mm9_v1_chr7_-_56892061_56892218	43.5248	SOX2.p2	BC082541|Dbx1|13172|developing brain homeobox 1	NM_001005232|Dbx1|13172|developing brain homeobox 1	S75837|Dbx1|13172|developing brain homeobox 1
mm9_v1_chr1_-_42749940_42749978	35.2297	SOX2.p2	BC059892|2610017I09Rik|66297|RIKEN cDNA 2610017I09 gene	BC058417|2610017I09Rik|66297|RIKEN cDNA 2610017I09 gene
mm9_v1_chr8_+_46593141_46593271	30.4315	SOX2.p2	AK171632|Sorbs2|234214|sorbin and SH3 domain containing 2	NM_172752|Sorbs2|234214|sorbin and SH3 domain containing 2	AK139388|Sorbs2|234214|sorbin and SH3 domain containing 2	BC151038|Sorbs2|234214|sorbin and SH3 domain containing 2	BC172140|Sorbs2|234214|sorbin and SH3 domain containing 2
mm9_v1_chr1_-_140739020_140739033	22.4329	SOX2.p2	AK031478|Lhx9|16876|LIM homeobox protein 9	NM_001025565|Lhx9|16876|LIM homeobox protein 9	NM_001042577|Lhx9|16876|LIM homeobox protein 9	BC072623|Lhx9|16876|LIM homeobox protein 9
mm9_v1_chr10_+_17516024_17516131	21.4625	SOX2.p2	AK084639|Txlnb|378431|taxilin beta	NM_138628|Txlnb|378431|taxilin beta	AK084579|Txlnb|378431|taxilin beta	AK052324|Txlnb|378431|taxilin beta	AF422244|Txlnb|378431|taxilin beta	AF422245|Txlnb|378431|taxilin beta	AK137442|Txlnb|378431|taxilin beta	BC141023|Txlnb|378431|taxilin beta	AK085904|Txlnb|378431|taxilin beta
mm9_v1_chr2_-_65405546_65405588	21.0461	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_chr10_+_43298969_43299042	20.9844	SOX2.p2	AK014279|Cd24a|12484|CD24a antigen	NM_009846|Cd24a|12484|CD24a antigen	AK133869|Cd24a|12484|CD24a antigen	AK168111|Cd24a|12484|CD24a antigen	AK169613|Cd24a|12484|CD24a antigen	BC026702|Cd24a|12484|CD24a antigen	M58661|Cd24a|12484|CD24a antigen	BC075622|Cd24a|12484|CD24a antigen	X53825|Cd24a|12484|CD24a antigen
mm9_v1_chr6_-_12699189_12699252	20.61	SOX2.p2	NM_001164805|Thsd7a|330267|thrombospondin, type I, domain containing 7A
mm9_v1_chr18_-_46372017_46372260	19.8489	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_chr1_-_12980994_12981257	19.7427	SOX2.p2	BC117943|Slco5a1|240726|solute carrier organic anion transporter family, member 5A1	BC117944|Slco5a1|240726|solute carrier organic anion transporter family, member 5A1	AK048882|Slco5a1|240726|solute carrier organic anion transporter family, member 5A1	AK041736|Slco5a1|240726|solute carrier organic anion transporter family, member 5A1	NM_172841|Slco5a1|240726|solute carrier organic anion transporter family, member 5A1	AK028758|Slco5a1|240726|solute carrier organic anion transporter family, member 5A1
mm9_v1_chr12_+_30219982_30220081	19.268	SOX2.p2	AK049624|Myt1l|17933|myelin transcription factor 1-like
mm9_v1_chrX_-_149078963_149079085	17.2361	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_chr10_+_119256444_119256567	16.6137	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_chr5_+_48374328_48374415	15.3387	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_chr18_-_43552694_43552984	15.0758	SOX2.p2	BC023003|Dpysl3|22240|dihydropyrimidinase-like 3	NM_009468|Dpysl3|22240|dihydropyrimidinase-like 3	X87817|Dpysl3|22240|dihydropyrimidinase-like 3
mm9_v1_chr2_+_181498036_181498036	14.3892	SOX2.p2	BC063252|Myt1|17932|myelin transcription factor 1	NM_001171615|Myt1|17932|myelin transcription factor 1
mm9_v1_chrX_+_106290703_106290922	14.1411	SOX2.p2	BC043055|Sh3bgrl|56726|SH3-binding domain glutamic acid-rich protein like	NM_019989|Sh3bgrl|56726|SH3-binding domain glutamic acid-rich protein like	AK218315|Sh3bgrl|56726|SH3-binding domain glutamic acid-rich protein like	BC034161|Sh3bgrl|56726|SH3-binding domain glutamic acid-rich protein like	AK151871|Sh3bgrl|56726|SH3-binding domain glutamic acid-rich protein like	AK165995|Sh3bgrl|56726|SH3-binding domain glutamic acid-rich protein like	AK146588|Sh3bgrl|56726|SH3-binding domain glutamic acid-rich protein like	AK150604|Sh3bgrl|56726|SH3-binding domain glutamic acid-rich protein like	AK151095|Sh3bgrl|56726|SH3-binding domain glutamic acid-rich protein like	AK049929|Sh3bgrl|56726|SH3-binding domain glutamic acid-rich protein like	AK151501|Sh3bgrl|56726|SH3-binding domain glutamic acid-rich protein like	AJ272504|Sh3bgrl|56726|SH3-binding domain glutamic acid-rich protein like
mm9_v1_chr11_+_93905557_93905590	13.8679	SOX2.p2	BC052058|Spag9|70834|sperm associated antigen 9	BC060100|Spag9|70834|sperm associated antigen 9	BC094670|Spag9|70834|sperm associated antigen 9
mm9_v1_chr7_-_91827857_91827907	13.8255	SOX2.p2	AK002775|Zfand6|65098|zinc finger, AN1-type domain 6	NM_022985|Zfand6|65098|zinc finger, AN1-type domain 6	AK144902|Zfand6|65098|zinc finger, AN1-type domain 6	AK009403|Zfand6|65098|zinc finger, AN1-type domain 6
mm9_v1_chr4_+_109015660_109015680	13.7129	SOX2.p2	NM_001159964|Eps15|13858|epidermal growth factor receptor pathway substrate 15	AK083176|Eps15|13858|epidermal growth factor receptor pathway substrate 15
mm9_v1_chr12_+_30213224_30213265	13.3313	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_chr2_-_59963586_59963753	13.0711	SOX2.p2	BC150814|Baz2b|407823|bromodomain adjacent to zinc finger domain, 2B	AK029386|Baz2b|407823|bromodomain adjacent to zinc finger domain, 2B	AK134250|Baz2b|407823|bromodomain adjacent to zinc finger domain, 2B	AK173180|Baz2b|407823|bromodomain adjacent to zinc finger domain, 2B	AK030867|Baz2b|407823|bromodomain adjacent to zinc finger domain, 2B
mm9_v1_chr5_-_135028197_135028344	12.8532	SOX2.p2	BC039162|Clip2|269713|CAP-GLY domain containing linker protein 2	BC053048|Clip2|269713|CAP-GLY domain containing linker protein 2	NM_001039162|Clip2|269713|CAP-GLY domain containing linker protein 2	NM_009990|Clip2|269713|CAP-GLY domain containing linker protein 2
mm9_v1_chr10_+_101621491_101621538	12.4281	SOX2.p2	NM_001162368|Mgat4c|67569|mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)	AK015051|4930402I19Rik|73798|RIKEN cDNA 4930402I19 gene
mm9_v1_chrX_+_139952975_139953253	12.3026	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_chr12_-_36769054_36769127	11.206	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_chr4_+_129190877_129190896	11.1446	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_chr4_-_109960078_109960115	10.8039	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_chr4_+_129190872_129190875	10.6019	SOX2.p2	AK083913|Marcksl1|17357|MARCKS-like 1
mm9_v1_chr8_+_63703064_63703069	10.5411	SOX2.p2	AF030131|Sh3rf1|59009|SH3 domain containing ring finger 1
mm9_v1_chr4_+_48598013_48598089	10.3528	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_chr3_-_107734481_107734662	10.0578	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_chr3_-_66100663_66100758	9.91938	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_chr6_-_138371302_138371390	9.85787	SOX2.p2	BC057086|Lmo3|109593|LIM domain only 3
mm9_v1_chr10_+_28863801_28863929	9.76738	SOX2.p2	NM_026138|6330407J23Rik|67412|RIKEN cDNA 6330407J23 gene	AK030682|6330407J23Rik|67412|RIKEN cDNA 6330407J23 gene
mm9_v1_chrX_+_130829929_130829942	9.66172	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_chr2_+_157385835_157385932	9.60085	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_chr5_+_143722032_143722059	9.5767	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_chr3_-_122322556_122322614	9.5187	SOX2.p2	AK151930|Fnbp1l|214459|formin binding protein 1-like	AK152002|Fnbp1l|214459|formin binding protein 1-like	NM_001114665|Fnbp1l|214459|formin binding protein 1-like	NM_153118|Fnbp1l|214459|formin binding protein 1-like
mm9_v1_chr19_-_19185685_19185685	9.42414	SOX2.p2	NM_001043354|Rorb|225998|RAR-related orphan receptor beta
mm9_v1_chr2_+_61642509_61642690	9.35122	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_chr8_-_86760940_86760953	9.33321	SOX2.p2	BC058080|Zswim4|212168|zinc finger, SWIM domain containing 4	NM_172503|Zswim4|212168|zinc finger, SWIM domain containing 4	AK041934|Zswim4|212168|zinc finger, SWIM domain containing 4	AK052168|Zswim4|212168|zinc finger, SWIM domain containing 4	AK053663|Zswim4|212168|zinc finger, SWIM domain containing 4	AK150221|Zswim4|212168|zinc finger, SWIM domain containing 4	AK155465|Zswim4|212168|zinc finger, SWIM domain containing 4
