty-two-three domain containing 1	NM_027226|Fyttd1|69823|forty-two-three domain containing 1	AK139638|Fyttd1|69823|forty-two-three domain containing 1	AK161252|Fyttd1|69823|forty-two-three domain containing 1	AK008130|Fyttd1|69823|forty-two-three domain containing 1	AK050479|Fyttd1|69823|forty-two-three domain containing 1	AK157602|Fyttd1|69823|forty-two-three domain containing 1	AK166032|Fyttd1|69823|forty-two-three domain containing 1	AK170511|Fyttd1|69823|forty-two-three domain containing 1	AK014447|Fyttd1|69823|forty-two-three domain containing 1	BC010204|Fyttd1|69823|forty-two-three domain containing 1	AK050448|Fyttd1|69823|forty-two-three domain containing 1	AK165633|Fyttd1|69823|forty-two-three domain containing 1	BC028253|Fyttd1|69823|forty-two-three domain containing 1	AK029785|Fyttd1|69823|forty-two-three domain containing 1	AJ344096|Fyttd1|69823|forty-two-three domain containing 1
mm9_v1_chr11_-_72609515_72609577	0.0752352	SOX2.p2	AK138991|Cyb5d2|192986|cytochrome b5 domain containing 2	AK034043|Cyb5d2|192986|cytochrome b5 domain containing 2	AK080730|Cyb5d2|192986|cytochrome b5 domain containing 2
mm9_v1_chr11_-_98054219_98054219	0.0744567	SOX2.p2	AF000294|Med1|19014|mediator complex subunit 1	NM_013634|Med1|19014|mediator complex subunit 1
mm9_v1_chr16_+_18392675_18392746	0.0743139	SOX2.p2	AK053865|Arvcf|11877|armadillo repeat gene deleted in velo-cardio-facial syndrome	BC051655|Arvcf|11877|armadillo repeat gene deleted in velo-cardio-facial syndrome	BC026727|Arvcf|11877|armadillo repeat gene deleted in velo-cardio-facial syndrome	AK051627|Arvcf|11877|armadillo repeat gene deleted in velo-cardio-facial syndrome	AK044982|Arvcf|11877|armadillo repeat gene deleted in velo-cardio-facial syndrome	AF286214|Arvcf|11877|armadillo repeat gene deleted in velo-cardio-facial syndrome	AF286215|Arvcf|11877|armadillo repeat gene deleted in velo-cardio-facial syndrome
mm9_v1_chr15_-_43002356_43002397	0.073688	SOX2.p2	AK087485|Rspo2|239405|R-spondin 2 homolog (Xenopus laevis)	NM_172815|Rspo2|239405|R-spondin 2 homolog (Xenopus laevis)	AK052457|Rspo2|239405|R-spondin 2 homolog (Xenopus laevis)	AK049891|Rspo2|239405|R-spondin 2 homolog (Xenopus laevis)
mm9_v1_chr12_-_84828657_84828685	0.0732887	SOX2.p2	AF362750|Dpf3|70127|D4, zinc and double PHD fingers, family 3	FJ151218|Dpf3|70127|D4, zinc and double PHD fingers, family 3	NM_058212|Dpf3|70127|D4, zinc and double PHD fingers, family 3	AK039011|Dpf3|70127|D4, zinc and double PHD fingers, family 3	AK032649|Dpf3|70127|D4, zinc and double PHD fingers, family 3	AK012970|Dpf3|70127|D4, zinc and double PHD fingers, family 3
mm9_v1_chr6_+_6813333_6813333	0.0732437	SOX2.p2	EF535989|Dlx6|13396|distal-less homeobox 6	EF535990|Dlx6|13396|distal-less homeobox 6	NM_010057|Dlx6|13396|distal-less homeobox 6
mm9_v1_chr14_-_52532988_52533037	0.0731441	SOX2.p2	BC012963|Ndrg2|29811|N-myc downstream regulated gene 2	AB033921|Ndrg2|29811|N-myc downstream regulated gene 2	AK168011|Ndrg2|29811|N-myc downstream regulated gene 2	AK154597|Ndrg2|29811|N-myc downstream regulated gene 2
mm9_v1_chr9_+_100978450_100978485	0.0728025	SOX2.p2	NM_001100451|Msl2|77853|male-specific lethal 2 homolog (Drosophila)	BC070432|Msl2|77853|male-specific lethal 2 homolog (Drosophila)
mm9_v1_chr18_+_67247937_67247965	0.0724355	SOX2.p2	AK043665|Gnal|14680|guanine nucleotide binding protein, alpha stimulating, olfactory type	AK035952|Gnal|14680|guanine nucleotide binding protein, alpha stimulating, olfactory type
mm9_v1_chr11_-_118074052_118074068	0.0719441	SOX2.p2	AK158216|Cyth1|19157|cytohesin 1	NM_001112700|Cyth1|19157|cytohesin 1
mm9_v1_chr11_-_6344445_6344467	0.0714986	SOX2.p2	NM_029938|H2afv|77605|H2A histone family, member V	AK155105|H2afv|77605|H2A histone family, member V
mm9_v1_chr15_-_81560302_81560307	0.0708912	SOX2.p2	AK159930|Rangap1|19387|RAN GTPase activating protein 1	BC014855|Rangap1|19387|RAN GTPase activating protein 1	AK146670|Rangap1|19387|RAN GTPase activating protein 1
mm9_v1_chr13_+_15555483_15555555	0.0706425	SOX2.p2	AK158261|Gli3|14634|GLI-Kruppel family member GLI3	NM_008130|Gli3|14634|GLI-Kruppel family member GLI3
mm9_v1_chr1_+_60466499_60466554	0.0701377	SOX2.p2	BC079646|Abi2|329165|abl-interactor 2
mm9_v1_chr11_-_120092784_120092898	0.0700853	SOX2.p2	AK034741|2900052L18Rik|76835|RIKEN cDNA 2900052L18 gene	AK162948|2900052L18Rik|76835|RIKEN cDNA 2900052L18 gene	AK013668|2900052L18Rik|76835|RIKEN cDNA 2900052L18 gene
mm9_v1_chr11_+_121168199_121168276	0.0696937	SOX2.p2	AK004247|Foxk2|68837|forkhead box K2
mm9_v1_chr10_+_42580317_42580598	0.0696835	SOX2.p2	NM_172938|Scml4|268297|sex comb on midleg-like 4 (Drosophila)	AF397911|Scml4|268297|sex comb on midleg-like 4 (Drosophila)	AK034171|Scml4|268297|sex comb on midleg-like 4 (Drosophila)	BC043310|Scml4|268297|sex comb on midleg-like 4 (Drosophila)	AK047972|Scml4|268297|sex comb on midleg-like 4 (Drosophila)
mm9_v1_chr13_+_89680240_89680277	0.0695958	SOX2.p2	AK032750|Hapln1|12950|hyaluronan and proteoglycan link protein 1	NM_013500|Hapln1|12950|hyaluronan and proteoglycan link protein 1
mm9_v1_chr4_+_41985509_41985545	0.0695307	SOX2.p2	BC087957|Ccl21c|65956|chemokine (C-C motif) ligand 21C (leucine)	NM_001193666|Gm13304|100504346|predicted gene 13304	NM_001193668|Gm10591|100504239|predicted gene 10591	NM_023052|Ccl21c|65956|chemokine (C-C motif) ligand 21C (leucine)	BC038120|Ccl21a|18829|chemokine (C-C motif) ligand 21A (serine)	NM_011335|Ccl21b|100042493|chemokine (C-C motif) ligand 21B (leucine)	U88322|Ccl21c|65956|chemokine (C-C motif) ligand 21C (leucine)
mm9_v1_chr17_+_5343877_5344040	0.0695299	SOX2.p2	AK049919|Arid1b|239985|AT rich interactive domain 1B (SWI-like)	AK021005|Arid1b|239985|AT rich interactive domain 1B (SWI-like)	AK048918|Arid1b|239985|AT rich interactive domain 1B (SWI-like)
mm9_v1_chr3_+_89586320_89586446	0.0692665	SOX2.p2	AK211403|Ube2q1|70093|ubiquitin-conjugating enzyme E2Q (putative) 1
mm9_v1_chr4_+_34562190_34562236	0.0691061	SOX2.p2	NM_181406|Rars2|109093|arginyl-tRNA synthetase 2, mitochondrial	AK075721|Rars2|109093|arginyl-tRNA synthetase 2, mitochondrial	AK166986|Rars2|109093|arginyl-tRNA synthetase 2, mitochondrial	BC024878|Rars2|109093|arginyl-tRNA synthetase 2, mitochondrial	AK156182|Rars2|109093|arginyl-tRNA synthetase 2, mitochondrial
mm9_v1_chr7_-_22919759_22919759	0.069026	SOX2.p2	NM_001167573|Gm10666|100043037|predicted gene 10666	NM_207547|Vmn1r93|404290|vomernasal 1 receptor Vmn1r93
mm9_v1_chr7_+_23656242_23656242	0.0686312	SOX2.p2	NM_001166724|Vmn1r160|620758|vomeronasal 1 receptor 160
mm9_v1_chr10_-_122550401_122550537	0.0684506	SOX2.p2	AK088952|Usp15|14479|ubiquitin specific peptidase 15
mm9_v1_chr5_+_150480804_150480876	0.0678793	SOX2.p2	NM_001081204|B3galtl|381694|beta 1,3-galactosyltransferase-like	AK089440|B3galtl|381694|beta 1,3-galactosyltransferase-like	AK145082|B3galtl|381694|beta 1,3-galactosyltransferase-like	AB253762|B3galtl|381694|beta 1,3-galactosyltransferase-like
mm9_v1_chr5_-_38871369_38871544	0.0677784	SOX2.p2	AF490463|Slc2a9|117591|solute carrier family 2 (facilitated glucose transporter), member 9	AK037093|Slc2a9|117591|solute carrier family 2 (facilitated glucose transporter), member 9	AK172234|Slc2a9|117591|solute carrier family 2 (facilitated glucose transporter), member 9	AK156740|Slc2a9|117591|solute carrier family 2 (facilitated glucose transporter), member 9	AF469480|Slc2a9|117591|solute carrier family 2 (facilitated glucose transporter), member 9	NM_001102414|Slc2a9|117591|solute carrier family 2 (facilitated glucose transporter), member 9	NM_001102415|Slc2a9|117591|solute carrier family 2 (facilitated glucose transporter), member 9
mm9_v1_chrX_-_101176600_101176631	0.0676952	SOX2.p2	AK013207|Rlim|19820|ring finger protein, LIM domain interacting	AK029295|Rlim|19820|ring finger protein, LIM domain interacting	AK163276|Rlim|19820|ring finger protein, LIM domain interacting	NM_011276|Rlim|19820|ring finger protein, LIM domain interacting
mm9_v1_chr9_-_62644026_62644272	0.0674925	SOX2.p2	AK078303|Fem1b|14155|feminization 1 homolog b (C. elegans)	AK160393|Fem1b|14155|feminization 1 homolog b (C. elegans)
mm9_v1_chrX_+_34666757_34666828	0.0674142	SOX2.p2	NM_025937|Nkap|67050|NFKB activating protein	BC026774|Nkap|67050|NFKB activating protein	AK011492|Nkap|67050|NFKB activating protein	AY388959|Nkap|67050|NFKB activating protein	AK038344|Nkap|67050|NFKB activating protein	AK076125|Nkap|67050|NFKB activating protein	AK012826|Nkap|67050|NFKB activating protein	AK089943|Nkap|67050|NFKB activating protein
mm9_v1_chr13_+_54676356_54676474	0.0671552	SOX2.p2	NM_019968|Arl10|56795|ADP-ribosylation factor-like 10	AK154684|Arl10|56795|ADP-ribosylation factor-like 10	AF205936|Arl10|56795|ADP-ribosylation factor-like 10	BC115498|Arl10|56795|ADP-ribosylation factor-like 10
mm9_v1_chr1_+_60466568_60466597	0.0667487	SOX2.p2	BC079545|Abi2|329165|abl-interactor 2
mm9_v1_chr2_-_131855722_131855755	0.0667204	SOX2.p2	NM_175445|Rassf2|215653|Ras association (RalGDS/AF-6) domain family member 2
mm9_v1_chr17_-_18020889_18020919	0.0666874	SOX2.p2	NM_013521|Fpr1|14293|formyl peptide receptor 1	AK137714|Fpr1|14293|formyl peptide receptor 1
mm9_v1_chr12_+_66176588_66176613	0.0666083	SOX2.p2	AK039944|Fancm|104806|Fanconi anemia, complementation group M	AK084697|Fancm|104806|Fanconi anemia, complementation group M	AK086395|Fancm|104806|Fanconi anemia, complementation group M	AK050306|Fancm|104806|Fanconi anemia, complementation group M	NM_178912|Fancm|104806|Fanconi anemia, complementation group M	AK053715|Fancm|104806|Fanconi anemia, complementation group M	BC150785|Fancm|104806|Fanconi anemia, complementation group M	AK173211|Fancm|104806|Fanconi anemia, complementation group M
mm9_v1_chr17_-_45706642_45706682	0.0663377	SOX2.p2	BC049951|Hsp90ab1|15516|heat shock protein 90 alpha (cytosolic), class B member 1	BC044888|Hsp90ab1|15516|heat shock protein 90 alpha (cytosolic), class B member 1