mm9_v1_chr13_-_56353523_56353523	9.18328	SOX2.p2	BC062148|Neurog1|18014|neurogenin 1	NM_010896|Neurog1|18014|neurogenin 1
mm9_v1_chr14_-_20796411_20796481	8.88075	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_chr2_-_73613381_73613446	8.73734	SOX2.p2	NM_001113246|Chn1|108699|chimerin (chimaerin) 1	NM_001166603|Chn1|108699|chimerin (chimaerin) 1
mm9_v1_chr4_+_13670582_13670631	8.66373	SOX2.p2	AK032132|Runx1t1|12395|runt-related transcription factor 1; translocated to, 1 (cyclin D-related)
mm9_v1_chr16_-_17125198_17125232	8.60559	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_chr18_+_59222034_59222186	8.57209	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_chr14_-_20796199_20796254	8.55069	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_chr10_+_68996455_68996596	8.47869	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_chr17_-_35975148_35975258	8.36024	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_chr5_+_89012547_89012592	8.31856	SOX2.p2	AK018184|Rufy3|52822|RUN and FYVE domain containing 3
mm9_v1_chrX_-_140367467_140367853	8.22792	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_chr12_-_32398730_32398790	8.21904	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_chr1_-_195196423_195196475	8.19202	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_chr3_+_127336055_127336062	8.19051	SOX2.p2	AK143190|Neurog2|11924|neurogenin 2	BC055743|Neurog2|11924|neurogenin 2	NM_009718|Neurog2|11924|neurogenin 2
mm9_v1_chr3_+_53959956_53960294	8.16477	SOX2.p2	AK084109|Trpc4|22066|transient receptor potential cation channel, subfamily C, member 4	AK080670|Trpc4|22066|transient receptor potential cation channel, subfamily C, member 4	AK084139|Trpc4|22066|transient receptor potential cation channel, subfamily C, member 4	NM_016984|Trpc4|22066|transient receptor potential cation channel, subfamily C, member 4	U50921|Trpc4|22066|transient receptor potential cation channel, subfamily C, member 4	U50922|Trpc4|22066|transient receptor potential cation channel, subfamily C, member 4	BC120729|Trpc4|22066|transient receptor potential cation channel, subfamily C, member 4	BC131915|Trpc4|22066|transient receptor potential cation channel, subfamily C, member 4	AK044265|Trpc4|22066|transient receptor potential cation channel, subfamily C, member 4	AF190646|Trpc4|22066|transient receptor potential cation channel, subfamily C, member 4	AF011543|Trpc4|22066|transient receptor potential cation channel, subfamily C, member 4	AF019663|Trpc4|22066|transient receptor potential cation channel, subfamily C, member 4	AK049788|Trpc4|22066|transient receptor potential cation channel, subfamily C, member 4
mm9_v1_chr17_+_17539832_17539856	8.06873	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_chr3_+_94282235_94282264	8.06148	SOX2.p2	AK044506|Celf3|78784|VCUGBP, Elav-like family member 3	AK087536|Celf3|78784|VCUGBP, Elav-like family member 3
mm9_v1_chr19_-_46114019_46114148	8.05954	SOX2.p2	NM_010697|Ldb1|16825|LIM domain binding 1	U69270|Ldb1|16825|LIM domain binding 1
mm9_v1_chr5_-_92512683_92512782	8.04257	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_chr10_+_79612410_79612424	8.00028	SOX2.p2	AK154535|Midn|59090|midnolin
mm9_v1_chr10_+_57206184_57206291	7.96468	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_chr2_+_37372112_37372145	7.91176	SOX2.p2	AK141999|Gpr21|338346|G protein-coupled receptor 21	AK048682|Gpr21|338346|G protein-coupled receptor 21	AK139361|Gpr21|338346|G protein-coupled receptor 21	NM_177383|Gpr21|338346|G protein-coupled receptor 21
mm9_v1_chr4_-_20705698_20705814	7.85001	SOX2.p2	AK051427|Nkain3|269513|Na+/K+ transporting ATPase interacting 3	AK053823|Nkain3|269513|Na+/K+ transporting ATPase interacting 3	AK141456|Nkain3|269513|Na+/K+ transporting ATPase interacting 3	BC075683|Nkain3|269513|Na+/K+ transporting ATPase interacting 3	NM_172987|Nkain3|269513|Na+/K+ transporting ATPase interacting 3
mm9_v1_chr1_+_19198994_19199078	7.789	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_chr16_-_44558929_44559002	7.76801	SOX2.p2	BC078631|Boc|117606|biregional cell adhesion molecule-related/down-regulated by oncogenes (Cdon) binding protein	BC062892|Boc|117606|biregional cell adhesion molecule-related/down-regulated by oncogenes (Cdon) binding protein	AK028889|Boc|117606|biregional cell adhesion molecule-related/down-regulated by oncogenes (Cdon) binding protein	NM_172506|Boc|117606|biregional cell adhesion molecule-related/down-regulated by oncogenes (Cdon) binding protein	AK043379|Boc|117606|biregional cell adhesion molecule-related/down-regulated by oncogenes (Cdon) binding protein	AK028770|Boc|117606|biregional cell adhesion molecule-related/down-regulated by oncogenes (Cdon) binding protein
mm9_v1_chr18_-_75120759_75120936	7.75943	SOX2.p2	BC020991|Lipg|16891|lipase, endothelial	AF118768|Lipg|16891|lipase, endothelial	AK090224|Lipg|16891|lipase, endothelial	AK152430|Lipg|16891|lipase, endothelial	AK152161|Lipg|16891|lipase, endothelial	AK153541|Lipg|16891|lipase, endothelial	AK152872|Lipg|16891|lipase, endothelial	AK172101|Lipg|16891|lipase, endothelial	NM_010720|Lipg|16891|lipase, endothelial
mm9_v1_chr18_-_16966954_16967033	7.70562	SOX2.p2	AK087418|Cdh2|12558|cadherin 2	BC022107|Cdh2|12558|cadherin 2	AK032826|Cdh2|12558|cadherin 2
mm9_v1_chr14_-_109313298_109313300	7.67405	SOX2.p2	AK144290|Slitrk1|76965|SLIT and NTRK-like family, member 1
mm9_v1_chr19_+_4756524_4756619	7.66011	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_chr2_-_56967331_56967448	7.63076	SOX2.p2	S53744|Nr4a2|18227|nuclear receptor subfamily 4, group A, member 2	AK158607|Nr4a2|18227|nuclear receptor subfamily 4, group A, member 2	NM_013613|Nr4a2|18227|nuclear receptor subfamily 4, group A, member 2
mm9_v1_chr5_+_67067477_67067482	7.53934	SOX2.p2	AK004066|Uchl1|22223|ubiquitin carboxy-terminal hydrolase L1	AK013729|Uchl1|22223|ubiquitin carboxy-terminal hydrolase L1
mm9_v1_chr11_+_93905443_93905464	7.47653	SOX2.p2	AK147537|Spag9|70834|sperm associated antigen 9	AK147431|Spag9|70834|sperm associated antigen 9
mm9_v1_chr4_-_91042997_91043190	7.4428	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_chr6_+_17015159_17015226	7.29152	SOX2.p2	AK083910|Tes|21753|testis derived transcript	AK132249|Tes|21753|testis derived transcript	AK167274|Tes|21753|testis derived transcript	BC010465|Tes|21753|testis derived transcript	AK145609|Tes|21753|testis derived transcript	AK167101|Tes|21753|testis derived transcript	BC051103|Tes|21753|testis derived transcript	BC003808|Tes|21753|testis derived transcript
mm9_v1_chr3_+_101814059_101814199	7.22142	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_chr3_-_143865162_143865359	7.16839	SOX2.p2	BC003488|Lmo4|16911|LIM domain only 4	BC100382|Lmo4|16911|LIM domain only 4	AF102817|Lmo4|16911|LIM domain only 4	AK138278|Lmo4|16911|LIM domain only 4	NM_001161770|Lmo4|16911|LIM domain only 4	NM_001161769|Lmo4|16911|LIM domain only 4
mm9_v1_chr13_-_54789064_54789098	7.1608	SOX2.p2	AK161651|Rnf44|105239|ring finger protein 44
mm9_v1_chr3_-_83844042_83844096	7.12345	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_chr5_+_13399492_13399661	7.07442	SOX2.p2	AK053115|Sema3a|20346|sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	BC057588|Sema3a|20346|sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A
mm9_v1_chr4_-_77857594_77857662	7.05433	SOX2.p2	AK086248|Ptprd|19266|protein tyrosine phosphatase, receptor type, D
mm9_v1_chr4_-_6917628_6917956	6.91928	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_chr10_-_26095736_26095813	6.77148	SOX2.p2	BC082309|L3mbtl3|237339|l(3)mbt-like 3 (Drosophila)	AK031398|L3mbtl3|237339|l(3)mbt-like 3 (Drosophila)
mm9_v1_chr12_+_53800369_53800393	6.73423	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_chr2_-_59963796_59963833	6.62832	SOX2.p2	NM_001001182|Baz2b|407823|bromodomain adjacent to zinc finger domain, 2B	AK147737|Baz2b|407823|bromodomain adjacent to zinc finger domain, 2B
mm9_v1_chr15_-_26825266_26825387	6.62228	SOX2.p2	AK129227|Fbxl7|448987|F-box and leucine-rich repeat protein 7	BC050864|Fbxl7|448987|F-box and leucine-rich repeat protein 7	BC091646|Fbxl7|448987|F-box and leucine-rich repeat protein 7	NM_176959|Fbxl7|448987|F-box and leucine-rich repeat protein 7	AK048688|Fbxl7|448987|F-box and leucine-rich repeat protein 7	AK051849|Fbxl7|448987|F-box and leucine-rich repeat protein 7
mm9_v1_chr12_+_3365147_3365223	6.61963	SOX2.p2	AK133649|Kif3c|16570|kinesin family member 3C	BC053053|Kif3c|16570|kinesin family member 3C
mm9_v1_chr12_+_96930429_96930467	6.60927	SOX2.p2	AK135149|Flrt2|399558|fibronectin leucine rich transmembrane protein 2	NM_201518|Flrt2|399558|fibronectin leucine rich transmembrane protein 2	AK136973|Flrt2|399558|fibronectin leucine rich transmembrane protein 2	BC067058|Flrt2|399558|fibronectin leucine rich transmembrane protein 2	AK041311|Flrt2|399558|fibronectin leucine rich transmembrane protein 2	BC096471|Flrt2|399558|fibronectin leucine rich transmembrane protein 2
mm9_v1_chr8_+_63702967_63703040	6.59556	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_chr7_-_111001598_111001720	6.58889	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_chr9_+_96159666_96159703	6.56088	SOX2.p2	NM_001184710|Tfdp2|211586|transcription factor Dp 2	NM_001184711|Tfdp2|211586|transcription factor Dp 2	AK158829|Tfdp2|211586|transcription factor Dp 2	BC092230|Tfdp2|211586|transcription factor Dp 2
mm9_v1_chr2_-_165710128_165710217	6.51552	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_chr6_+_64992584_64992660	6.46893	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_chr9_+_96159123_96159160	6.43279	SOX2.p2	NM_001184709|Tfdp2|211586|transcription factor Dp 2	AK033356|Tfdp2|211586|transcription factor Dp 2
mm9_v1_chr7_+_69493148_69493265	6.43121	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_chr15_+_98465193_98465247	6.4255	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_chr3_+_89019126_89019154	6.38602	SOX2.p2	L04302|Thbs3|21827|thrombospondin 3	L24434|Thbs3|21827|thrombospondin 3	BC060104|Thbs3|21827|thrombospondin 3	BC053023|Thbs3|21827|thrombospondin 3
mm9_v1_chr9_+_74823917_74823980	6.3859	SOX2.p2	BC031353|BC031353|235493|cDNA sequence BC031353	NM_153584|BC031353|235493|cDNA sequence BC031353
mm9_v1_chr8_-_42140113_42140147	6.31402	SOX2.p2	BC043321|Mtus1|102103|mitochondrial tumor suppressor 1	AK043214|Mtus1|102103|mitochondrial tumor suppressor 1	AY626782|Mtus1|102103|mitochondrial tumor suppressor 1	NM_001005864|Mtus1|102103|mitochondrial tumor suppressor 1
mm9_v1_chr1_+_9591550_9591585	6.30197	SOX2.p2	BC066997|3110035E14Rik|76982|RIKEN cDNA 3110035E14 gene
mm9_v1_chr12_+_30219769_30219800	6.28189	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_chr1_+_155596555_155596633	6.26735	SOX2.p2	AK140815|Rnasel|24014|ribonuclease L (2', 5'-oligoisoadenylate synthetase-dependent)	NM_011882|Rnasel|24014|ribonuclease L (2', 5'-oligoisoadenylate synthetase-dependent)	BC003873|Rnasel|24014|ribonuclease L (2', 5'-oligoisoadenylate synthetase-dependent)
mm9_v1_chr5_-_92566671_92566678	6.24442	SOX2.p2	
mm9_v1_chr9_-_71743854_71743929	6.23881	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_chr4_-_77857753_77857864	6.20614	SOX2.p2	AK083789|Ptprd|19266|protein tyrosine phosphatase, receptor type, D	AK045658|Ptprd|19266|protein tyrosine phosphatase, receptor type, D	AK034145|Ptprd|19266|protein tyrosine phosphatase, receptor type, D	AK080973|Ptprd|19266|protein tyrosine phosphatase, receptor type, D
mm9_v1_chr4_+_13670425_13670448	6.17822	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_chr1_+_62749850_62750115	6.13949	SOX2.p2	NM_001077403|Nrp2|18187|neuropilin 2	NM_001077404|Nrp2|18187|neuropilin 2	NM_001077405|Nrp2|18187|neuropilin 2	NM_001077406|Nrp2|18187|neuropilin 2	NM_001077407|Nrp2|18187|neuropilin 2	NM_010939|Nrp2|18187|neuropilin 2	AK149643|Nrp2|18187|neuropilin 2	AK051873|Nrp2|18187|neuropilin 2
mm9_v1_chr11_-_95867076_95867257	6.10569	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_chr11_+_93905501_93905545	6.10249	SOX2.p2	AK014060|Spag9|70834|sperm associated antigen 9	AK079365|Spag9|70834|sperm associated antigen 9	NM_001025428|Spag9|70834|sperm associated antigen 9	NM_001025429|Spag9|70834|sperm associated antigen 9	NM_001025430|Spag9|70834|sperm associated antigen 9	AK172961|Spag9|70834|sperm associated antigen 9
mm9_v1_chr2_-_51004604_51004631	6.10163	SOX2.p2	BC009002|Rnd3|74194|Rho family GTPase 3	AK035195|Rnd3|74194|Rho family GTPase 3	AK048635|Rnd3|74194|Rho family GTPase 3	AK011442|Rnd3|74194|Rho family GTPase 3	NM_028810|Rnd3|74194|Rho family GTPase 3
mm9_v1_chr4_+_111087610_111087629	6.02879	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_chr7_-_112936063_112936159	6.01481	SOX2.p2	NM_001162943|Dchs1|233651|dachsous 1 (Drosophila)	AK048080|Dchs1|233651|dachsous 1 (Drosophila)
mm9_v1_chr16_+_17070249_17070422	6.00458	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_chr18_+_65048630_65048682	5.99564	SOX2.p2	AK042621|Nedd4l|83814|neural precursor cell expressed, developmentally down-regulated gene 4-like
mm9_v1_chr2_+_14976877_14977152	5.97328	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_chr5_+_89012600_89012641	5.9186	SOX2.p2	AK045610|Rufy3|52822|RUN and FYVE domain containing 3	AK083242|Rufy3|52822|RUN and FYVE domain containing 3
mm9_v1_chr4_-_155571450_155571620	5.86788	SOX2.p2	U84407|Agrn|11603|agrin	AY914875|Agrn|11603|agrin	AF190858|Agrn|11603|agrin	AK134826|Agrn|11603|agrin
mm9_v1_chr7_-_134758707_134758785	5.84632	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_chr5_+_19413335_19413335	5.82622	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_chr18_-_33623527_33623549	5.81395	SOX2.p2	AK020629|D0H4S114|27528|DNA segment, human D4S114
mm9_v1_chrX_-_103124651_103124717	5.77349	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_chrX_+_104115963_104116162	5.76832	SOX2.p2	NM_175271|Lpar4|78134|lysophosphatidic acid receptor 4	BC052178|Lpar4|78134|lysophosphatidic acid receptor 4	AK051709|Lpar4|78134|lysophosphatidic acid receptor 4	AK019967|Lpar4|78134|lysophosphatidic acid receptor 4	AK045289|Lpar4|78134|lysophosphatidic acid receptor 4	BC069178|Lpar4|78134|lysophosphatidic acid receptor 4	BC138893|Lpar4|78134|lysophosphatidic acid receptor 4	BC138894|Lpar4|78134|lysophosphatidic acid receptor 4
mm9_v1_chr5_+_111846284_111846381	5.73352	SOX2.p2	AK142207|Mn1|433938|meningioma 1
mm9_v1_chr9_-_117161564_117161606	5.7137	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_chr1_-_135817945_135817982	5.70176	SOX2.p2	AK037150|Prelp|116847|proline arginine-rich end leucine-rich repeat	BC019775|Prelp|116847|proline arginine-rich end leucine-rich repeat	AK047480|Prelp|116847|proline arginine-rich end leucine-rich repeat	NM_054077|Prelp|116847|proline arginine-rich end leucine-rich repeat
mm9_v1_chr5_+_36236113_36236140	5.70062	SOX2.p2	AK043209|Afap1|70292|actin filament associated protein 1	AK148000|Afap1|70292|actin filament associated protein 1	AK011153|Afap1|70292|actin filament associated protein 1
mm9_v1_chr7_+_134376574_134376794	5.65448	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_chr12_-_14158843_14158897	5.64362	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_chr13_-_55589377_55589460	5.63265	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_chr6_-_31513817_31513936	5.5489	SOX2.p2	AB028048|Podxl|27205|podocalyxin-like	AF290209|Podxl|27205|podocalyxin-like	BC052442|Podxl|27205|podocalyxin-like	BC054530|Podxl|27205|podocalyxin-like	NM_013723|Podxl|27205|podocalyxin-like