mm9_v1_chr15_-_85652162_85652162	0.0662721	SOX2.p2	NM_011105|Pkdrej|18766|polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like
mm9_v1_chr9_+_58430210_58430222	0.0662022	SOX2.p2	AK075610|Nptn|20320|neuroplastin	AK153930|Nptn|20320|neuroplastin	D50463|Nptn|20320|neuroplastin
mm9_v1_chr19_+_46227052_46227083	0.0661637	SOX2.p2	BC082336|Gbf1|107338|golgi-specific brefeldin A-resistance factor 1	AK019933|Gbf1|107338|golgi-specific brefeldin A-resistance factor 1	BC011335|Gbf1|107338|golgi-specific brefeldin A-resistance factor 1
mm9_v1_chr7_-_22045635_22045635	0.0656917	SOX2.p2	NM_001166757|Vmn1r124|670764|vomeronasal 1 receptor 124
mm9_v1_chr8_-_72149357_72149431	0.0654401	SOX2.p2	AK083009|Zfp868|234362|zinc finger protein 868
mm9_v1_chr2_+_128793137_128793209	0.0650872	SOX2.p2	AK050503|Zc3h6|78751|zinc finger CCCH type containing 6	NM_178404|Zc3h6|78751|zinc finger CCCH type containing 6	AK013610|Zc3h6|78751|zinc finger CCCH type containing 6	AK019345|Zc3h6|78751|zinc finger CCCH type containing 6	AK039171|Zc3h6|78751|zinc finger CCCH type containing 6	AK014766|Zc3h6|78751|zinc finger CCCH type containing 6	BC058173|Zc3h6|78751|zinc finger CCCH type containing 6
mm9_v1_chr11_-_97883924_97884006	0.0647767	SOX2.p2	BC077713|Cacnb1|12295|calcium channel, voltage-dependent, beta 1 subunit	AK155193|Cacnb1|12295|calcium channel, voltage-dependent, beta 1 subunit	NM_001159319|Cacnb1|12295|calcium channel, voltage-dependent, beta 1 subunit	NM_031173|Cacnb1|12295|calcium channel, voltage-dependent, beta 1 subunit	NM_145121|Cacnb1|12295|calcium channel, voltage-dependent, beta 1 subunit	AF322905|Cacnb1|12295|calcium channel, voltage-dependent, beta 1 subunit
mm9_v1_chr11_-_81387006_81387040	0.0646293	SOX2.p2	BC139179|1700071K01Rik|237880|RIKEN cDNA 1700071K01 gene	BC139181|1700071K01Rik|237880|RIKEN cDNA 1700071K01 gene	AK131752|1700071K01Rik|237880|RIKEN cDNA 1700071K01 gene	NM_001033765|1700071K01Rik|237880|RIKEN cDNA 1700071K01 gene
mm9_v1_chr12_+_58331537_58331633	0.0640913	SOX2.p2	AK020763|Mipol1|73490|mirror-image polydactyly gene 1 homolog (human)	AK006974|Mipol1|73490|mirror-image polydactyly gene 1 homolog (human)
mm9_v1_chr12_-_47919695_47919761	0.0633072	SOX2.p2	AF232828|Nova1|664883|neuro-oncological ventral antigen 1	NM_021361|Nova1|664883|neuro-oncological ventral antigen 1
mm9_v1_chr13_+_43880475_43880582	0.0632616	SOX2.p2	NM_009856|Cd83|12522|CD83 antigen	AK075888|Cd83|12522|CD83 antigen	AK139410|Cd83|12522|CD83 antigen	AK154862|Cd83|12522|CD83 antigen	AK156386|Cd83|12522|CD83 antigen	AK171716|Cd83|12522|CD83 antigen	AK172122|Cd83|12522|CD83 antigen	AK172449|Cd83|12522|CD83 antigen	AK172515|Cd83|12522|CD83 antigen	AK172466|Cd83|12522|CD83 antigen	BC072615|Cd83|12522|CD83 antigen	AK172396|Cd83|12522|CD83 antigen	AJ245551|Cd83|12522|CD83 antigen	BC107344|Cd83|12522|CD83 antigen	BC107345|Cd83|12522|CD83 antigen	AF001036|Cd83|12522|CD83 antigen
mm9_v1_chr6_-_130330679_130330825	0.0632163	SOX2.p2	AF146571|Klra15|27423|killer cell lectin-like receptor, subfamily A, member 15	NM_013793|Klra15|27423|killer cell lectin-like receptor, subfamily A, member 15	U34890|Klra1|16627|killer cell lectin-like receptor, subfamily A, member 1	AF218077|Klra1|16627|killer cell lectin-like receptor, subfamily A, member 1	BC125466|Klra15|27423|killer cell lectin-like receptor, subfamily A, member 15	BC125494|Klra15|27423|killer cell lectin-like receptor, subfamily A, member 15	BC140968|Klra1|16627|killer cell lectin-like receptor, subfamily A, member 1	BC144929|Klra1|16627|killer cell lectin-like receptor, subfamily A, member 1	AF288381|Klra22|93969|killer cell lectin-like receptor subfamily A, member 22	NM_053152|Klra22|93969|killer cell lectin-like receptor subfamily A, member 22
mm9_v1_chr15_-_79272478_79272599	0.0631111	SOX2.p2	NM_013767|Csnk1e|27373|casein kinase 1, epsilon
mm9_v1_chr6_+_114081375_114081412	0.0623013	SOX2.p2	AK053261|Slc6a11|243616|solute carrier family 6 (neurotransmitter transporter, GABA), member 11	AK021402|Slc6a11|243616|solute carrier family 6 (neurotransmitter transporter, GABA), member 11
mm9_v1_chr8_-_72149443_72149460	0.0622266	SOX2.p2	AK079745|Zfp868|234362|zinc finger protein 868	AK168306|Zfp868|234362|zinc finger protein 868	NM_172754|Zfp868|234362|zinc finger protein 868
mm9_v1_chr18_+_37514924_37514931	0.0621704	SOX2.p2	AY013790|Pcdhb8|93879|protocadherin beta 8	BC116268|Pcdhb8|93879|protocadherin beta 8	BC127160|Pcdhb8|93879|protocadherin beta 8	NM_053133|Pcdhb8|93879|protocadherin beta 8	BC116269|Pcdhb8|93879|protocadherin beta 8
mm9_v1_chr18_+_34490797_34490849	0.0617854	SOX2.p2	AK004118|Srp19|66384|signal recognition particle 19	AK037009|Srp19|66384|signal recognition particle 19	NM_025527|Srp19|66384|signal recognition particle 19	AK010760|Srp19|66384|signal recognition particle 19	AK152322|Srp19|66384|signal recognition particle 19	AK135508|Srp19|66384|signal recognition particle 19	AK162107|Srp19|66384|signal recognition particle 19	BC051932|Srp19|66384|signal recognition particle 19	AK009412|Srp19|66384|signal recognition particle 19
mm9_v1_chr7_+_51136529_51136569	0.0614233	SOX2.p2	AK087426|Klk4|56640|kallikrein related-peptidase 4 (prostase, enamel matrix, prostate)	AF019979|Klk4|56640|kallikrein related-peptidase 4 (prostase, enamel matrix, prostate)	NM_019928|Klk4|56640|kallikrein related-peptidase 4 (prostase, enamel matrix, prostate)	BC100716|Klk4|56640|kallikrein related-peptidase 4 (prostase, enamel matrix, prostate)	BC100717|Klk4|56640|kallikrein related-peptidase 4 (prostase, enamel matrix, prostate)	BC100718|Klk4|56640|kallikrein related-peptidase 4 (prostase, enamel matrix, prostate)	BC100719|Klk4|56640|kallikrein related-peptidase 4 (prostase, enamel matrix, prostate)
mm9_v1_chr19_+_46227029_46227030	0.0613059	SOX2.p2	AK039570|Gbf1|107338|golgi-specific brefeldin A-resistance factor 1
mm9_v1_chr3_-_93480189_93480204	0.0607353	SOX2.p2	AF290198|Tdpoz1|207213|TD and POZ domain containing 1	NM_148949|Tdpoz1|207213|TD and POZ domain containing 1
mm9_v1_chr19_-_7315495_7315711	0.0601758	SOX2.p2	AK202154|Naa40|70999|N(alpha)-acetyltransferase 40, NatD catalytic subunit, homolog (S. cerevisiae)	AK035418|Naa40|70999|N(alpha)-acetyltransferase 40, NatD catalytic subunit, homolog (S. cerevisiae)	AK033510|Naa40|70999|N(alpha)-acetyltransferase 40, NatD catalytic subunit, homolog (S. cerevisiae)	AK170548|Naa40|70999|N(alpha)-acetyltransferase 40, NatD catalytic subunit, homolog (S. cerevisiae)	AK033896|Naa40|70999|N(alpha)-acetyltransferase 40, NatD catalytic subunit, homolog (S. cerevisiae)	AK089209|Naa40|70999|N(alpha)-acetyltransferase 40, NatD catalytic subunit, homolog (S. cerevisiae)	AK162625|Naa40|70999|N(alpha)-acetyltransferase 40, NatD catalytic subunit, homolog (S. cerevisiae)	BC020020|Naa40|70999|N(alpha)-acetyltransferase 40, NatD catalytic subunit, homolog (S. cerevisiae)	AK016504|Naa40|70999|N(alpha)-acetyltransferase 40, NatD catalytic subunit, homolog (S. cerevisiae)	NM_027643|Naa40|70999|N(alpha)-acetyltransferase 40, NatD catalytic subunit, homolog (S. cerevisiae)
mm9_v1_chr3_+_27215949_27216031	0.0597332	SOX2.p2	AK153581|Tnfsf10|22035|tumor necrosis factor (ligand) superfamily, member 10	AK144931|Tnfsf10|22035|tumor necrosis factor (ligand) superfamily, member 10	AK142960|Tnfsf10|22035|tumor necrosis factor (ligand) superfamily, member 10	AK157633|Tnfsf10|22035|tumor necrosis factor (ligand) superfamily, member 10	NM_009425|Tnfsf10|22035|tumor necrosis factor (ligand) superfamily, member 10	U37522|Tnfsf10|22035|tumor necrosis factor (ligand) superfamily, member 10	BC138807|Tnfsf10|22035|tumor necrosis factor (ligand) superfamily, member 10	BC138808|Tnfsf10|22035|tumor necrosis factor (ligand) superfamily, member 10	BC011469|Tnfsf10|22035|tumor necrosis factor (ligand) superfamily, member 10
mm9_v1_chr7_+_31017092_31017092	0.0595596	SOX2.p2	BC062812|Polr2i|69920|polymerase (RNA) II (DNA directed) polypeptide I	NM_027259|Polr2i|69920|polymerase (RNA) II (DNA directed) polypeptide I
mm9_v1_chr8_+_96738448_96738479	0.0594613	SOX2.p2	AK169693|Nup93|71805|nucleoporin 93
mm9_v1_chr14_-_47441795_47441916	0.0590582	SOX2.p2	AB001732|Gmfb|63985|glia maturation factor, beta	BC040233|Gmfb|63985|glia maturation factor, beta	AB050013|Gmfb|63985|glia maturation factor, beta	BC049134|Gmfb|63985|glia maturation factor, beta	AK013970|Gmfb|63985|glia maturation factor, beta	AK013947|Gmfb|63985|glia maturation factor, beta	AF297220|Gmfb|63985|glia maturation factor, beta	AK142014|Gmfb|63985|glia maturation factor, beta	NM_022023|Gmfb|63985|glia maturation factor, beta
mm9_v1_chr13_-_58494637_58494692	0.0582547	SOX2.p2	AK207611|Hnrnpk|15387|heterogeneous nuclear ribonucleoprotein K
mm9_v1_chr13_-_61107271_61107285	0.0581871	SOX2.p2	AF136272|Ctsj|26898|cathepsin J	NM_012007|Ctsj|26898|cathepsin J	BC103769|Ctsj|26898|cathepsin J	AK005526|Ctsj|26898|cathepsin J	AK131661|Ctsj|26898|cathepsin J
mm9_v1_chr4_+_102243272_102243317	0.0580939	SOX2.p2	AK011999|Pde4b|18578|phosphodiesterase 4B, cAMP specific	BC007155|Pde4b|18578|phosphodiesterase 4B, cAMP specific
mm9_v1_chr2_-_34813680_34813690	0.0579698	SOX2.p2	AK172598|Traf1|22029|TNF receptor-associated factor 1
mm9_v1_chr5_+_37729746_37729775	0.0562606	SOX2.p2	BC037473|Evc2|68525|Ellis van Creveld syndrome 2 homolog (human)
mm9_v1_chr14_-_64162509_64162554	0.0561177	SOX2.p2	BC145946|Mtmr9|210376|myotubularin related protein 9	BC145948|Mtmr9|210376|myotubularin related protein 9
mm9_v1_chr5_+_98758322_98758388	0.055641	SOX2.p2	BC049770|1700007G11Rik|75784|RIKEN cDNA 1700007G11 gene	NM_001024614|1700007G11Rik|75784|RIKEN cDNA 1700007G11 gene	AK005711|1700007G11Rik|75784|RIKEN cDNA 1700007G11 gene
mm9_v1_chr5_+_75471625_75471626	0.0544883	SOX2.p2	NM_133256|Gsx2|14843|GS homeobox 2	S79041|Gsx2|14843|GS homeobox 2	BC119464|Gsx2|14843|GS homeobox 2	BC119465|Gsx2|14843|GS homeobox 2