mm9_v1_chr9_-_49606959_49607009	5.54397	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_+_59969845_59969868	5.543	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_chr15_-_76983985_76984241	5.52851	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_chr9_+_55388955_55389013	5.51182	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_chr15_-_98783909_98783984	5.51142	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_chr16_+_19760300_19760490	5.46029	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_chr6_+_17015148_17015148	5.43247	SOX2.p2	NM_207176|Tes|21753|testis derived transcript
mm9_v1_chr5_+_28492235_28492251	5.41651	SOX2.p2	AK157766|En2|13799|engrailed 2	NM_010134|En2|13799|engrailed 2
mm9_v1_chr10_-_25798768_25798857	5.37445	SOX2.p2	AK048673|Tmem200a|77220|transmembrane protein 200A	AK173299|Tmem200a|77220|transmembrane protein 200A	NM_029881|Tmem200a|77220|transmembrane protein 200A
mm9_v1_chr10_-_61246611_61246701	5.34353	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_chr1_-_33871349_33871443	5.3388	SOX2.p2	AK015797|Zfp451|98403|zinc finger protein 451
mm9_v1_chr13_+_88961161_88961261	5.3257	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_chr6_+_64992810_64992853	5.30081	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_chr3_-_84024766_84024812	5.29597	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_chr7_+_90015842_90015842	5.21454	SOX2.p2	NM_175366|Mex3b|108797|mex3 homolog B (C. elegans)
mm9_v1_chr3_+_5218545_5218658	5.16297	SOX2.p2	AK084213|Zfhx4|80892|zinc finger homeodomain 4	BC061199|Zfhx4|80892|zinc finger homeodomain 4	NM_030708|Zfhx4|80892|zinc finger homeodomain 4	AK044540|Zfhx4|80892|zinc finger homeodomain 4
mm9_v1_chr16_+_93608058_93608176	5.15723	SOX2.p2	NM_007620|Cbr1|12408|carbonyl reductase 1	U31966|Cbr1|12408|carbonyl reductase 1	BC158026|Cbr1|12408|carbonyl reductase 1	BC158029|Cbr1|12408|carbonyl reductase 1	AK146805|Cbr1|12408|carbonyl reductase 1	BC012714|Cbr1|12408|carbonyl reductase 1
mm9_v1_chrX_+_140098931_140098937	5.15661	SOX2.p2	
mm9_v1_chr5_+_67067497_67067526	5.15042	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_chrY_-_582062_582201	5.07871	SOX2.p2	AK162410|Uty|22290|ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome	AK220463|Uty|22290|ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome	AK155922|Uty|22290|ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome	AF057367|Uty|22290|ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome	BC053061|Uty|22290|ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome	AK043154|Uty|22290|ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome	NM_009484|Uty|22290|ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome	AK142344|Uty|22290|ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome	AK142512|Uty|22290|ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome
mm9_v1_chr7_-_91558468_91558528	5.07238	SOX2.p2	BC054546|Arnt2|11864|aryl hydrocarbon receptor nuclear translocator 2	NM_007488|Arnt2|11864|aryl hydrocarbon receptor nuclear translocator 2
mm9_v1_chr5_-_103640272_103640352	5.04195	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_chr2_+_65683823_65683911	4.92516	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_chr8_-_64238879_64238894	4.9156	SOX2.p2	AK031696|Palld|72333|palladin, cytoskeletal associated protein	AK162050|Palld|72333|palladin, cytoskeletal associated protein	AK087270|Palld|72333|palladin, cytoskeletal associated protein
mm9_v1_chr19_-_47036782_47036852	4.87718	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_chr10_+_27794664_27794727	4.86544	SOX2.p2	AK052275|Ptprk|19272|protein tyrosine phosphatase, receptor type, K	AK019870|Ptprk|19272|protein tyrosine phosphatase, receptor type, K
mm9_v1_chr1_-_97564064_97564129	4.86012	SOX2.p2	AK041723|St8sia4|20452|ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	AK003690|St8sia4|20452|ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4
mm9_v1_chr12_-_15822792_15822800	4.84668	SOX2.p2	AK080064|Trib2|217410|tribbles homolog 2 (Drosophila)	AK082329|Trib2|217410|tribbles homolog 2 (Drosophila)
mm9_v1_chr5_-_115750940_115750978	4.83282	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_chr10_-_93498449_93498481	4.83106	SOX2.p2	AY753561|Vezt|215008|vezatin, adherens junctions transmembrane protein	AY753562|Vezt|215008|vezatin, adherens junctions transmembrane protein	DQ025533|Vezt|215008|vezatin, adherens junctions transmembrane protein	BC056428|Vezt|215008|vezatin, adherens junctions transmembrane protein
mm9_v1_chr3_-_95032039_95032230	4.82578	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_chr16_+_78301923_78302076	4.80605	SOX2.p2	NM_001025192|Cxadr|13052|coxsackie virus and adenovirus receptor	NM_009988|Cxadr|13052|coxsackie virus and adenovirus receptor	AK004908|Cxadr|13052|coxsackie virus and adenovirus receptor	AK145569|Cxadr|13052|coxsackie virus and adenovirus receptor	AK160457|Cxadr|13052|coxsackie virus and adenovirus receptor	BC016457|Cxadr|13052|coxsackie virus and adenovirus receptor	BC004680|Cxadr|13052|coxsackie virus and adenovirus receptor	U90715|Cxadr|13052|coxsackie virus and adenovirus receptor	Y10320|Cxadr|13052|coxsackie virus and adenovirus receptor
mm9_v1_chr1_+_139795165_139795180	4.76306	SOX2.p2	AK080376|A630083H20Rik|320863|RIKEN cDNA A630083H20 gene	AK040011|A630083H20Rik|320863|RIKEN cDNA A630083H20 gene
mm9_v1_chr13_-_111070344_111070365	4.73764	SOX2.p2	AK164316|Rab3c|67295|RAB3C, member RAS oncogene family
mm9_v1_chr5_+_31014229_31014273	4.73606	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_chr8_-_87461251_87461273	4.72699	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_chr3_+_121129396_121129492	4.71058	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_chr7_+_103358652_103358694	4.68814	SOX2.p2	AK031375|Odz4|23966|odd Oz/ten-m homolog 4 (Drosophila)
mm9_v1_chr3_+_7503409_7503519	4.67072	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_chr10_+_17443024_17443226	4.62682	SOX2.p2	AK131664|Cited2|17684|Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	AK133791|Cited2|17684|Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	NM_010828|Cited2|17684|Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	BC057126|Cited2|17684|Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	U86445|Cited2|17684|Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	Y15163|Cited2|17684|Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2
mm9_v1_chr7_+_106614513_106614536	4.60229	SOX2.p2	NM_028145|Klhl35|72184|kelch-like 35 (Drosophila)	AK013012|Klhl35|72184|kelch-like 35 (Drosophila)
mm9_v1_chr1_-_128634766_128634787	4.57187	SOX2.p2	AK083792|Nckap5|210356|NCK-associated protein 5
mm9_v1_chr14_-_20796255_20796277	4.57112	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_chr15_-_95358674_95358735	4.56823	SOX2.p2	U59230|Nell2|54003|NEL-like 2 (chicken)
mm9_v1_chr10_-_93498482_93498486	4.52945	SOX2.p2	AK042540|Vezt|215008|vezatin, adherens junctions transmembrane protein
mm9_v1_chr6_+_64992861_64992872	4.51322	SOX2.p2	AK147884|Smarcad1|13990|SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1
mm9_v1_chr10_-_93498488_93498564	4.51156	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_chrX_+_35542969_35543017	4.50856	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_chr9_-_49607017_49607038	4.47917	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_chr11_+_117193732_117193733	4.46824	SOX2.p2	
mm9_v1_chr5_+_89012537_89012542	4.44882	SOX2.p2	AK013185|Rufy3|52822|RUN and FYVE domain containing 3
mm9_v1_chr18_-_15309939_15309954	4.41667	SOX2.p2	AY899808|Kctd1|106931|potassium channel tetramerisation domain containing 1	NM_134112|Kctd1|106931|potassium channel tetramerisation domain containing 1
mm9_v1_chr4_+_11083585_11083598	4.35846	SOX2.p2	AJ131776|Trp53inp1|60599|transformation related protein 53 inducible nuclear protein 1	AY034611|Trp53inp1|60599|transformation related protein 53 inducible nuclear protein 1	AY034612|Trp53inp1|60599|transformation related protein 53 inducible nuclear protein 1	NM_021897|Trp53inp1|60599|transformation related protein 53 inducible nuclear protein 1	AK054214|Trp53inp1|60599|transformation related protein 53 inducible nuclear protein 1	AK142321|Trp53inp1|60599|transformation related protein 53 inducible nuclear protein 1
mm9_v1_chr4_+_122673318_122673349	4.31393	SOX2.p2	AK146959|Mycl1|16918|v-myc myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian)	BC053059|Mycl1|16918|v-myc myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian)	BC089346|Mycl1|16918|v-myc myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian)	NM_008506|Mycl1|16918|v-myc myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian)
mm9_v1_chr5_+_37637027_37637257	4.3038	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_chr3_+_8509479_8509599	4.28028	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_chr13_-_111070225_111070335	4.2772	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_+_71657791_71657963	4.2751	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_+_15135505_15135508	4.27284	SOX2.p2	BC062926|Foxp2|114142|forkhead box P2	NM_212435|Foxp2|114142|forkhead box P2	BC058960|Foxp2|114142|forkhead box P2
mm9_v1_chr1_-_167865030_167865141	4.21178	SOX2.p2	AJ296212|Pou2f1|18986|POU domain, class 2, transcription factor 1	NM_198933|Pou2f1|18986|POU domain, class 2, transcription factor 1	NM_198934|Pou2f1|18986|POU domain, class 2, transcription factor 1	AJ489475|Pou2f1|18986|POU domain, class 2, transcription factor 1	AJ489474|Pou2f1|18986|POU domain, class 2, transcription factor 1	X56230|Pou2f1|18986|POU domain, class 2, transcription factor 1
mm9_v1_chr1_-_135817867_135817935	4.19937	SOX2.p2	
mm9_v1_chrX_-_131285919_131285957	4.19887	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_chr11_-_107655777_107655857	4.16767	SOX2.p2	AJ272045|Cacng4|54377|calcium channel, voltage-dependent, gamma subunit 4	NM_019431|Cacng4|54377|calcium channel, voltage-dependent, gamma subunit 4	BC138503|Cacng4|54377|calcium channel, voltage-dependent, gamma subunit 4	BC138506|Cacng4|54377|calcium channel, voltage-dependent, gamma subunit 4
mm9_v1_chr5_+_73398142_73398230	4.16617	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_chr17_-_35975075_35975143	4.1609	SOX2.p2	X04663|Tubb5|22154|tubulin, beta 5
mm9_v1_chr11_+_23978110_23978267	4.1523	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_chr9_+_61220162_61220251	4.13581	SOX2.p2	NM_001083927|Tle3|21887|transducin-like enhancer of split 3, homolog of Drosophila E(spl)	NM_001083928|Tle3|21887|transducin-like enhancer of split 3, homolog of Drosophila E(spl)	NM_009389|Tle3|21887|transducin-like enhancer of split 3, homolog of Drosophila E(spl)
mm9_v1_chr13_-_40829082_40829191	4.12518	SOX2.p2	AB221578|Tcfap2a|21418|transcription factor AP-2, alpha	U17286|Tcfap2a|21418|transcription factor AP-2, alpha	AK145772|Tcfap2a|21418|transcription factor AP-2, alpha	X74216|Tcfap2a|21418|transcription factor AP-2, alpha	BC007471|Tcfap2a|21418|transcription factor AP-2, alpha	U17285|Tcfap2a|21418|transcription factor AP-2, alpha	NM_011547|Tcfap2a|21418|transcription factor AP-2, alpha
mm9_v1_chr5_+_34326081_34326346	4.12303	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_chr5_+_77694506_77694565	4.12171	SOX2.p2	AK004945|Rest|19712|RE1-silencing transcription factor	NM_011263|Rest|19712|RE1-silencing transcription factor	AK156514|Rest|19712|RE1-silencing transcription factor
mm9_v1_chr12_+_3365295_3365555	4.12045	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_chr4_+_100449274_100449299	4.11964	SOX2.p2	AK080923|Cachd1|320508|cache domain containing 1	BC058676|Cachd1|320508|cache domain containing 1	NM_198037|Cachd1|320508|cache domain containing 1
mm9_v1_chr17_-_71199129_71199153	4.08774	SOX2.p2	NM_001164076|Tgif1|21815|TGFB-induced factor homeobox 1
mm9_v1_chr1_-_141273617_141273676	4.07831	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_chr2_+_25036276_25036300	4.07328	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_chr1_-_46910333_46910455	4.07221	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_chr8_+_37157910_37157939	4.06921	SOX2.p2	AK036672|D8Ertd82e|244418|DNA segment, Chr 8, ERATO Doi 82, expressed	AK052494|D8Ertd82e|244418|DNA segment, Chr 8, ERATO Doi 82, expressed	AK089749|D8Ertd82e|244418|DNA segment, Chr 8, ERATO Doi 82, expressed
mm9_v1_chr2_-_74497475_74497613	4.06543	SOX2.p2	M93128|Evx2|14029|even skipped homeotic gene 2 homolog	NM_007967|Evx2|14029|even skipped homeotic gene 2 homolog	BC061467|Evx2|14029|even skipped homeotic gene 2 homolog
mm9_v1_chr1_+_70772288_70772496	4.05542	SOX2.p2	BC094541|Vwc2l|320460|von Willebrand factor C domain-containing protein 2-like	NM_177164|Vwc2l|320460|von Willebrand factor C domain-containing protein 2-like	AK083856|Vwc2l|320460|von Willebrand factor C domain-containing protein 2-like	BC064448|Vwc2l|320460|von Willebrand factor C domain-containing protein 2-like	AK080585|Vwc2l|320460|von Willebrand factor C domain-containing protein 2-like
mm9_v1_chr14_-_80171003_80171120	4.05262	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_chr6_-_148893155_148893361	4.04182	SOX2.p2	AK046519|Fam60a|56306|family with sequence similarity 60, member A
mm9_v1_chr14_+_27852148_27852279	4.03718	SOX2.p2	AF494210|Il17rd|171463|interleukin 17 receptor D	NM_134437|Il17rd|171463|interleukin 17 receptor D	BC138629|Il17rd|171463|interleukin 17 receptor D	BC066804|Il17rd|171463|interleukin 17 receptor D	AF459444|Il17rd|171463|interleukin 17 receptor D
mm9_v1_chr11_+_103635438_103635563	4.03717	SOX2.p2	AK132516|Wnt3|22415|wingless-related MMTV integration site 3	NM_009521|Wnt3|22415|wingless-related MMTV integration site 3	M32502|Wnt3|22415|wingless-related MMTV integration site 3	BC152305|Wnt3|22415|wingless-related MMTV integration site 3	BC152537|Wnt3|22415|wingless-related MMTV integration site 3	BC152304|Wnt3|22415|wingless-related MMTV integration site 3	AK141154|Wnt3|22415|wingless-related MMTV integration site 3	BC141271|Wnt3|22415|wingless-related MMTV integration site 3	BC141274|Wnt3|22415|wingless-related MMTV integration site 3
mm9_v1_chr10_+_42580317_42580598	4.02967	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_chr4_-_6917964_6917984	4.01917	SOX2.p2	AK169546|Tox|252838|thymocyte selection-associated high mobility group box
mm9_v1_chr2_+_4322020_4322021	4.0059	SOX2.p2	BC082808|Frmd4a|209630|FERM domain containing 4A	NM_001177843|Frmd4a|209630|FERM domain containing 4A
mm9_v1_chrX_-_92853721_92853847	3.98055	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_chr16_+_23224804_23224864	3.97301	SOX2.p2	BC092222|St6gal1|20440|beta galactoside alpha 2,6 sialyltransferase 1	NM_145933|St6gal1|20440|beta galactoside alpha 2,6 sialyltransferase 1
mm9_v1_chr11_-_77707282_77707373	3.97056	SOX2.p2	U94700|Pipox|19193|pipecolic acid oxidase	BC013525|Pipox|19193|pipecolic acid oxidase	AK135009|Pipox|19193|pipecolic acid oxidase	AK149488|Pipox|19193|pipecolic acid oxidase	AK008555|Pipox|19193|pipecolic acid oxidase	NM_008952|Pipox|19193|pipecolic acid oxidase
mm9_v1_chr16_+_17452048_17452310	3.95193	SOX2.p2	AK052315|Crkl|12929|v-crk sarcoma virus CT10 oncogene homolog (avian)-like	AK048641|Crkl|12929|v-crk sarcoma virus CT10 oncogene homolog (avian)-like	NM_007764|Crkl|12929|v-crk sarcoma virus CT10 oncogene homolog (avian)-like	AK163981|Crkl|12929|v-crk sarcoma virus CT10 oncogene homolog (avian)-like	BC023080|Crkl|12929|v-crk sarcoma virus CT10 oncogene homolog (avian)-like	X90648|Crkl|12929|v-crk sarcoma virus CT10 oncogene homolog (avian)-like	BC131984|Crkl|12929|v-crk sarcoma virus CT10 oncogene homolog (avian)-like	BC131986|Crkl|12929|v-crk sarcoma virus CT10 oncogene homolog (avian)-like