mm9_v1_chr19_+_46227031_46227037	0.0544139	SOX2.p2	AK143358|Gbf1|107338|golgi-specific brefeldin A-resistance factor 1
mm9_v1_chr7_+_24416996_24417006	0.053976	SOX2.p2	AF324871|Vmn1r171|81012|vomeronasal 1 receptor 171	BC111911|Vmn1r171|81012|vomeronasal 1 receptor 171	NM_030737|Vmn1r171|81012|vomeronasal 1 receptor 171
mm9_v1_chr15_-_36724292_36724292	0.053616	SOX2.p2	NM_011740|Ywhaz|22631|tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide
mm9_v1_chr2_+_130232255_130232267	0.0535142	SOX2.p2	AK016923|4933425O20Rik|66766|RIKEN cDNA 4933425O20 gene	BC049728|4933425O20Rik|66766|RIKEN cDNA 4933425O20 gene	NM_025753|4933425O20Rik|66766|RIKEN cDNA 4933425O20 gene	AK006188|4933425O20Rik|66766|RIKEN cDNA 4933425O20 gene
mm9_v1_chr7_+_18557472_18557527	0.0526166	SOX2.p2	AF221099|Ceacam11|66996|carcinoembryonic antigen-related cell adhesion molecule 11	AK004142|Ceacam11|66996|carcinoembryonic antigen-related cell adhesion molecule 11	AK005432|Ceacam11|66996|carcinoembryonic antigen-related cell adhesion molecule 11	AK005463|Ceacam11|66996|carcinoembryonic antigen-related cell adhesion molecule 11	NM_023289|Ceacam11|66996|carcinoembryonic antigen-related cell adhesion molecule 11	AK145847|Ceacam11|66996|carcinoembryonic antigen-related cell adhesion molecule 11	BC099452|Ceacam11|66996|carcinoembryonic antigen-related cell adhesion molecule 11
mm9_v1_chr1_+_133807034_133807132	0.0522522	SOX2.p2	NM_001145804|Nucks1|98415|nuclear casein kinase and cyclin-dependent kinase substrate 1	NM_175294|Nucks1|98415|nuclear casein kinase and cyclin-dependent kinase substrate 1	AB049825|Nucks1|98415|nuclear casein kinase and cyclin-dependent kinase substrate 1	AK078816|Nucks1|98415|nuclear casein kinase and cyclin-dependent kinase substrate 1	BC039951|Nucks1|98415|nuclear casein kinase and cyclin-dependent kinase substrate 1
mm9_v1_chr9_-_82868992_82869032	0.0521368	SOX2.p2	AJ303103|Phip|83946|pleckstrin homology domain interacting protein	AB049460|Phip|83946|pleckstrin homology domain interacting protein	BC037036|Phip|83946|pleckstrin homology domain interacting protein	AK044935|Phip|83946|pleckstrin homology domain interacting protein	BC049950|Phip|83946|pleckstrin homology domain interacting protein	AK049736|Phip|83946|pleckstrin homology domain interacting protein	AK136530|Phip|83946|pleckstrin homology domain interacting protein
mm9_v1_chr7_+_5626844_5626923	0.051794	SOX2.p2	BC147681|Vmn1r62|81016|vomeronasal 1 receptor 62	BC147684|Vmn1r62|81016|vomeronasal 1 receptor 62	NM_001167567|Vmn1r186|100039479|vomeronasal 1 receptor Vmn1r186
mm9_v1_chr1_-_197002841_197002908	0.0517674	SOX2.p2	BC109344|Cr2|12902|complement receptor 2	BC109345|Cr2|12902|complement receptor 2	AK003072|Cr2|12902|complement receptor 2	NM_007758|Cr2|12902|complement receptor 2
mm9_v1_chr16_-_18248701_18248813	0.0505027	SOX2.p2	AK008276|Ranbp1|19385|RAN binding protein 1	AK002989|Ranbp1|19385|RAN binding protein 1	AK151167|Ranbp1|19385|RAN binding protein 1	AK153074|Ranbp1|19385|RAN binding protein 1	AK167053|Ranbp1|19385|RAN binding protein 1	AK088781|Ranbp1|19385|RAN binding protein 1	AK166642|Ranbp1|19385|RAN binding protein 1	NM_011239|Ranbp1|19385|RAN binding protein 1	X56045|Ranbp1|19385|RAN binding protein 1	X56046|Ranbp1|19385|RAN binding protein 1	BC061140|Ranbp1|19385|RAN binding protein 1
mm9_v1_chr12_-_52930506_52930535	0.0502001	SOX2.p2	AK172326|Hectd1|207304|HECT domain containing 1	NM_144788|Hectd1|207304|HECT domain containing 1
mm9_v1_chr12_-_86518229_86518247	0.0496546	SOX2.p2	X96793|Pgf|18654|placental growth factor	BC016567|Pgf|18654|placental growth factor	NM_008827|Pgf|18654|placental growth factor	AK042891|Pgf|18654|placental growth factor	AK088943|Pgf|18654|placental growth factor
mm9_v1_chr2_-_84510822_84510901	0.0493208	SOX2.p2	AK167638|2700094K13Rik|72657|RIKEN cDNA 2700094K13 gene	AK012609|2700094K13Rik|72657|RIKEN cDNA 2700094K13 gene	AK142622|2700094K13Rik|72657|RIKEN cDNA 2700094K13 gene	AK171972|2700094K13Rik|72657|RIKEN cDNA 2700094K13 gene	BC056177|2700094K13Rik|72657|RIKEN cDNA 2700094K13 gene	NM_001033166|2700094K13Rik|72657|RIKEN cDNA 2700094K13 gene	NM_001037279|2700094K13Rik|72657|RIKEN cDNA 2700094K13 gene
mm9_v1_chr7_+_13609462_13609530	0.0492758	SOX2.p2	BC089337|Trim28|21849|tripartite motif-containing 28	NM_011588|Trim28|21849|tripartite motif-containing 28	U67303|Trim28|21849|tripartite motif-containing 28
mm9_v1_chrX_+_137212566_137212566	0.0490927	SOX2.p2	AF196480|Mid2|23947|midline 2	NM_011845|Mid2|23947|midline 2
mm9_v1_chr2_-_118305356_118305444	0.0490499	SOX2.p2	M29264|Srp14|20813|signal recognition particle 14	AK156845|Srp14|20813|signal recognition particle 14	AK167821|Srp14|20813|signal recognition particle 14	BC021537|Srp14|20813|signal recognition particle 14	AK168144|Srp14|20813|signal recognition particle 14	AK019310|Srp14|20813|signal recognition particle 14	NM_009273|Srp14|20813|signal recognition particle 14
mm9_v1_chr17_-_24210437_24210453	0.0487412	SOX2.p2	AK052960|Kctd5|69259|potassium channel tetramerisation domain containing 5	NM_027008|Kctd5|69259|potassium channel tetramerisation domain containing 5
mm9_v1_chr2_-_27330917_27330977	0.0486586	SOX2.p2	NM_023336|Brd3|67382|bromodomain containing 3
mm9_v1_chr3_-_119486305_119486325	0.0484355	SOX2.p2	AK135738|Ptbp2|56195|polypyrimidine tract binding protein 2	NM_019550|Ptbp2|56195|polypyrimidine tract binding protein 2
mm9_v1_chr4_+_128365981_128366038	0.048314	SOX2.p2	NM_018774|Phc2|54383|polyhomeotic-like 2 (Drosophila)	BC057571|Phc2|54383|polyhomeotic-like 2 (Drosophila)
mm9_v1_chr6_-_126116761_126116761	0.0481933	SOX2.p2	NM_001164034|Ntf3|18205|neurotrophin 3	NM_008742|Ntf3|18205|neurotrophin 3
mm9_v1_chr5_+_58109246_58109263	0.0480755	SOX2.p2	NM_001122758|Pcdh7|54216|protocadherin 7	NM_018764|Pcdh7|54216|protocadherin 7
mm9_v1_chr2_-_37225800_37225813	0.0478544	SOX2.p2	AK046886|Rc3h2|319817|ring finger and CCCH-type zinc finger domains 2
mm9_v1_chr17_+_74888823_74888973	0.0477986	SOX2.p2	AK166347|Yipf4|67864|Yip1 domain family, member 4	AK009618|Yipf4|67864|Yip1 domain family, member 4	AK083301|Yipf4|67864|Yip1 domain family, member 4	NM_026417|Yipf4|67864|Yip1 domain family, member 4	AK017721|Yipf4|67864|Yip1 domain family, member 4	AK017722|Yipf4|67864|Yip1 domain family, member 4	AK159227|Yipf4|67864|Yip1 domain family, member 4	BC003936|Yipf4|67864|Yip1 domain family, member 4
mm9_v1_chr11_-_121084021_121084125	0.0475781	SOX2.p2	AK215969|BC017643|217370|cDNA sequence BC017643
mm9_v1_chr5_+_96221657_96221657	0.0473525	SOX2.p2	NM_001122678|Gm3286|100041354|predicted gene 3286	NM_001167793|Gm3286|100041354|predicted gene 3286
mm9_v1_chr8_+_96738490_96738507	0.0469295	SOX2.p2	AK010450|Nup93|71805|nucleoporin 93	AK167105|Nup93|71805|nucleoporin 93	AK028864|Nup93|71805|nucleoporin 93	NM_172410|Nup93|71805|nucleoporin 93	BC023140|Nup93|71805|nucleoporin 93
mm9_v1_chr9_-_14588941_14589004	0.0467185	SOX2.p2	AK155932|Ankrd49|56503|ankyrin repeat domain 49	AK137504|Ankrd49|56503|ankyrin repeat domain 49	AK153923|Ankrd49|56503|ankyrin repeat domain 49	AK157315|Ankrd49|56503|ankyrin repeat domain 49	AK132850|Ankrd49|56503|ankyrin repeat domain 49	AF028722|Ankrd49|56503|ankyrin repeat domain 49
mm9_v1_chr10_+_101974855_101975051	0.0465698	SOX2.p2	AK041688|Rassf9|237504|Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	NM_146240|Rassf9|237504|Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	BC028805|Rassf9|237504|Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	AK086855|Rassf9|237504|Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	AK033464|Rassf9|237504|Ras association (RalGDS/AF-6) domain family (N-terminal) member 9
mm9_v1_chr11_+_119129280_119129348	0.0463275	SOX2.p2	NM_001159324|Gaa|14387|glucosidase, alpha, acid	AK146538|Gaa|14387|glucosidase, alpha, acid	NM_008064|Gaa|14387|glucosidase, alpha, acid	U49351|Gaa|14387|glucosidase, alpha, acid	AK052211|Gaa|14387|glucosidase, alpha, acid	AK054057|Gaa|14387|glucosidase, alpha, acid	AK141546|Gaa|14387|glucosidase, alpha, acid	AK088481|Gaa|14387|glucosidase, alpha, acid
mm9_v1_chr7_+_5626205_5626228	0.0462887	SOX2.p2	AF324867|Vmn1r62|81016|vomeronasal 1 receptor 62	NM_030741|Vmn1r62|81016|vomeronasal 1 receptor 62	BC113757|Vmn1r62|81016|vomeronasal 1 receptor 62
mm9_v1_chr2_-_33226946_33226968	0.0462313	SOX2.p2	BC072656|Ralgps1|241308|Ral GEF with PH domain and SH3 binding motif 1	AK170248|Ralgps1|241308|Ral GEF with PH domain and SH3 binding motif 1
mm9_v1_chr14_-_14793678_14793804	0.0460583	SOX2.p2	AK147003|Thoc7|66231|THO complex 7 homolog (Drosophila)	AK007440|Thoc7|66231|THO complex 7 homolog (Drosophila)	AK008899|Thoc7|66231|THO complex 7 homolog (Drosophila)	NM_001013578|Thoc7|66231|THO complex 7 homolog (Drosophila)	NM_025435|Thoc7|66231|THO complex 7 homolog (Drosophila)	AK013319|Thoc7|66231|THO complex 7 homolog (Drosophila)	AK005176|Thoc7|66231|THO complex 7 homolog (Drosophila)	BC042209|Thoc7|66231|THO complex 7 homolog (Drosophila)	AK010958|Thoc7|66231|THO complex 7 homolog (Drosophila)	BC027113|Thoc7|66231|THO complex 7 homolog (Drosophila)	BC054419|Thoc7|66231|THO complex 7 homolog (Drosophila)	BC116919|Thoc7|66231|THO complex 7 homolog (Drosophila)	BC116945|Thoc7|66231|THO complex 7 homolog (Drosophila)
mm9_v1_chr6_-_72382855_72382865	0.0456102	SOX2.p2	
mm9_v1_chr16_-_11137100_11137212	0.0451719	SOX2.p2	AK218593|Zc3h7a|106205|zinc finger CCCH type containing 7 A
mm9_v1_chr14_+_47380287_47380301	0.0449598	SOX2.p2	AK146312|Cdkn3|72391|cyclin-dependent kinase inhibitor 3
mm9_v1_chr13_-_107726930_107727002	0.044853	SOX2.p2	BC031900|Ipo11|76582|importin 11	BC029746|Ipo11|76582|importin 11	NM_029665|Ipo11|76582|importin 11
mm9_v1_chr2_-_157835086_157835095	0.0444815	SOX2.p2	AF332067|Tti1|75425|Tel2 interacting protein 1 homolog (S. pombe)	AF332068|Tti1|75425|Tel2 interacting protein 1 homolog (S. pombe)	BC053067|Tti1|75425|Tel2 interacting protein 1 homolog (S. pombe)	NM_029282|Tti1|75425|Tel2 interacting protein 1 homolog (S. pombe)