mm9_v1_chr1_+_160292470_160292548	3.9292	SOX2.p2	AK164117|Astn1|11899|astrotactin 1	NM_007495|Astn1|11899|astrotactin 1	BC094666|Astn1|11899|astrotactin 1
mm9_v1_chr1_-_192802869_192802928	3.91595	SOX2.p2	AK140989|Vash2|226841|vasohibin 2	NM_144879|Vash2|226841|vasohibin 2
mm9_v1_chr3_+_31801595_31801757	3.85819	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_chr3_+_94964364_94964444	3.85724	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_chr5_+_89012596_89012599	3.84552	SOX2.p2	BC049127|Rufy3|52822|RUN and FYVE domain containing 3	NM_027530|Rufy3|52822|RUN and FYVE domain containing 3
mm9_v1_chr13_+_40982534_40982735	3.84085	SOX2.p2	NM_008105|Gcnt2|14538|glucosaminyl (N-acetyl) transferase 2, I-branching enzyme	AK080061|Gcnt2|14538|glucosaminyl (N-acetyl) transferase 2, I-branching enzyme	AK054226|Gcnt2|14538|glucosaminyl (N-acetyl) transferase 2, I-branching enzyme	AB037597|Gcnt2|14538|glucosaminyl (N-acetyl) transferase 2, I-branching enzyme	AY435149|Gcnt2|14538|glucosaminyl (N-acetyl) transferase 2, I-branching enzyme
mm9_v1_chr6_+_47194393_47194453	3.8287	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_chr9_-_50535949_50536088	3.81486	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_chrX_+_155897136_155897153	3.78417	SOX2.p2	AK005554|Mtap7d2|78283|MAP7 domain containing 2	AK030316|Mtap7d2|78283|MAP7 domain containing 2
mm9_v1_chr12_-_35213738_35213753	3.77333	SOX2.p2	BC098187|Hdac9|79221|histone deacetylase 9	NM_024124|Hdac9|79221|histone deacetylase 9
mm9_v1_chr2_-_130985746_130985825	3.75679	SOX2.p2	AK003406|1700037H04Rik|67326|RIKEN cDNA 1700037H04 gene	NM_026091|1700037H04Rik|67326|RIKEN cDNA 1700037H04 gene	BC071212|1700037H04Rik|67326|RIKEN cDNA 1700037H04 gene	AK006622|1700037H04Rik|67326|RIKEN cDNA 1700037H04 gene
mm9_v1_chr12_-_86113948_86114061	3.74677	SOX2.p2	AK158624|Npc2|67963|Niemann Pick type C2	NM_023409|Npc2|67963|Niemann Pick type C2
mm9_v1_chr12_-_56087322_56087322	3.73968	SOX2.p2	AK135668|Baz1a|217578|bromodomain adjacent to zinc finger domain 1A	NM_013815|Baz1a|217578|bromodomain adjacent to zinc finger domain 1A
mm9_v1_chr9_-_75257729_75257901	3.73914	SOX2.p2	AK011505|Mapk6|50772|mitogen-activated protein kinase 6	AK044752|Mapk6|50772|mitogen-activated protein kinase 6	BC100385|Mapk6|50772|mitogen-activated protein kinase 6	NM_015806|Mapk6|50772|mitogen-activated protein kinase 6
mm9_v1_chr9_+_54711492_54711604	3.73419	SOX2.p2	NM_022655|Ireb2|64602|iron responsive element binding protein 2	BC044665|Ireb2|64602|iron responsive element binding protein 2
mm9_v1_chr5_+_3928177_3928370	3.70622	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_-_117252126_117252166	3.6683	SOX2.p2	
mm9_v1_chr11_-_86621074_86621127	3.66283	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_chr2_+_181599126_181599193	3.66241	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_-_6516073_6516084	3.61128	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_chr11_+_80290571_80290592	3.60802	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_chr13_+_88961034_88961117	3.57319	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_chr15_-_39775173_39775370	3.52008	SOX2.p2	AK050512|Lrp12|239393|low density lipoprotein-related protein 12	NM_172814|Lrp12|239393|low density lipoprotein-related protein 12
mm9_v1_chr12_-_73337534_73337705	3.51767	SOX2.p2	AK013731|Rtn1|104001|reticulon 1	AK014358|Rtn1|104001|reticulon 1
mm9_v1_chr2_-_119096952_119096961	3.5118	SOX2.p2	BC021307|Rhov|228543|ras homolog gene family, member V	AK036775|Rhov|228543|ras homolog gene family, member V	AK037170|Rhov|228543|ras homolog gene family, member V	NM_145530|Rhov|228543|ras homolog gene family, member V
mm9_v1_chr2_+_179777187_179777250	3.49617	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_chr5_+_65522325_65522469	3.4926	SOX2.p2	BC057606|Klhl5|71778|kelch-like 5 (Drosophila)	NM_175174|Klhl5|71778|kelch-like 5 (Drosophila)
mm9_v1_chr13_-_99696254_99696340	3.48935	SOX2.p2	AK030580|Tnpo1|238799|transportin 1	AK087194|Tnpo1|238799|transportin 1	AK037001|Tnpo1|238799|transportin 1	AK029953|Tnpo1|238799|transportin 1	NM_178716|Tnpo1|238799|transportin 1
mm9_v1_chr10_+_79611013_79611064	3.48511	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_chr2_-_52414072_52414117	3.47899	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_chr6_-_49164469_49164732	3.46865	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_chr2_+_179777418_179777493	3.46765	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_chr16_-_23520662_23520727	3.44215	SOX2.p2	BC131637|Masp1|17174|mannan-binding lectin serine peptidase 1	BC131638|Masp1|17174|mannan-binding lectin serine peptidase 1	NM_008555|Masp1|17174|mannan-binding lectin serine peptidase 1	AK032944|Masp1|17174|mannan-binding lectin serine peptidase 1	AB049755|Masp1|17174|mannan-binding lectin serine peptidase 1	D16492|Masp1|17174|mannan-binding lectin serine peptidase 1	AK043055|Masp1|17174|mannan-binding lectin serine peptidase 1	AK031598|Masp1|17174|mannan-binding lectin serine peptidase 1
mm9_v1_chr11_-_77303157_77303183	3.43981	SOX2.p2	BC151158|Ankrd13b|268445|ankyrin repeat domain 13b	BC172028|Ankrd13b|268445|ankyrin repeat domain 13b	NM_172945|Ankrd13b|268445|ankyrin repeat domain 13b
mm9_v1_chr16_+_17146981_17147071	3.43711	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_chr2_-_63936044_63936094	3.43168	SOX2.p2	AF263913|Fign|60344|fidgetin	AK163474|Fign|60344|fidgetin	AK164536|Fign|60344|fidgetin	NM_021716|Fign|60344|fidgetin	AK143787|Fign|60344|fidgetin	BC059266|Fign|60344|fidgetin
mm9_v1_chr3_+_132754791_132754924	3.42633	SOX2.p2	AK012829|Ints12|71793|integrator complex subunit 12	AK003874|Ints12|71793|integrator complex subunit 12	AK155162|Ints12|71793|integrator complex subunit 12	AK038713|Ints12|71793|integrator complex subunit 12	BC046996|Ints12|71793|integrator complex subunit 12	BC023801|Ints12|71793|integrator complex subunit 12	NM_027927|Ints12|71793|integrator complex subunit 12
mm9_v1_chr4_+_13678443_13678575	3.39903	SOX2.p2	NM_001111027|Runx1t1|12395|runt-related transcription factor 1; translocated to, 1 (cyclin D-related)
mm9_v1_chrX_-_91787353_91787369	3.39675	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_chr1_-_183950050_183950110	3.39487	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_chr18_+_37127284_37127409	3.37709	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_chr4_+_85699818_85699939	3.37561	SOX2.p2	NM_029967|Adamtsl1|77739|ADAMTS-like 1	AK020115|Adamtsl1|77739|ADAMTS-like 1	BC062814|Adamtsl1|77739|ADAMTS-like 1	AK045085|Adamtsl1|77739|ADAMTS-like 1	BC139339|Adamtsl1|77739|ADAMTS-like 1	BC139367|Adamtsl1|77739|ADAMTS-like 1
mm9_v1_chr11_-_40508405_40508442	3.36845	SOX2.p2	AK075600|Mat2b|108645|methionine adenosyltransferase II, beta	AK075947|Mat2b|108645|methionine adenosyltransferase II, beta	AK162087|Mat2b|108645|methionine adenosyltransferase II, beta
mm9_v1_chr7_+_52471161_52471287	3.35371	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_+_58877199_58877199	3.35193	SOX2.p2	NM_080853|Slc17a6|140919|solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6
mm9_v1_chr17_-_80689434_80689517	3.34513	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_chr5_+_147042806_147042851	3.33213	SOX2.p2	AK131948|Cdk8|264064|cyclin-dependent kinase 8