mm9_v1_chr2_+_157250020_157250043	0.0444549	SOX2.p2	NM_001025395|Src|20779|Rous sarcoma oncogene	NM_009271|Src|20779|Rous sarcoma oncogene	BC039953|Src|20779|Rous sarcoma oncogene
mm9_v1_chr17_+_56098521_56098583	0.0443835	SOX2.p2	AK168621|Ccdc94|72886|coiled-coil domain containing 94
mm9_v1_chr5_+_90947970_90948068	0.044267	SOX2.p2	AK143987|Afm|280662|afamin	BC100597|Afm|280662|afamin	NM_145146|Afm|280662|afamin	BC026681|Afm|280662|afamin
mm9_v1_chrX_+_50265390_50265552	0.0432763	SOX2.p2	AK157045|Phf6|70998|PHD finger protein 6	AK012211|Phf6|70998|PHD finger protein 6	AK077803|Phf6|70998|PHD finger protein 6	AK163345|Phf6|70998|PHD finger protein 6	BC043127|Phf6|70998|PHD finger protein 6	NM_027642|Phf6|70998|PHD finger protein 6	AK141804|Phf6|70998|PHD finger protein 6	BC055330|Phf6|70998|PHD finger protein 6	AK122560|Phf6|70998|PHD finger protein 6	AK028498|Phf6|70998|PHD finger protein 6	AK038320|Phf6|70998|PHD finger protein 6	BC057374|Phf6|70998|PHD finger protein 6	AK192342|Phf6|70998|PHD finger protein 6	AK213676|Phf6|70998|PHD finger protein 6
mm9_v1_chr9_-_20700331_20700394	0.0432456	SOX2.p2	
mm9_v1_chr1_-_36200401_36200606	0.0426132	SOX2.p2	AK044321|Uggt1|320011|UDP-glucose glycoprotein glucosyltransferase 1
mm9_v1_chr18_+_3383216_3383321	0.0422212	SOX2.p2	AK004875|Cul2|71745|cullin 2	NM_029402|Cul2|71745|cullin 2	AK160597|Cul2|71745|cullin 2	AK220287|Cul2|71745|cullin 2	AK144693|Cul2|71745|cullin 2	AK028589|Cul2|71745|cullin 2	BC027428|Cul2|71745|cullin 2	BC026779|Cul2|71745|cullin 2
mm9_v1_chr5_+_64550623_64550689	0.0419271	SOX2.p2	AK122445|Tbc1d1|57915|TBC1 domain family, member 1
mm9_v1_chr12_-_13255934_13256032	0.0417851	SOX2.p2	BC008570|Ddx1|104721|DEAD (Asp-Glu-Ala-Asp) box polypeptide 1	AK166146|Ddx1|104721|DEAD (Asp-Glu-Ala-Asp) box polypeptide 1	AK028341|Ddx1|104721|DEAD (Asp-Glu-Ala-Asp) box polypeptide 1	AK053259|Ddx1|104721|DEAD (Asp-Glu-Ala-Asp) box polypeptide 1	AK160982|Ddx1|104721|DEAD (Asp-Glu-Ala-Asp) box polypeptide 1	BC010624|Ddx1|104721|DEAD (Asp-Glu-Ala-Asp) box polypeptide 1	NM_134040|Ddx1|104721|DEAD (Asp-Glu-Ala-Asp) box polypeptide 1	AK153335|Ddx1|104721|DEAD (Asp-Glu-Ala-Asp) box polypeptide 1	AK132157|Ddx1|104721|DEAD (Asp-Glu-Ala-Asp) box polypeptide 1
mm9_v1_chr3_+_51028368_51028391	0.0417185	SOX2.p2	AK087790|Ccrn4l|12457|CCR4 carbon catabolite repression 4-like (S. cerevisiae)	NM_009834|Ccrn4l|12457|CCR4 carbon catabolite repression 4-like (S. cerevisiae)	AF183960|Ccrn4l|12457|CCR4 carbon catabolite repression 4-like (S. cerevisiae)	AK149340|Ccrn4l|12457|CCR4 carbon catabolite repression 4-like (S. cerevisiae)
mm9_v1_chr9_-_107516538_107516684	0.0414986	SOX2.p2	
mm9_v1_chr11_-_70223517_70223527	0.0414938	SOX2.p2	BC090620|Pelp1|75273|proline, glutamic acid and leucine rich protein 1
mm9_v1_chr12_+_101350539_101350540	0.0413985	SOX2.p2	U39302|Psmc1|19179|protease (prosome, macropain) 26S subunit, ATPase 1	NM_008947|Psmc1|19179|protease (prosome, macropain) 26S subunit, ATPase 1
mm9_v1_chr3_-_66785692_66785692	0.0413565	SOX2.p2	NM_013665|Shox2|20429|short stature homeobox 2	U66918|Shox2|20429|short stature homeobox 2
mm9_v1_chr7_-_20724436_20724436	0.0412625	SOX2.p2	NM_001167573|Gm10666|100043037|predicted gene 10666	NM_207547|Vmn1r93|404290|vomernasal 1 receptor Vmn1r93
mm9_v1_chr17_+_87682206_87682305	0.0411266	SOX2.p2	AK040578|Ttc7|225049|tetratricopeptide repeat domain 7	NM_028639|Ttc7|225049|tetratricopeptide repeat domain 7	AK050263|Ttc7|225049|tetratricopeptide repeat domain 7	AK090252|Ttc7|225049|tetratricopeptide repeat domain 7	AK153704|Ttc7|225049|tetratricopeptide repeat domain 7	AK080284|Ttc7|225049|tetratricopeptide repeat domain 7	AK040610|Ttc7|225049|tetratricopeptide repeat domain 7	AK004107|Ttc7|225049|tetratricopeptide repeat domain 7
mm9_v1_chr1_-_153275461_153275510	0.0406607	SOX2.p2	BC028449|1200016B10Rik|66875|RIKEN cDNA 1200016B10 gene	BC060204|1200016B10Rik|66875|RIKEN cDNA 1200016B10 gene	AK013686|1200016B10Rik|66875|RIKEN cDNA 1200016B10 gene	AK004803|1200016B10Rik|66875|RIKEN cDNA 1200016B10 gene
mm9_v1_chr10_+_127529818_127529845	0.0401943	SOX2.p2	AK133149|Baz2a|116848|bromodomain adjacent to zinc finger domain, 2A	BC048415|Baz2a|116848|bromodomain adjacent to zinc finger domain, 2A	NM_054078|Baz2a|116848|bromodomain adjacent to zinc finger domain, 2A
mm9_v1_chr5_+_37729712_37729738	0.0398126	SOX2.p2	NM_145920|Evc2|68525|Ellis van Creveld syndrome 2 homolog (human)	AK134298|Evc2|68525|Ellis van Creveld syndrome 2 homolog (human)	BC064473|Evc2|68525|Ellis van Creveld syndrome 2 homolog (human)
mm9_v1_chr13_-_29045399_29045574	0.0397729	SOX2.p2	AK187111|Sox4|20677|SRY-box containing gene 4	BC060669|Sox4|20677|SRY-box containing gene 4	X70298|Sox4|20677|SRY-box containing gene 4	BC052736|Sox4|20677|SRY-box containing gene 4	NM_009238|Sox4|20677|SRY-box containing gene 4	AK053840|Sox4|20677|SRY-box containing gene 4	AK028989|Sox4|20677|SRY-box containing gene 4
mm9_v1_chr17_+_56098594_56098609	0.0397576	SOX2.p2	AK078481|Ccdc94|72886|coiled-coil domain containing 94	AK013533|Ccdc94|72886|coiled-coil domain containing 94	BC031400|Ccdc94|72886|coiled-coil domain containing 94	NM_028381|Ccdc94|72886|coiled-coil domain containing 94
mm9_v1_chr11_+_74644479_74644499	0.0396073	SOX2.p2	Y07609|Mnt|17428|max binding protein	BC054534|Mnt|17428|max binding protein
mm9_v1_chr6_-_51419726_51419880	0.0392337	SOX2.p2	BC141253|Hnrnpa2b1|53379|heterogeneous nuclear ribonucleoprotein A2/B1	BC145588|Hnrnpa2b1|53379|heterogeneous nuclear ribonucleoprotein A2/B1	AF073993|Hnrnpa2b1|53379|heterogeneous nuclear ribonucleoprotein A2/B1	AK089012|Hnrnpa2b1|53379|heterogeneous nuclear ribonucleoprotein A2/B1
mm9_v1_chr5_+_110681753_110681764	0.0389925	SOX2.p2	AK134966|Ankle2|71782|ankyrin repeat and LEM domain containing 2
mm9_v1_chr1_+_88600370_88600431	0.0388053	SOX2.p2	AK050762|Dis3l2|208718|DIS3 mitotic control homolog (S. cerevisiae)-like 2	NM_001172157|Dis3l2|208718|DIS3 mitotic control homolog (S. cerevisiae)-like 2	NM_153530|Dis3l2|208718|DIS3 mitotic control homolog (S. cerevisiae)-like 2	AK079867|Dis3l2|208718|DIS3 mitotic control homolog (S. cerevisiae)-like 2	AK031180|Dis3l2|208718|DIS3 mitotic control homolog (S. cerevisiae)-like 2	AK029652|Dis3l2|208718|DIS3 mitotic control homolog (S. cerevisiae)-like 2	AK040613|Dis3l2|208718|DIS3 mitotic control homolog (S. cerevisiae)-like 2	BC036177|Dis3l2|208718|DIS3 mitotic control homolog (S. cerevisiae)-like 2
mm9_v1_chr13_+_24895094_24895151	0.0387402	SOX2.p2	BC002217|BC005537|79555|cDNA sequence BC005537
mm9_v1_chr14_-_52533114_52533162	0.0382529	SOX2.p2	NM_001145959|Ndrg2|29811|N-myc downstream regulated gene 2	NM_013864|Ndrg2|29811|N-myc downstream regulated gene 2
mm9_v1_chr7_-_110809831_110809831	0.0381963	SOX2.p2	BC119275|Olfr623|259126|olfactory receptor 623	NM_147122|Olfr623|259126|olfactory receptor 623
mm9_v1_chr11_+_101594342_101594372	0.0381449	SOX2.p2	AK170616|Dhx8|217207|DEAH (Asp-Glu-Ala-His) box polypeptide 8
mm9_v1_chr15_-_73455173_73455173	0.0379102	SOX2.p2	AK133269|Slc45a4|106068|solute carrier family 45, member 4	NM_001033219|Slc45a4|106068|solute carrier family 45, member 4
mm9_v1_chr12_-_99497498_99497616	0.0378874	SOX2.p2	AK077475|Galc|14420|galactosylceramidase	BC065140|Galc|14420|galactosylceramidase	BC086671|Galc|14420|galactosylceramidase	NM_008079|Galc|14420|galactosylceramidase	AK165478|Galc|14420|galactosylceramidase	D38557|Galc|14420|galactosylceramidase
mm9_v1_chr5_-_109224353_109224381	0.0374363	SOX2.p2	BC132664|Tmed11|67366|transmembrane emp24 protein transport domain containing	BC132666|Tmed11|67366|transmembrane emp24 protein transport domain containing	AK019032|Tmed11|67366|transmembrane emp24 protein transport domain containing	AK007381|Tmed11|67366|transmembrane emp24 protein transport domain containing	NM_026109|Tmed11|67366|transmembrane emp24 protein transport domain containing
mm9_v1_chr9_+_43875103_43875168	0.0373678	SOX2.p2	NM_198092|Usp2|53376|ubiquitin specific peptidase 2	AK138799|Usp2|53376|ubiquitin specific peptidase 2
mm9_v1_chr7_+_109118356_109118356	0.0373066	SOX2.p2	BC049791|Numa1|101706|nuclear mitotic apparatus protein 1	NM_133947|Numa1|101706|nuclear mitotic apparatus protein 1
mm9_v1_chr5_+_138462503_138462503	0.0370876	SOX2.p2	AJ245454|Smok3a|545814|sperm motility kinase 3A	NM_001168602|Smok3a|545814|sperm motility kinase 3A
mm9_v1_chr8_-_127093601_127093609	0.0370076	SOX2.p2	AK018763|Agt|11606|angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	AK139179|Agt|11606|angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	AK005354|Agt|11606|angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	NM_007428|Agt|11606|angiotensinogen (serpin peptidase inhibitor, clade A, member 8)
mm9_v1_chr11_+_29030725_29030774	0.03684	SOX2.p2	AK161833|Pnpt1|71701|polyribonucleotide nucleotidyltransferase 1	AJ507387|Pnpt1|71701|polyribonucleotide nucleotidyltransferase 1	AK144151|Pnpt1|71701|polyribonucleotide nucleotidyltransferase 1	AK149419|Pnpt1|71701|polyribonucleotide nucleotidyltransferase 1	AK165566|Pnpt1|71701|polyribonucleotide nucleotidyltransferase 1	NM_027869|Pnpt1|71701|polyribonucleotide nucleotidyltransferase 1	AF465249|Pnpt1|71701|polyribonucleotide nucleotidyltransferase 1	AK152445|Pnpt1|71701|polyribonucleotide nucleotidyltransferase 1
mm9_v1_chr5_+_37729786_37729846	0.0368015	SOX2.p2	AB083066|Evc2|68525|Ellis van Creveld syndrome 2 homolog (human)	AK165051|Evc2|68525|Ellis van Creveld syndrome 2 homolog (human)	AK044977|Evc2|68525|Ellis van Creveld syndrome 2 homolog (human)
mm9_v1_chr11_-_70223528_70223535	0.0366834	SOX2.p2	AK005027|Pelp1|75273|proline, glutamic acid and leucine rich protein 1	AK016197|Pelp1|75273|proline, glutamic acid and leucine rich protein 1	AK128966|Pelp1|75273|proline, glutamic acid and leucine rich protein 1	NM_029231|Pelp1|75273|proline, glutamic acid and leucine rich protein 1