mm9_v1_chr9_-_35075338_35075393	3.32871	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_chr4_+_83063621_83063661	3.32834	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_chr4_-_34830178_34830200	3.32716	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_chr14_+_62218348_62218392	3.32075	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_chrX_-_161764912_161765057	3.31016	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_chr9_+_90057930_90058082	3.30183	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_chr5_+_36235967_36236084	3.29131	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_chr4_+_154335029_154335081	3.29102	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_chr1_+_66368409_66368422	3.28622	SOX2.p2	AK079618|Mtap2|17756|microtubule-associated protein 2
mm9_v1_chr12_+_41172675_41172679	3.2828	SOX2.p2	AK082607|Dock4|238130|dedicator of cytokinesis 4
mm9_v1_chr7_-_128125714_128125825	3.26625	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_chrX_+_90920450_90920749	3.23624	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_chr13_-_54789148_54789168	3.21638	SOX2.p2	AK147349|Rnf44|105239|ring finger protein 44	NM_001146025|Rnf44|105239|ring finger protein 44	NM_001146026|Rnf44|105239|ring finger protein 44	NM_134064|Rnf44|105239|ring finger protein 44
mm9_v1_chr6_-_38826156_38826247	3.2143	SOX2.p2	NM_010433|Hipk2|15258|homeodomain interacting protein kinase 2
mm9_v1_chr3_-_126928844_126928867	3.21209	SOX2.p2	AK044093|Ank2|109676|ankyrin 2, brain
mm9_v1_chr17_-_36046961_36047023	3.21063	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_chr2_-_37558818_37558881	3.20097	SOX2.p2	AK043648|Strbp|20744|spermatid perinuclear RNA binding protein
mm9_v1_chr6_-_18464792_18464824	3.19806	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_chr1_+_34062720_34062743	3.16667	SOX2.p2	AK039885|Dst|13518|dystonin
mm9_v1_chr1_-_168339909_168339980	3.16476	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_chr14_+_73637697_73637874	3.14848	SOX2.p2	NM_175116|Lpar6|67168|lysophosphatidic acid receptor 6	AK032901|Lpar6|67168|lysophosphatidic acid receptor 6	AK011967|Lpar6|67168|lysophosphatidic acid receptor 6	AK169602|Lpar6|67168|lysophosphatidic acid receptor 6	BC047931|Lpar6|67168|lysophosphatidic acid receptor 6	AK008952|Lpar6|67168|lysophosphatidic acid receptor 6	BC057175|Lpar6|67168|lysophosphatidic acid receptor 6	BC069991|Lpar6|67168|lysophosphatidic acid receptor 6
mm9_v1_chr19_-_42160732_42160861	3.12236	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_chr2_+_48669677_48669740	3.11817	SOX2.p2	AK050252|Acvr2a|11480|activin receptor IIA	AK143186|Acvr2a|11480|activin receptor IIA
mm9_v1_chr7_+_25292105_25292148	3.10527	SOX2.p2	NM_146183|Zfp428|232969|zinc finger protein 428	AK080517|Zfp428|232969|zinc finger protein 428
mm9_v1_chr15_-_73253617_73253652	3.08895	SOX2.p2	AK220543|Ptk2|14083|PTK2 protein tyrosine kinase 2	NM_001130409|Ptk2|14083|PTK2 protein tyrosine kinase 2	NM_007982|Ptk2|14083|PTK2 protein tyrosine kinase 2	AK005468|Ptk2|14083|PTK2 protein tyrosine kinase 2
mm9_v1_chr7_+_30088984_30089023	3.08092	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_chr3_-_116126853_116126921	3.04063	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_chr5_+_31754808_31754902	3.03972	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_chr1_+_64579358_64579513	3.03567	SOX2.p2	NM_001037726|Creb1|12912|cAMP responsive element binding protein 1	NM_009952|Creb1|12912|cAMP responsive element binding protein 1	NM_133828|Creb1|12912|cAMP responsive element binding protein 1	AK079223|Creb1|12912|cAMP responsive element binding protein 1	X92497|Creb1|12912|cAMP responsive element binding protein 1	AK042595|Creb1|12912|cAMP responsive element binding protein 1	BC021649|Creb1|12912|cAMP responsive element binding protein 1	M95106|Creb1|12912|cAMP responsive element binding protein 1	AF448507|Creb1|12912|cAMP responsive element binding protein 1
mm9_v1_chr18_-_16967100_16967238	3.02759	SOX2.p2	AB008811|Cdh2|12558|cadherin 2	M31131|Cdh2|12558|cadherin 2
mm9_v1_chr1_-_153192360_153192399	3.00854	SOX2.p2	
mm9_v1_chr14_-_71166340_71166465	2.99454	SOX2.p2	AJ297360|Xpo7|65246|exportin 7	AK041768|Xpo7|65246|exportin 7	AK051105|Xpo7|65246|exportin 7	AK035775|Xpo7|65246|exportin 7	BC029702|Xpo7|65246|exportin 7	AK164595|Xpo7|65246|exportin 7	NM_023045|Xpo7|65246|exportin 7
mm9_v1_chr14_-_109313333_109313374	2.98741	SOX2.p2	AK173296|Slitrk1|76965|SLIT and NTRK-like family, member 1
mm9_v1_chr18_+_37098858_37098971	2.97543	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_chr8_-_90483392_90483493	2.96106	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_chr14_-_11285927_11285966	2.953	SOX2.p2	BC012662|Fhit|14198|fragile histidine triad gene
mm9_v1_chr14_+_65885454_65885579	2.94854	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_chr4_-_136604609_136604715	2.92525	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_chrX_+_130829763_130829919	2.92215	SOX2.p2	BC042623|Tmem35|67564|transmembrane protein 35	NM_026239|Tmem35|67564|transmembrane protein 35	BC050880|Tmem35|67564|transmembrane protein 35
mm9_v1_chr15_+_99532698_99532771	2.92109	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_chr6_+_83087016_83087103	2.92011	SOX2.p2	NM_009106|Rtkn|20166|rhotekin	NM_133641|Rtkn|20166|rhotekin	U54638|Rtkn|20166|rhotekin	BC013820|Rtkn|20166|rhotekin
mm9_v1_chr1_-_64167952_64168022	2.91881	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_chr11_+_80290509_80290569	2.91834	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_chr16_+_87699143_87699302	2.91535	SOX2.p2	D86603|Bach1|12013|BTB and CNC homology 1	AK140765|Bach1|12013|BTB and CNC homology 1	AK140903|Bach1|12013|BTB and CNC homology 1	NM_007520|Bach1|12013|BTB and CNC homology 1	AK030871|Bach1|12013|BTB and CNC homology 1	AK141405|Bach1|12013|BTB and CNC homology 1	BC057894|Bach1|12013|BTB and CNC homology 1
mm9_v1_chrX_-_69901382_69901584	2.88175	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_chrX_+_155897056_155897081	2.87507	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_chr8_+_108042645_108042656	2.87157	SOX2.p2	AK155153|Hsd11b2|15484|hydroxysteroid 11-beta dehydrogenase 2	NM_008289|Hsd11b2|15484|hydroxysteroid 11-beta dehydrogenase 2	BC014753|Hsd11b2|15484|hydroxysteroid 11-beta dehydrogenase 2	BC066209|Hsd11b2|15484|hydroxysteroid 11-beta dehydrogenase 2
mm9_v1_chr1_-_155334737_155334791	2.85481	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_chr7_-_91558407_91558432	2.84752	SOX2.p2	D63644|Arnt2|11864|aryl hydrocarbon receptor nuclear translocator 2
mm9_v1_chr2_-_84490827_84490896	2.84383	SOX2.p2	BC054544|Ctnnd1|12388|catenin (cadherin associated protein), delta 1	BC043108|Ctnnd1|12388|catenin (cadherin associated protein), delta 1	AK161790|Ctnnd1|12388|catenin (cadherin associated protein), delta 1	AK164485|Ctnnd1|12388|catenin (cadherin associated protein), delta 1	AK168453|Ctnnd1|12388|catenin (cadherin associated protein), delta 1	NM_001085448|Ctnnd1|12388|catenin (cadherin associated protein), delta 1	NM_001085449|Ctnnd1|12388|catenin (cadherin associated protein), delta 1	NM_001085450|Ctnnd1|12388|catenin (cadherin associated protein), delta 1	NM_007615|Ctnnd1|12388|catenin (cadherin associated protein), delta 1
mm9_v1_chr6_-_42660031_42660117	2.83947	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_chr3_-_145312928_145312948	2.83795	SOX2.p2	BC066019|Cyr61|16007|cysteine rich protein 61	BC003205|Cyr61|16007|cysteine rich protein 61	AK156723|Cyr61|16007|cysteine rich protein 61	AK159452|Cyr61|16007|cysteine rich protein 61	M32490|Cyr61|16007|cysteine rich protein 61	NM_010516|Cyr61|16007|cysteine rich protein 61