mm9_v1_chr2_+_26775279_26775409	0.0366597	SOX2.p2	AK215042|Surf2|20931|surfeit gene 2
mm9_v1_chr17_+_47027553_47027615	0.0360602	SOX2.p2	NM_178385|Tbcc|72726|tubulin-specific chaperone C
mm9_v1_chr6_-_131243197_131243269	0.0359328	SOX2.p2	BC027505|Magohb|66441|mago-nashi homolog B (Drosophila)	AK007769|Magohb|66441|mago-nashi homolog B (Drosophila)	AK013310|Magohb|66441|mago-nashi homolog B (Drosophila)	AK006303|Magohb|66441|mago-nashi homolog B (Drosophila)	AK008200|Magohb|66441|mago-nashi homolog B (Drosophila)	NM_025564|Magohb|66441|mago-nashi homolog B (Drosophila)
mm9_v1_chr7_+_134388006_134388047	0.0358436	SOX2.p2	AK090240|Zfp771|244216|zinc finger protein 771	NM_177362|Zfp771|244216|zinc finger protein 771	AK159461|Zfp771|244216|zinc finger protein 771
mm9_v1_chr2_-_120434984_120435243	0.0346856	SOX2.p2	AK003592|Lrrc57|66606|leucine rich repeat containing 57	AK169249|Lrrc57|66606|leucine rich repeat containing 57	BC034894|Lrrc57|66606|leucine rich repeat containing 57	AK003037|Lrrc57|66606|leucine rich repeat containing 57	NM_025657|Lrrc57|66606|leucine rich repeat containing 57	AK012637|Lrrc57|66606|leucine rich repeat containing 57	AK033084|Lrrc57|66606|leucine rich repeat containing 57	AK134971|Lrrc57|66606|leucine rich repeat containing 57	NM_001159612|Lrrc57|66606|leucine rich repeat containing 57	AK015684|Lrrc57|66606|leucine rich repeat containing 57	AK019566|Lrrc57|66606|leucine rich repeat containing 57	NM_001159609|Lrrc57|66606|leucine rich repeat containing 57	NM_001159610|Lrrc57|66606|leucine rich repeat containing 57
mm9_v1_chr8_-_70498472_70498472	0.0344648	SOX2.p2	AB220685|Psd3|234353|pleckstrin and Sec7 domain containing 3	NM_177698|Psd3|234353|pleckstrin and Sec7 domain containing 3
mm9_v1_chr12_+_41172639_41172648	0.0344592	SOX2.p2	AK043666|Dock4|238130|dedicator of cytokinesis 4	NM_172803|Dock4|238130|dedicator of cytokinesis 4
mm9_v1_chr5_+_138478451_138478466	0.0343627	SOX2.p2	AK133180|Smok3b|622474|sperm motility kinase 3B	NM_001039889|Smok3b|622474|sperm motility kinase 3B	AJ245454|Smok3a|545814|sperm motility kinase 3A
mm9_v1_chr14_-_67627598_67627723	0.0331198	SOX2.p2	AK220143|Bnip3l|12177|BCL2/adenovirus E1B interacting protein 3-like	BC049081|Bnip3l|12177|BCL2/adenovirus E1B interacting protein 3-like	AK139950|Bnip3l|12177|BCL2/adenovirus E1B interacting protein 3-like	AK004667|Bnip3l|12177|BCL2/adenovirus E1B interacting protein 3-like	BC085237|Bnip3l|12177|BCL2/adenovirus E1B interacting protein 3-like	AK018668|Bnip3l|12177|BCL2/adenovirus E1B interacting protein 3-like	AK155040|Bnip3l|12177|BCL2/adenovirus E1B interacting protein 3-like	AY057069|Bnip3l|12177|BCL2/adenovirus E1B interacting protein 3-like	AK013467|Bnip3l|12177|BCL2/adenovirus E1B interacting protein 3-like	AK007920|Bnip3l|12177|BCL2/adenovirus E1B interacting protein 3-like	AF067395|Bnip3l|12177|BCL2/adenovirus E1B interacting protein 3-like	AK168482|Bnip3l|12177|BCL2/adenovirus E1B interacting protein 3-like	AK169391|Bnip3l|12177|BCL2/adenovirus E1B interacting protein 3-like	NM_009761|Bnip3l|12177|BCL2/adenovirus E1B interacting protein 3-like
mm9_v1_chr6_+_113257130_113257306	0.033038	SOX2.p2	AK043372|Brpf1|78783|bromodomain and PHD finger containing, 1	AK156375|Brpf1|78783|bromodomain and PHD finger containing, 1	BC046521|Brpf1|78783|bromodomain and PHD finger containing, 1	NM_030178|Brpf1|78783|bromodomain and PHD finger containing, 1	AK177868|Brpf1|78783|bromodomain and PHD finger containing, 1	BC138361|Brpf1|78783|bromodomain and PHD finger containing, 1	BC145256|Brpf1|78783|bromodomain and PHD finger containing, 1
mm9_v1_chr9_-_108551631_108551731	0.0325445	SOX2.p2	AK165028|Arih2|23807|ariadne homolog 2 (Drosophila)	AK149936|Arih2|23807|ariadne homolog 2 (Drosophila)	BC051998|Arih2|23807|ariadne homolog 2 (Drosophila)	BC052422|Arih2|23807|ariadne homolog 2 (Drosophila)	NM_011790|Arih2|23807|ariadne homolog 2 (Drosophila)	AK011094|Arih2|23807|ariadne homolog 2 (Drosophila)	AK168055|Arih2|23807|ariadne homolog 2 (Drosophila)
mm9_v1_chr14_+_55713789_55713939	0.0316626	SOX2.p2	AF432864|Thtpa|105663|thiamine triphosphatase	AK085173|Thtpa|105663|thiamine triphosphatase	AK132479|Thtpa|105663|thiamine triphosphatase
mm9_v1_chr8_+_73017009_73017206	0.0316203	SOX2.p2	NM_018827|Crlf1|12931|cytokine receptor-like factor 1	AB040038|Crlf1|12931|cytokine receptor-like factor 1	BC107376|Crlf1|12931|cytokine receptor-like factor 1	BC107377|Crlf1|12931|cytokine receptor-like factor 1	BC114407|Crlf1|12931|cytokine receptor-like factor 1
mm9_v1_chr8_-_106772390_106772476	0.0309128	SOX2.p2	AF105217|Tk2|57813|thymidine kinase 2, mitochondrial	AJ249341|Tk2|57813|thymidine kinase 2, mitochondrial	BC019982|Tk2|57813|thymidine kinase 2, mitochondrial	AK041651|Tk2|57813|thymidine kinase 2, mitochondrial	AK051286|Tk2|57813|thymidine kinase 2, mitochondrial	AK154160|Tk2|57813|thymidine kinase 2, mitochondrial	AK087557|Tk2|57813|thymidine kinase 2, mitochondrial	NM_021028|Tk2|57813|thymidine kinase 2, mitochondrial
mm9_v1_chr17_-_33897428_33897430	0.0308926	SOX2.p2	NM_008997|Rab11b|19326|RAB11B, member RAS oncogene family
mm9_v1_chr19_-_8293322_8293389	0.030709	SOX2.p2	AF536196|D630002G06Rik|236293|RIKEN cDNA D630002G06 gene	AK052597|D630002G06Rik|236293|RIKEN cDNA D630002G06 gene	BC126952|D630002G06Rik|236293|RIKEN cDNA D630002G06 gene	NM_172776|D630002G06Rik|236293|RIKEN cDNA D630002G06 gene	AF536195|D630002G06Rik|236293|RIKEN cDNA D630002G06 gene
mm9_v1_chr5_+_95902559_95902571	0.0306779	SOX2.p2	NM_001122678|Gm3286|100041354|predicted gene 3286	NM_001167792|Gm3286|100041354|predicted gene 3286	NM_001167793|Gm3286|100041354|predicted gene 3286	BC099941|D5Ertd577e|320549|DNA segment, Chr 5, ERATO Doi 577, expressed
mm9_v1_chr10_+_90545782_90545789	0.0304736	SOX2.p2	NM_026166|Ikbip|67454|IKBKB interacting protein	NM_027078|Ikbip|67454|IKBKB interacting protein
mm9_v1_chr13_-_21494493_21494508	0.030291	SOX2.p2	AK220177|Zkscan3|72739|zinc finger with KRAB and SCAN domains 3
mm9_v1_chr11_-_69619087_69619125	0.0294793	SOX2.p2	BC144871|Tmem102|380705|transmembrane protein 102	AK143262|Tmem102|380705|transmembrane protein 102	NM_001033433|Tmem102|380705|transmembrane protein 102
mm9_v1_chr12_+_53617063_53617093	0.0292326	SOX2.p2	NM_009706|Arhgap5|11855|Rho GTPase activating protein 5	BC150823|Arhgap5|11855|Rho GTPase activating protein 5
mm9_v1_chr6_+_65621583_65621630	0.0289515	SOX2.p2	AK049802|A930038C07Rik|68169|RIKEN cDNA A930038C07 gene	AK029210|A930038C07Rik|68169|RIKEN cDNA A930038C07 gene	NM_172399|A930038C07Rik|68169|RIKEN cDNA A930038C07 gene	BC047154|A930038C07Rik|68169|RIKEN cDNA A930038C07 gene
mm9_v1_chr4_-_148000832_148000895	0.0288139	SOX2.p2	BC027772|Tardbp|230908|TAR DNA binding protein	BC012873|Tardbp|230908|TAR DNA binding protein	BC033475|Tardbp|230908|TAR DNA binding protein	BC029728|Tardbp|230908|TAR DNA binding protein	BC025544|Tardbp|230908|TAR DNA binding protein	BC027105|Tardbp|230908|TAR DNA binding protein	BC031126|Tardbp|230908|TAR DNA binding protein	AK032199|Tardbp|230908|TAR DNA binding protein	AK045495|Tardbp|230908|TAR DNA binding protein	AK076208|Tardbp|230908|TAR DNA binding protein	AK146002|Tardbp|230908|TAR DNA binding protein	AK146997|Tardbp|230908|TAR DNA binding protein	AK083312|Tardbp|230908|TAR DNA binding protein	AK153803|Tardbp|230908|TAR DNA binding protein	AK133207|Tardbp|230908|TAR DNA binding protein
mm9_v1_chr2_+_181599056_181599106	0.028683	SOX2.p2	NM_025901|Polr3k|67005|polymerase (RNA) III (DNA directed) polypeptide K
mm9_v1_chr8_-_108861850_108861887	0.0282686	SOX2.p2	AK087515|Smpd3|58994|sphingomyelin phosphodiesterase 3, neutral	AK076416|Smpd3|58994|sphingomyelin phosphodiesterase 3, neutral	AK139226|Smpd3|58994|sphingomyelin phosphodiesterase 3, neutral	AK019476|Smpd3|58994|sphingomyelin phosphodiesterase 3, neutral	AK162894|Smpd3|58994|sphingomyelin phosphodiesterase 3, neutral	BC043077|Smpd3|58994|sphingomyelin phosphodiesterase 3, neutral	NM_021491|Smpd3|58994|sphingomyelin phosphodiesterase 3, neutral
mm9_v1_chr6_-_123600652_123600652	0.0279873	SOX2.p2	NM_001104637|Vmn2r22|546913|vomeronasal 2, receptor 22
mm9_v1_chr2_-_26766145_26766181	0.0279019	SOX2.p2	BC018225|Med22|20933|mediator complex subunit 22	NM_001033908|Med22|20933|mediator complex subunit 22	NM_011513|Med22|20933|mediator complex subunit 22
mm9_v1_chr12_-_71212591_71212711	0.0275808	SOX2.p2	AK141891|Nin|18080|ninein	AK134860|Nin|18080|ninein
mm9_v1_chr16_+_59148654_59148677	0.0268144	SOX2.p2	BC119110|Olfr195|259000|olfactory receptor 195	NM_146998|Olfr195|259000|olfactory receptor 195
mm9_v1_chr7_-_54175214_54175352	0.0264938	SOX2.p2	AK185554|Tsg101|22088|tumor susceptibility gene 101	AK179695|Tsg101|22088|tumor susceptibility gene 101	AK014049|Tsg101|22088|tumor susceptibility gene 101	U52945|Tsg101|22088|tumor susceptibility gene 101	BC085308|Tsg101|22088|tumor susceptibility gene 101	AK146602|Tsg101|22088|tumor susceptibility gene 101	NM_021884|Tsg101|22088|tumor susceptibility gene 101	BC005424|Tsg101|22088|tumor susceptibility gene 101	AK146229|Tsg101|22088|tumor susceptibility gene 101	AK150369|Tsg101|22088|tumor susceptibility gene 101
mm9_v1_chr12_+_78339071_78339134	0.0262187	SOX2.p2	BC010666|Fut8|53618|fucosyltransferase 8	AK051811|Fut8|53618|fucosyltransferase 8
mm9_v1_chr17_+_46818005_46818130	0.0261873	SOX2.p2	AK010863|Mea1|17256|male enhanced antigen 1	AK008305|Mea1|17256|male enhanced antigen 1	AK008194|Mea1|17256|male enhanced antigen 1	AK010904|Mea1|17256|male enhanced antigen 1	AK010962|Mea1|17256|male enhanced antigen 1	AK012617|Mea1|17256|male enhanced antigen 1	AK005369|Mea1|17256|male enhanced antigen 1	AK005106|Mea1|17256|male enhanced antigen 1	L10401|Mea1|17256|male enhanced antigen 1	M27938|Mea1|17256|male enhanced antigen 1	NM_010787|Mea1|17256|male enhanced antigen 1	AK011189|Mea1|17256|male enhanced antigen 1	D17341|Mea1|17256|male enhanced antigen 1
mm9_v1_chrX_+_132779615_132779721	0.0261742	SOX2.p2	NM_011712|Wbp5|22381|WW domain binding protein 5	AY459189|Wbp5|22381|WW domain binding protein 5	AK017717|Wbp5|22381|WW domain binding protein 5	AK002214|Wbp5|22381|WW domain binding protein 5	BC020289|Wbp5|22381|WW domain binding protein 5	BC007478|Wbp5|22381|WW domain binding protein 5
mm9_v1_chr3_+_137528537_137528637	0.0261705	SOX2.p2	AK204242|H2afz|51788|H2A histone family, member Z
mm9_v1_chr5_-_149862867_149863025	0.0255157	SOX2.p2	BC110667|Hmgb1|15289|high mobility group box 1	AK037928|Hmgb1|15289|high mobility group box 1
mm9_v1_chr9_-_65756482_65756602	0.0251628	SOX2.p2	AF539614|Trip4|56404|thyroid hormone receptor interactor 4	AK016170|Trip4|56404|thyroid hormone receptor interactor 4	AK139423|Trip4|56404|thyroid hormone receptor interactor 4	AK166192|Trip4|56404|thyroid hormone receptor interactor 4	NM_019797|Trip4|56404|thyroid hormone receptor interactor 4
mm9_v1_chr10_-_116500780_116500882	0.0251343	SOX2.p2	AK181482|Cct2|12461|chaperonin containing Tcp1, subunit 2 (beta)	AK012295|Cct2|12461|chaperonin containing Tcp1, subunit 2 (beta)	Z31553|Cct2|12461|chaperonin containing Tcp1, subunit 2 (beta)	AK088145|Cct2|12461|chaperonin containing Tcp1, subunit 2 (beta)	BC007470|Cct2|12461|chaperonin containing Tcp1, subunit 2 (beta)	BC026918|Cct2|12461|chaperonin containing Tcp1, subunit 2 (beta)	AB041570|Cct2|12461|chaperonin containing Tcp1, subunit 2 (beta)	AK075581|Cct2|12461|chaperonin containing Tcp1, subunit 2 (beta)	AK166891|Cct2|12461|chaperonin containing Tcp1, subunit 2 (beta)	AK145406|Cct2|12461|chaperonin containing Tcp1, subunit 2 (beta)	NM_007636|Cct2|12461|chaperonin containing Tcp1, subunit 2 (beta)
mm9_v1_chr18_+_65185527_65185593	0.0248549	SOX2.p2	AK004969|Nedd4l|83814|neural precursor cell expressed, developmentally down-regulated gene 4-like
mm9_v1_chr6_+_123258350_123258350	0.024528	SOX2.p2	NM_001104632|Vmn2r19|232358|vomeronasal 2, receptor 19
mm9_v1_chr2_-_156005873_156005985	0.0245222	SOX2.p2	AY061882|Rbm39|170791|RNA binding motif protein 39	BC023205|Rbm39|170791|RNA binding motif protein 39	AK156737|Rbm39|170791|RNA binding motif protein 39	AK009719|Rbm39|170791|RNA binding motif protein 39	BC086645|Rbm39|170791|RNA binding motif protein 39	AK154989|Rbm39|170791|RNA binding motif protein 39	AK147076|Rbm39|170791|RNA binding motif protein 39	AK167355|Rbm39|170791|RNA binding motif protein 39	AK005227|Rbm39|170791|RNA binding motif protein 39	AK005234|Rbm39|170791|RNA binding motif protein 39	AK155976|Rbm39|170791|RNA binding motif protein 39	NM_133242|Rbm39|170791|RNA binding motif protein 39
mm9_v1_chr7_-_52378270_52378281	0.0242537	SOX2.p2	AK002987|Rps11|27207|ribosomal protein S11
mm9_v1_chr5_-_123438517_123438541	0.023589	SOX2.p2	NM_001005866|Kdm2b|30841|lysine (K)-specific demethylase 2B
mm9_v1_chr2_-_63022140_63022343	0.0235559	SOX2.p2	AJ291608|Kcnh7|170738|potassium voltage-gated channel, subfamily H (eag-related), member 7	AK052366|Kcnh7|170738|potassium voltage-gated channel, subfamily H (eag-related), member 7	AK043768|Kcnh7|170738|potassium voltage-gated channel, subfamily H (eag-related), member 7	AK034003|Kcnh7|170738|potassium voltage-gated channel, subfamily H (eag-related), member 7	NM_133207|Kcnh7|170738|potassium voltage-gated channel, subfamily H (eag-related), member 7
mm9_v1_chr7_+_52071438_52071457	0.0229647	SOX2.p2	AK171455|Nup62|18226|nucleoporin 62	AK171611|Nup62|18226|nucleoporin 62
mm9_v1_chr5_+_65194814_65194820	0.0229585	SOX2.p2	AK010713|Klf3|16599|Kruppel-like factor 3 (basic)
mm9_v1_chr14_+_31832374_31832396	0.0229095	SOX2.p2	AK030781|Pbrm1|66923|polybromo 1
mm9_v1_chr8_-_72425538_72425567	0.022895	SOX2.p2	AF286698|Ndufa13|67184|NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13	BC037149|Ndufa13|67184|NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13	AK003012|Ndufa13|67184|NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13	AK010517|Ndufa13|67184|NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13	AK012422|Ndufa13|67184|NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13	BC055435|Ndufa13|67184|NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13
mm9_v1_chr7_-_133540239_133540250	0.0225579	SOX2.p2	U76759|Nfatc2ip|18020|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2 interacting protein	AK005947|Nfatc2ip|18020|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2 interacting protein	AK030107|Nfatc2ip|18020|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2 interacting protein	BC113761|Nfatc2ip|18020|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2 interacting protein	NM_010900|Nfatc2ip|18020|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2 interacting protein
mm9_v1_chr12_-_85489188_85489438	0.0218979	SOX2.p2	BC116688|Pnma1|70481|paraneoplastic antigen MA1	BC116687|Pnma1|70481|paraneoplastic antigen MA1	AK017476|Pnma1|70481|paraneoplastic antigen MA1	AK028331|Pnma1|70481|paraneoplastic antigen MA1	AK136933|Pnma1|70481|paraneoplastic antigen MA1	NM_027438|Pnma1|70481|paraneoplastic antigen MA1
mm9_v1_chrX_+_106029995_106030017	0.0217219	SOX2.p2	AK007586|2810403D21Rik|69964|RIKEN cDNA 2810403D21 gene	AK155344|2810403D21Rik|69964|RIKEN cDNA 2810403D21 gene	AK012972|2810403D21Rik|69964|RIKEN cDNA 2810403D21 gene
mm9_v1_chr1_-_137271539_137271700	0.0217077	SOX2.p2	BC044813|Shisa4|77552|shisa homolog 4 (Xenopus laevis)	NM_175259|Shisa4|77552|shisa homolog 4 (Xenopus laevis)	AK039457|Shisa4|77552|shisa homolog 4 (Xenopus laevis)	AK020369|Shisa4|77552|shisa homolog 4 (Xenopus laevis)
mm9_v1_chr17_+_23816331_23816354	0.0214254	SOX2.p2	AK010560|Cldn6|54419|claudin 6	NM_018777|Cldn6|54419|claudin 6	AK010682|Cldn6|54419|claudin 6	BC050138|Cldn6|54419|claudin 6	BC005718|Cldn6|54419|claudin 6
mm9_v1_chr10_-_80828534_80828564	0.0214043	SOX2.p2	AK015088|4930404N11Rik|432479|RIKEN cDNA 4930404N11 gene	BC049656|4930404N11Rik|432479|RIKEN cDNA 4930404N11 gene	BC139256|4930404N11Rik|432479|RIKEN cDNA 4930404N11 gene	BC145589|4930404N11Rik|432479|RIKEN cDNA 4930404N11 gene	BC145960|4930404N11Rik|432479|RIKEN cDNA 4930404N11 gene	NM_001014836|4930404N11Rik|432479|RIKEN cDNA 4930404N11 gene
mm9_v1_chr11_-_87811778_87811799	0.0211127	SOX2.p2	BC049621|Dynll2|68097|dynein light chain LC8-type 2	AK006876|Dynll2|68097|dynein light chain LC8-type 2	NM_001168471|Dynll2|68097|dynein light chain LC8-type 2
mm9_v1_chr17_-_34258691_34258691	0.0205365	SOX2.p2	AK158970|Brd2|14312|bromodomain containing 2	NM_010238|Brd2|14312|bromodomain containing 2
mm9_v1_chr7_+_140175699_140175731	0.0204704	SOX2.p2	AJ250693|Zranb1|360216|zinc finger, RAN-binding domain containing 1
mm9_v1_chr18_-_61173753_61173875	0.0202333	SOX2.p2	BC050103|Slc6a7|240332|solute carrier family 6 (neurotransmitter transporter, L-proline), member 7	BC057070|Slc6a7|240332|solute carrier family 6 (neurotransmitter transporter, L-proline), member 7	NM_201353|Slc6a7|240332|solute carrier family 6 (neurotransmitter transporter, L-proline), member 7	AK141581|Slc6a7|240332|solute carrier family 6 (neurotransmitter transporter, L-proline), member 7
mm9_v1_chr18_+_78546492_78546501	0.0196599	SOX2.p2	BC158101|Gm6133|620155|60S ribosomal protein L17 pseudogene
mm9_v1_chr11_+_53246787_53246879	0.0191406	SOX2.p2	NM_008110|Gdf9|14566|growth differentiation factor 9	AK136145|Gdf9|14566|growth differentiation factor 9	BC052667|Gdf9|14566|growth differentiation factor 9	L06444|Gdf9|14566|growth differentiation factor 9
mm9_v1_chr2_+_166840778_166840830	0.0186981	SOX2.p2	AK138442|Ddx27|228889|DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	AK146469|Ddx27|228889|DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	AK134274|Ddx27|228889|DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	BC024730|Ddx27|228889|DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	BC024981|Ddx27|228889|DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	BC033398|Ddx27|228889|DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	NM_153065|Ddx27|228889|DEAD (Asp-Glu-Ala-Asp) box polypeptide 27
mm9_v1_chr18_+_83080270_83080270	0.0184022	SOX2.p2	NM_183033|Zfp516|329003|zinc finger protein 516
mm9_v1_chr19_-_24299471_24299519	0.0175432	SOX2.p2	NM_011597|Tjp2|21873|tight junction protein 2
mm9_v1_chr17_-_75951137_75951285	0.0174051	SOX2.p2	AK167224|Fam98a|72722|family with sequence similarity 98, member A	BC004626|Fam98a|72722|family with sequence similarity 98, member A	AK146955|Fam98a|72722|family with sequence similarity 98, member A	AK046481|Fam98a|72722|family with sequence similarity 98, member A	AK012997|Fam98a|72722|family with sequence similarity 98, member A	AK146215|Fam98a|72722|family with sequence similarity 98, member A	AK146761|Fam98a|72722|family with sequence similarity 98, member A	NM_133747|Fam98a|72722|family with sequence similarity 98, member A
mm9_v1_chr15_-_85412250_85412299	0.0171901	SOX2.p2	BC058398|Wnt7b|22422|wingless-related MMTV integration site 7B	NM_009528|Wnt7b|22422|wingless-related MMTV integration site 7B
mm9_v1_chr3_+_137880777_137880845	0.0169717	SOX2.p2	AK009588|Adh7|11529|alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide	AK144795|Adh7|11529|alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide	BC047267|Adh7|11529|alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide	U20257|Adh7|11529|alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide
mm9_v1_chr7_-_49948087_49948135	0.0169557	SOX2.p2	BC068175|Gm5595|434179|predicted gene 5595	NM_001008427|Gm5595|434179|predicted gene 5595
mm9_v1_chr11_+_99740500_99740500	0.0168742	SOX2.p2	AK003994|Gm11567|670533|predicted gene 11567	NM_001101613|Gm11567|670533|predicted gene 11567
mm9_v1_chr10_+_80102813_80103107	0.0164052	SOX2.p2	AK180542|Csnk1g2|103236|casein kinase 1, gamma 2	AK182278|Csnk1g2|103236|casein kinase 1, gamma 2	AK184141|Csnk1g2|103236|casein kinase 1, gamma 2	AK184876|Csnk1g2|103236|casein kinase 1, gamma 2	AK013192|Csnk1g2|103236|casein kinase 1, gamma 2
mm9_v1_chr17_+_47027617_47027637	0.0156519	SOX2.p2	AK132036|Tbcc|72726|tubulin-specific chaperone C	AK012950|Tbcc|72726|tubulin-specific chaperone C	BC019476|Tbcc|72726|tubulin-specific chaperone C	BC083164|Tbcc|72726|tubulin-specific chaperone C
mm9_v1_chr2_+_169459145_169459258	0.0146177	SOX2.p2	NM_080455|Tshz2|228911|teashirt zinc finger family member 2	BC079550|Tshz2|228911|teashirt zinc finger family member 2
mm9_v1_chr2_+_29202327_29202356	0.0135068	SOX2.p2	AK147181|Med27|68975|mediator complex subunit 27	BC016537|Med27|68975|mediator complex subunit 27	AK009764|Med27|68975|mediator complex subunit 27	AK005251|Med27|68975|mediator complex subunit 27	NM_026896|Med27|68975|mediator complex subunit 27
mm9_v1_chr2_-_75819804_75820023	0.0133136	SOX2.p2	BC004773|Ttc30a1|78802|tetratricopeptide repeat domain 30A1	AK045096|Ttc30a1|78802|tetratricopeptide repeat domain 30A1	AK029535|Ttc30a1|78802|tetratricopeptide repeat domain 30A1	AK019670|Ttc30a1|78802|tetratricopeptide repeat domain 30A1	NM_030188|Ttc30a1|78802|tetratricopeptide repeat domain 30A1
mm9_v1_chr11_+_8948594_8948715	0.0129547	SOX2.p2	NM_001037928|Gm11992|626870|predicted gene 11992	AK154909|Gm11992|626870|predicted gene 11992	AK160996|Gm11992|626870|predicted gene 11992	BC147253|Gm11992|626870|predicted gene 11992	BC147254|Gm11992|626870|predicted gene 11992
mm9_v1_chr2_-_168415690_168415866	0.0128436	SOX2.p2	AF289078|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	EU887582|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	EU887588|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	EU887594|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	EU887600|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	NM_001136073|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	U36575|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	U36576|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	NM_010899|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	BC064006|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	AK081853|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	EU887584|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	EU887586|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	EU887590|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	EU887592|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	EU887596|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	EU887602|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	EU887604|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	NM_001037177|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	AK135414|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	EU887598|Nfatc2|18019|nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2
mm9_v1_chr1_-_162964371_162964389	0.0124135	SOX2.p2	BC113763|Zbtb37|240869|zinc finger and BTB domain containing 37	AK084871|Zbtb37|240869|zinc finger and BTB domain containing 37	NM_173424|Zbtb37|240869|zinc finger and BTB domain containing 37
mm9_v1_chr8_+_108380603_108380698	0.0123633	SOX2.p2	AK210001|Thap11|59016|THAP domain containing 11
mm9_v1_chr11_-_79344055_79344121	0.0120417	SOX2.p2	AK046407|Evi2a|14017|ecotropic viral integration site 2a	BC038124|Evi2a|14017|ecotropic viral integration site 2a	AK170527|Evi2a|14017|ecotropic viral integration site 2a	AK005353|Evi2a|14017|ecotropic viral integration site 2a	NM_146023|Evi2b|216984|ecotropic viral integration site 2b	NM_001033711|Evi2a|14017|ecotropic viral integration site 2a	NM_010161|Evi2a|14017|ecotropic viral integration site 2a
mm9_v1_chr4_+_116480325_116480357	0.0114022	SOX2.p2	NM_001159581|Mutyh|70603|mutY homolog (E. coli)	NM_133250|Mutyh|70603|mutY homolog (E. coli)	AK077546|Mutyh|70603|mutY homolog (E. coli)	AK156790|Mutyh|70603|mutY homolog (E. coli)	AK017730|Mutyh|70603|mutY homolog (E. coli)	AB117939|Mutyh|70603|mutY homolog (E. coli)	BC057942|Mutyh|70603|mutY homolog (E. coli)
mm9_v1_chr1_-_135557925_135557932	0.0112347	SOX2.p2	BC066163|Zc3h11a|70579|zinc finger CCCH type containing 11A
mm9_v1_chr9_+_58430031_58430196	0.0106292	SOX2.p2	NM_009145|Nptn|20320|neuroplastin	BC039191|Nptn|20320|neuroplastin
mm9_v1_chr5_-_138721164_138721212	0.0104999	SOX2.p2	AK049639|Gpc2|71951|glypican 2 (cerebroglycan)	NM_172412|Gpc2|71951|glypican 2 (cerebroglycan)	BC083180|Gpc2|71951|glypican 2 (cerebroglycan)	AK048605|Gpc2|71951|glypican 2 (cerebroglycan)	AK010515|Gpc2|71951|glypican 2 (cerebroglycan)	AK160959|Gpc2|71951|glypican 2 (cerebroglycan)	BC056941|Gpc2|71951|glypican 2 (cerebroglycan)
mm9_v1_chr5_+_138526376_138526387	0.0103378	SOX2.p2	AK028932|Zkscan1|74570|zinc finger with KRAB and SCAN domains 1
mm9_v1_chr3_+_32335072_32335127	0.0097975	SOX2.p2	BC089038|Pik3ca|18706|phosphatidylinositol 3-kinase, catalytic, alpha polypeptide	NM_008839|Pik3ca|18706|phosphatidylinositol 3-kinase, catalytic, alpha polypeptide	BC130228|Pik3ca|18706|phosphatidylinositol 3-kinase, catalytic, alpha polypeptide	U03279|Pik3ca|18706|phosphatidylinositol 3-kinase, catalytic, alpha polypeptide
mm9_v1_chr2_-_152657392_152657404	0.00947661	SOX2.p2	AK150028|Bcl2l1|12048|BCL2-like 1
mm9_v1_chr8_-_81923238_81923251	0.00937604	SOX2.p2	U74359|Smad1|17125|MAD homolog 1 (Drosophila)
mm9_v1_chr5_-_124482223_124482295	0.00905244	SOX2.p2	AK082658|Vps37b|330192|vacuolar protein sorting 37B (yeast)	AK172114|Vps37b|330192|vacuolar protein sorting 37B (yeast)	AK172337|Vps37b|330192|vacuolar protein sorting 37B (yeast)	AK149893|Vps37b|330192|vacuolar protein sorting 37B (yeast)	AK166359|Vps37b|330192|vacuolar protein sorting 37B (yeast)	BC026744|Vps37b|330192|vacuolar protein sorting 37B (yeast)	NM_177876|Vps37b|330192|vacuolar protein sorting 37B (yeast)
mm9_v1_chr17_-_25023253_25023304	0.00834955	SOX2.p2	AK169896|Nubp2|26426|nucleotide binding protein 2	AF114169|Nubp2|26426|nucleotide binding protein 2	BC012635|Nubp2|26426|nucleotide binding protein 2	AK003816|Nubp2|26426|nucleotide binding protein 2	NM_011956|Nubp2|26426|nucleotide binding protein 2
mm9_v1_chr11_+_64792527_64792682	0.00720948	SOX2.p2	AK156730|Elac2|68626|elaC homolog 2 (E. coli)	NM_023479|Elac2|68626|elaC homolog 2 (E. coli)	AK172604|Elac2|68626|elaC homolog 2 (E. coli)	BC023134|Elac2|68626|elaC homolog 2 (E. coli)	AF308696|Elac2|68626|elaC homolog 2 (E. coli)	BC048235|Elac2|68626|elaC homolog 2 (E. coli)
mm9_v1_chr19_+_45005658_45005755	0.00693786	SOX2.p2	BC150999|Fam178a|226151|family with sequence similarity 178, member A	BC157937|Fam178a|226151|family with sequence similarity 178, member A	BC172097|Fam178a|226151|family with sequence similarity 178, member A
mm9_v1_chr2_-_121282428_121282516	0.0069255	SOX2.p2	BC026459|Serinc4|574418|serine incorporator 4	BC083132|Serinc4|574418|serine incorporator 4	NM_001025371|Serinc4|574418|serine incorporator 4	AK044479|Serinc4|574418|serine incorporator 4
mm9_v1_chr19_+_56948738_56948999	0.00650586	SOX2.p2	AK145058|Vwa2|240675|von Willebrand factor A domain containing 2	AK166339|Vwa2|240675|von Willebrand factor A domain containing 2	AK160971|Vwa2|240675|von Willebrand factor A domain containing 2	AJ536329|Vwa2|240675|von Willebrand factor A domain containing 2	NM_172840|Vwa2|240675|von Willebrand factor A domain containing 2	BC116636|Vwa2|240675|von Willebrand factor A domain containing 2	BC115868|Vwa2|240675|von Willebrand factor A domain containing 2	AK029297|Vwa2|240675|von Willebrand factor A domain containing 2	AK133486|Vwa2|240675|von Willebrand factor A domain containing 2
mm9_v1_chr11_-_96838940_96839063	0.00646068	SOX2.p2	GU126673|Sp2|78912|Sp2 transcription factor	AK139302|Sp2|78912|Sp2 transcription factor	BC086457|Sp2|78912|Sp2 transcription factor	BC021759|Sp2|78912|Sp2 transcription factor	AK078246|Sp2|78912|Sp2 transcription factor	AK156580|Sp2|78912|Sp2 transcription factor	NM_001080964|Sp2|78912|Sp2 transcription factor	NM_030220|Sp2|78912|Sp2 transcription factor
mm9_v1_chr14_-_49865069_49865102	0.00609029	SOX2.p2	AK005866|1700011H14Rik|67082|RIKEN cDNA 1700011H14 gene	BC026534|1700011H14Rik|67082|RIKEN cDNA 1700011H14 gene	AK007176|1700011H14Rik|67082|RIKEN cDNA 1700011H14 gene	NM_025956|1700011H14Rik|67082|RIKEN cDNA 1700011H14 gene
mm9_v1_chr19_+_41986360_41986656	0.005972	SOX2.p2	NM_023418|Pgam1|18648|phosphoglycerate mutase 1	BC002241|Pgam1|18648|phosphoglycerate mutase 1	BC106139|Pgam1|18648|phosphoglycerate mutase 1	BC005661|Pgam1|18648|phosphoglycerate mutase 1	AF283667|Pgam1|18648|phosphoglycerate mutase 1	AK004921|Pgam1|18648|phosphoglycerate mutase 1	AK009905|Pgam1|18648|phosphoglycerate mutase 1	AK144681|Pgam1|18648|phosphoglycerate mutase 1	AK153202|Pgam1|18648|phosphoglycerate mutase 1	AK159305|Pgam1|18648|phosphoglycerate mutase 1	AK150716|Pgam1|18648|phosphoglycerate mutase 1	AK152443|Pgam1|18648|phosphoglycerate mutase 1	AK165410|Pgam1|18648|phosphoglycerate mutase 1	AK168949|Pgam1|18648|phosphoglycerate mutase 1	BC083090|Pgam1|18648|phosphoglycerate mutase 1	BC066844|Pgam1|18648|phosphoglycerate mutase 1
mm9_v1_chr16_-_38800293_38800318	0.00565161	SOX2.p2	BC046604|Upk1b|22268|uroplakin 1B	AK083101|Upk1b|22268|uroplakin 1B	AK086926|Upk1b|22268|uroplakin 1B	AK053004|Upk1b|22268|uroplakin 1B	NM_178924|Upk1b|22268|uroplakin 1B
mm9_v1_chr19_+_45122065_45122176	0.00561021	SOX2.p2	NM_001178012|Sfxn3|94280|sideroflexin 3	NM_001178013|Sfxn3|94280|sideroflexin 3	NM_053197|Sfxn3|94280|sideroflexin 3	BC012208|Sfxn3|94280|sideroflexin 3
mm9_v1_chr7_+_53152425_53152567	0.00553974	SOX2.p2	NM_144801|Tmem143|70209|transmembrane protein 143	BC017618|Tmem143|70209|transmembrane protein 143	AK035836|Tmem143|70209|transmembrane protein 143	AK010209|Tmem143|70209|transmembrane protein 143	AK171908|Tmem143|70209|transmembrane protein 143	AK087636|Tmem143|70209|transmembrane protein 143
mm9_v1_chr7_+_13609719_13609899	0.00498614	SOX2.p2	AK141357|Trim28|21849|tripartite motif-containing 28	BC023335|Trim28|21849|tripartite motif-containing 28	AF230391|Trim28|21849|tripartite motif-containing 28	AF230392|Trim28|21849|tripartite motif-containing 28	X99644|Trim28|21849|tripartite motif-containing 28
mm9_v1_chr7_+_134388053_134388144	0.00473957	SOX2.p2	BC139048|Zfp771|244216|zinc finger protein 771	BC139049|Zfp771|244216|zinc finger protein 771	BC145524|Zfp771|244216|zinc finger protein 771
mm9_v1_chr4_-_117354829_117354891	0.00468336	SOX2.p2	AF438610|Dmap1|66233|DNA methyltransferase 1-associated protein 1	NM_023178|Dmap1|66233|DNA methyltransferase 1-associated protein 1	AK012055|Dmap1|66233|DNA methyltransferase 1-associated protein 1	AK005270|Dmap1|66233|DNA methyltransferase 1-associated protein 1
mm9_v1_chr18_+_77303920_77303957	0.00465363	SOX2.p2	AK029716|Pias2|17344|protein inhibitor of activated STAT 2	NM_001164167|Pias2|17344|protein inhibitor of activated STAT 2	NM_001164169|Pias2|17344|protein inhibitor of activated STAT 2	NM_008602|Pias2|17344|protein inhibitor of activated STAT 2	AK014871|Pias2|17344|protein inhibitor of activated STAT 2
mm9_v1_chr11_-_3795097_3795128	0.00457684	SOX2.p2	AK049235|4921536K21Rik|67430|RIKEN cDNA 4921536K21 gene	BC048445|4921536K21Rik|67430|RIKEN cDNA 4921536K21 gene	AK006513|4921536K21Rik|67430|RIKEN cDNA 4921536K21 gene	AK015005|4921536K21Rik|67430|RIKEN cDNA 4921536K21 gene	AK081396|4921536K21Rik|67430|RIKEN cDNA 4921536K21 gene	NM_026150|4921536K21Rik|67430|RIKEN cDNA 4921536K21 gene
mm9_v1_chr9_-_62828677_62828715	0.00440216	SOX2.p2	AF077950|Pias1|56469|protein inhibitor of activated STAT 1	BC051417|Pias1|56469|protein inhibitor of activated STAT 1	AK075708|Pias1|56469|protein inhibitor of activated STAT 1	NM_019663|Pias1|56469|protein inhibitor of activated STAT 1	AK153871|Pias1|56469|protein inhibitor of activated STAT 1
mm9_v1_chr19_+_5878465_5878648	0.00361967	SOX2.p2	NM_134154|Slc25a45|107375|solute carrier family 25, member 45	BC037680|Slc25a45|107375|solute carrier family 25, member 45	BC022156|Slc25a45|107375|solute carrier family 25, member 45
mm9_v1_chr15_-_83180585_83180713	0.0032891	SOX2.p2	AK169107|Arfgap3|66251|ADP-ribosylation factor GTPase activating protein 3	AK007732|Arfgap3|66251|ADP-ribosylation factor GTPase activating protein 3	BC060369|Arfgap3|66251|ADP-ribosylation factor GTPase activating protein 3	BC004081|Arfgap3|66251|ADP-ribosylation factor GTPase activating protein 3	AK018680|Arfgap3|66251|ADP-ribosylation factor GTPase activating protein 3	AK075788|Arfgap3|66251|ADP-ribosylation factor GTPase activating protein 3	AK028990|Arfgap3|66251|ADP-ribosylation factor GTPase activating protein 3	NM_025445|Arfgap3|66251|ADP-ribosylation factor GTPase activating protein 3
mm9_v1_chr18_-_62915799_62916000	0.00293231	SOX2.p2	BC072581|2700046A07Rik|78449|RIKEN cDNA 2700046A07 gene	AK012381|2700046A07Rik|78449|RIKEN cDNA 2700046A07 gene	AK020725|2700046A07Rik|78449|RIKEN cDNA 2700046A07 gene
mm9_v1_chr7_-_26443700_26443803	0.00279183	SOX2.p2	L47335|Bckdha|12039|branched chain ketoacid dehydrogenase E1, alpha polypeptide	AK002435|Bckdha|12039|branched chain ketoacid dehydrogenase E1, alpha polypeptide	AK154734|Bckdha|12039|branched chain ketoacid dehydrogenase E1, alpha polypeptide	NM_007533|Bckdha|12039|branched chain ketoacid dehydrogenase E1, alpha polypeptide
mm9_v1_chr13_-_73838142_73838227	0.00268508	SOX2.p2	AK014544|Slc6a19|74338|solute carrier family 6 (neurotransmitter transporter), member 19	AK028784|Slc6a19|74338|solute carrier family 6 (neurotransmitter transporter), member 19	AK128923|Slc6a19|74338|solute carrier family 6 (neurotransmitter transporter), member 19	NM_028878|Slc6a19|74338|solute carrier family 6 (neurotransmitter transporter), member 19	BC107411|Slc6a19|74338|solute carrier family 6 (neurotransmitter transporter), member 19	BC107412|Slc6a19|74338|solute carrier family 6 (neurotransmitter transporter), member 19	AJ633679|Slc6a19|74338|solute carrier family 6 (neurotransmitter transporter), member 19	AB096860|Slc6a19|74338|solute carrier family 6 (neurotransmitter transporter), member 19
mm9_v1_chr5_+_114185982_114186036	0.00241112	SOX2.p2	AK044446|Ficd|231630|FIC domain containing	AK054325|Ficd|231630|FIC domain containing
mm9_v1_chr7_+_26466176_26466176	0.00179153	SOX2.p2	BC028440|B9d2|232987|B9 protein domain 2	NM_172148|B9d2|232987|B9 protein domain 2
mm9_v1_chr2_-_155183133_155183168	0.0015838	SOX2.p2	AK162913|Pigu|228812|phosphatidylinositol glycan anchor biosynthesis, class U	AK171988|Pigu|228812|phosphatidylinositol glycan anchor biosynthesis, class U	BC120680|Pigu|228812|phosphatidylinositol glycan anchor biosynthesis, class U	BC120682|Pigu|228812|phosphatidylinositol glycan anchor biosynthesis, class U	AK140955|Pigu|228812|phosphatidylinositol glycan anchor biosynthesis, class U	AK143517|Pigu|228812|phosphatidylinositol glycan anchor biosynthesis, class U	NM_001004721|Pigu|228812|phosphatidylinositol glycan anchor biosynthesis, class U
mm9_v1_chr16_-_33961960_33961990	0.00135539	SOX2.p2	M29395|Umps|22247|uridine monophosphate synthetase
mm9_v1_chr8_+_70047752_70047752	0.00126269	SOX2.p2	AK077364|Nat3|17962|N-acetyltransferase 3	NM_008674|Nat3|17962|N-acetyltransferase 3
mm9_v1_chr19_-_25036047_25036105	0.000907178	SOX2.p2	BC018472|Cbwd1|226043|COBW domain containing 1	AK076027|Cbwd1|226043|COBW domain containing 1	BC053745|Cbwd1|226043|COBW domain containing 1	AK132291|Cbwd1|226043|COBW domain containing 1	NM_146097|Cbwd1|226043|COBW domain containing 1
mm9_v1_chr14_+_99498642_99498692	0.000621567	SOX2.p2	AK017107|Pibf1|52023|progesterone immunomodulatory binding factor 1	NM_029320|Pibf1|52023|progesterone immunomodulatory binding factor 1	NM_029454|Pibf1|52023|progesterone immunomodulatory binding factor 1
mm9_v1_chr2_+_83795612_83795648	0.000522022	SOX2.p2	NM_001177418|Gm13698|668096|predicted gene 13698	NM_001177422|Gm13693|668100|predicted gene 13693	NM_001177424|Gm13696|668107|predicted gene 13696	NM_001177429|Gm13694|668113|predicted gene 13694	NM_001177430|Gm13697|668115|predicted gene 13697	NM_001177432|Gm13691|668119|predicted gene 13691	NM_001177434|Gm13695|545432|predicted gene 13695	AK139594|Gm13698|668096|predicted gene 13698
mm9_v1_chr18_+_77168765_77168895	0.00044067	SOX2.p2	NM_025409|Ier3ip1|66191|immediate early response 3 interacting protein 1	AK004281|Ier3ip1|66191|immediate early response 3 interacting protein 1	BC021512|Ier3ip1|66191|immediate early response 3 interacting protein 1	AK007388|Ier3ip1|66191|immediate early response 3 interacting protein 1	AK007862|Ier3ip1|66191|immediate early response 3 interacting protein 1	AK009116|Ier3ip1|66191|immediate early response 3 interacting protein 1	AK182132|Ier3ip1|66191|immediate early response 3 interacting protein 1	AK190140|Ier3ip1|66191|immediate early response 3 interacting protein 1	AK210106|Ier3ip1|66191|immediate early response 3 interacting protein 1
mm9_v1_chr2_+_83807232_83807268	0.000400645	SOX2.p2	NM_001177418|Gm13698|668096|predicted gene 13698	NM_001177422|Gm13693|668100|predicted gene 13693	NM_001177424|Gm13696|668107|predicted gene 13696	NM_001177429|Gm13694|668113|predicted gene 13694	NM_001177430|Gm13697|668115|predicted gene 13697	NM_001177432|Gm13691|668119|predicted gene 13691	NM_001177434|Gm13695|545432|predicted gene 13695	AK139594|Gm13698|668096|predicted gene 13698
mm9_v1_chr2_+_83824662_83824698	0.000400645	SOX2.p2	NM_001177418|Gm13698|668096|predicted gene 13698	NM_001177422|Gm13693|668100|predicted gene 13693	NM_001177424|Gm13696|668107|predicted gene 13696	NM_001177429|Gm13694|668113|predicted gene 13694	NM_001177430|Gm13697|668115|predicted gene 13697	NM_001177432|Gm13691|668119|predicted gene 13691	NM_001177434|Gm13695|545432|predicted gene 13695	AK139594|Gm13698|668096|predicted gene 13698
mm9_v1_chr2_+_83801422_83801458	0.000400645	SOX2.p2	NM_001177418|Gm13698|668096|predicted gene 13698	NM_001177422|Gm13693|668100|predicted gene 13693	NM_001177424|Gm13696|668107|predicted gene 13696	NM_001177429|Gm13694|668113|predicted gene 13694	NM_001177430|Gm13697|668115|predicted gene 13697	NM_001177432|Gm13691|668119|predicted gene 13691	NM_001177434|Gm13695|545432|predicted gene 13695	AK139594|Gm13698|668096|predicted gene 13698
mm9_v1_chr2_+_83813042_83813078	0.000400645	SOX2.p2	NM_001177418|Gm13698|668096|predicted gene 13698	NM_001177422|Gm13693|668100|predicted gene 13693	NM_001177424|Gm13696|668107|predicted gene 13696	NM_001177429|Gm13694|668113|predicted gene 13694	NM_001177430|Gm13697|668115|predicted gene 13697	NM_001177432|Gm13691|668119|predicted gene 13691	NM_001177434|Gm13695|545432|predicted gene 13695	AK139594|Gm13698|668096|predicted gene 13698
mm9_v1_chr2_+_83830472_83830508	0.000400645	SOX2.p2	NM_001177418|Gm13698|668096|predicted gene 13698	NM_001177422|Gm13693|668100|predicted gene 13693	NM_001177424|Gm13696|668107|predicted gene 13696	NM_001177429|Gm13694|668113|predicted gene 13694	NM_001177430|Gm13697|668115|predicted gene 13697	NM_001177432|Gm13691|668119|predicted gene 13691	NM_001177434|Gm13695|545432|predicted gene 13695	AK139594|Gm13698|668096|predicted gene 13698
mm9_v1_chr2_+_83818852_83818888	0.000400645	SOX2.p2	NM_001177418|Gm13698|668096|predicted gene 13698	NM_001177422|Gm13693|668100|predicted gene 13693	NM_001177424|Gm13696|668107|predicted gene 13696	NM_001177429|Gm13694|668113|predicted gene 13694	NM_001177430|Gm13697|668115|predicted gene 13697	NM_001177432|Gm13691|668119|predicted gene 13691	NM_001177434|Gm13695|545432|predicted gene 13695	AK139594|Gm13698|668096|predicted gene 13698
mm9_v1_chr1_+_89346303_89346444	3.22243e-05	SOX2.p2	AK044009|Gigyf2|227331|GRB10 interacting GYF protein 2