mm9_v1_chr18_+_23910833_23910892	2.82967	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_chrX_-_54646073_54646213	2.82863	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_chr14_-_63796620_63796725	2.81884	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_chr4_-_114659706_114659870	2.80417	SOX2.p2	AK004827|Cmpk1|66588|cytidine monophosphate (UMP-CMP) kinase 1	AK146436|Cmpk1|66588|cytidine monophosphate (UMP-CMP) kinase 1	AK002526|Cmpk1|66588|cytidine monophosphate (UMP-CMP) kinase 1	BC017684|Cmpk1|66588|cytidine monophosphate (UMP-CMP) kinase 1	AK162173|Cmpk1|66588|cytidine monophosphate (UMP-CMP) kinase 1	AK150162|Cmpk1|66588|cytidine monophosphate (UMP-CMP) kinase 1	NM_025647|Cmpk1|66588|cytidine monophosphate (UMP-CMP) kinase 1	AK077534|Cmpk1|66588|cytidine monophosphate (UMP-CMP) kinase 1
mm9_v1_chr1_+_138028025_138028071	2.79885	SOX2.p2	AK089400|Kif21b|16565|kinesin family member 21B
mm9_v1_chr12_+_41172669_41172674	2.79558	SOX2.p2	AK030653|Dock4|238130|dedicator of cytokinesis 4	AK031713|Dock4|238130|dedicator of cytokinesis 4
mm9_v1_chr11_+_69805051_69805216	2.78618	SOX2.p2	BC002126|Gabarap|56486|gamma-aminobutyric acid receptor associated protein	BC024621|Gabarap|56486|gamma-aminobutyric acid receptor associated protein	AK002879|Gabarap|56486|gamma-aminobutyric acid receptor associated protein	AF161587|Gabarap|56486|gamma-aminobutyric acid receptor associated protein	BC029329|Gabarap|56486|gamma-aminobutyric acid receptor associated protein	AK011731|Gabarap|56486|gamma-aminobutyric acid receptor associated protein
mm9_v1_chrX_-_137077133_137077229	2.78046	SOX2.p2	AF201287|Tsc22d3|14605|TSC22 domain family, member 3
mm9_v1_chr12_+_25516433_25516564	2.77816	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_chr12_+_114378688_114378782	2.77735	SOX2.p2	AF469648|Crip2|68337|cysteine rich protein 2	BC002093|Crip2|68337|cysteine rich protein 2	AK002484|Crip2|68337|cysteine rich protein 2	BC002096|Crip2|68337|cysteine rich protein 2	BC007149|Crip2|68337|cysteine rich protein 2	CT010309|Crip2|68337|cysteine rich protein 2
mm9_v1_chr6_-_134837738_134837876	2.76105	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_chr4_-_134409149_134409155	2.75163	SOX2.p2	AK038972|Tmem57|66146|transmembrane protein 57	BC054769|Tmem57|66146|transmembrane protein 57
mm9_v1_chr17_+_74738195_74738352	2.73789	SOX2.p2	BC046286|Spast|50850|spastin	NM_001162870|Spast|50850|spastin	NM_016962|Spast|50850|spastin	AK129282|Spast|50850|spastin
mm9_v1_chr6_-_3444484_3444497	2.72598	SOX2.p2	BC096374|Hepacam2|101202|HEPACAM family member 2	AK033728|Hepacam2|101202|HEPACAM family member 2	AK050501|Hepacam2|101202|HEPACAM family member 2	NM_178899|Hepacam2|101202|HEPACAM family member 2
mm9_v1_chr7_+_98239427_98239516	2.71238	SOX2.p2	AF388675|Dlg2|23859|discs, large homolog 2 (Drosophila)
mm9_v1_chr6_+_124989841_124989878	2.70759	SOX2.p2	AK046126|Ing4|28019|inhibitor of growth family, member 4	AK050522|Ing4|28019|inhibitor of growth family, member 4	AK031633|Ing4|28019|inhibitor of growth family, member 4	AK002821|Ing4|28019|inhibitor of growth family, member 4	AK009267|Ing4|28019|inhibitor of growth family, member 4	NM_133345|Ing4|28019|inhibitor of growth family, member 4	BC009127|Ing4|28019|inhibitor of growth family, member 4	AY035880|Ing4|28019|inhibitor of growth family, member 4	AY035881|Ing4|28019|inhibitor of growth family, member 4	AY036107|Ing4|28019|inhibitor of growth family, member 4
mm9_v1_chr4_-_134409199_134409236	2.699	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_chr11_-_115674905_115674973	2.69392	SOX2.p2	BC053083|Caskin2|140721|CASK-interacting protein 2	NM_080643|Caskin2|140721|CASK-interacting protein 2	AK129297|Caskin2|140721|CASK-interacting protein 2
mm9_v1_chr6_-_47544925_47545028	2.68574	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_chr2_-_11423673_11423729	2.68141	SOX2.p2	BC052400|Pfkfb3|170768|6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	AK054285|Pfkfb3|170768|6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	NM_001177752|Pfkfb3|170768|6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	NM_001177753|Pfkfb3|170768|6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	NM_001177754|Pfkfb3|170768|6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	NM_001177755|Pfkfb3|170768|6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	NM_001177756|Pfkfb3|170768|6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	NM_001177757|Pfkfb3|170768|6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	NM_133232|Pfkfb3|170768|6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3
mm9_v1_chr15_-_24957039_24957112	2.68067	SOX2.p2	AK033069|Gm2824|100040529|predicted gene 2824	AK083927|Gm2824|100040529|predicted gene 2824
mm9_v1_chr3_+_130813214_130813388	2.67961	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_chr11_-_31571811_31571918	2.67931	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_chr17_-_71202829_71202871	2.67636	SOX2.p2	AK160193|Tgif1|21815|TGFB-induced factor homeobox 1	NM_001164074|Tgif1|21815|TGFB-induced factor homeobox 1
mm9_v1_chr5_+_108494692_108494781	2.6758	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_chr4_-_44180769_44180855	2.6594	SOX2.p2	
mm9_v1_chr11_-_86887549_86887638	2.65781	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_chr18_+_37839910_37840111	2.65145	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_chr9_+_43552046_43552085	2.64588	SOX2.p2	AK147479|Pvrl1|58235|poliovirus receptor-related 1
mm9_v1_chr14_-_48188088_48188108	2.62428	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_chr2_+_143741243_143741349	2.6239	SOX2.p2	AK078898|Dstn|56431|destrin	AB025406|Dstn|56431|destrin	BC131926|Dstn|56431|destrin
mm9_v1_chr6_+_17699145_17699592	2.61174	SOX2.p2	AK079107|St7|64213|suppression of tumorigenicity 7	AK132103|St7|64213|suppression of tumorigenicity 7	AK151550|St7|64213|suppression of tumorigenicity 7	NM_001083315|St7|64213|suppression of tumorigenicity 7	NM_022332|St7|64213|suppression of tumorigenicity 7	BC108418|St7|64213|suppression of tumorigenicity 7	AF234884|St7|64213|suppression of tumorigenicity 7	AF234885|St7|64213|suppression of tumorigenicity 7	AY007794|St7|64213|suppression of tumorigenicity 7	AY007795|St7|64213|suppression of tumorigenicity 7	AK036248|St7|64213|suppression of tumorigenicity 7	BC060630|St7|64213|suppression of tumorigenicity 7	BC051429|St7|64213|suppression of tumorigenicity 7	AY551821|St7|64213|suppression of tumorigenicity 7	AY551822|St7|64213|suppression of tumorigenicity 7	CT010245|St7|64213|suppression of tumorigenicity 7
mm9_v1_chr3_+_17695743_17695745	2.61088	SOX2.p2	AK046405|6430547I21Rik|320521|RIKEN cDNA 6430547I21 gene	AK032443|6430547I21Rik|320521|RIKEN cDNA 6430547I21 gene
mm9_v1_chrX_+_98624989_98625073	2.60764	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_chr13_-_104899571_104899748	2.58916	SOX2.p2	AK146364|Nln|75805|neurolysin (metallopeptidase M3 family)	BC016224|Nln|75805|neurolysin (metallopeptidase M3 family)	AK138399|Nln|75805|neurolysin (metallopeptidase M3 family)	AK170508|Nln|75805|neurolysin (metallopeptidase M3 family)	AK171432|Nln|75805|neurolysin (metallopeptidase M3 family)	AK079090|Nln|75805|neurolysin (metallopeptidase M3 family)	NM_029447|Nln|75805|neurolysin (metallopeptidase M3 family)
mm9_v1_chr3_+_121129588_121129727	2.58528	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_chr4_-_147504787_147504806	2.57675	SOX2.p2	BC060239|2610109H07Rik|70433|RIKEN cDNA 2610109H07 gene	AK086198|2610109H07Rik|70433|RIKEN cDNA 2610109H07 gene	NM_027426|2610109H07Rik|70433|RIKEN cDNA 2610109H07 gene
mm9_v1_chr9_-_82868992_82869032	2.57587	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_chr11_+_32355355_32355458	2.57168	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_chr4_-_21612991_21613109	2.56814	SOX2.p2	AK149252|Prdm13|230025|PR domain containing 13	BC017632|Prdm13|230025|PR domain containing 13	NM_001080771|Prdm13|230025|PR domain containing 13
mm9_v1_chr15_-_95358989_95359075	2.56373	SOX2.p2	AK039790|Nell2|54003|NEL-like 2 (chicken)
mm9_v1_chr10_+_84218792_84218938	2.55807	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_chr8_+_3493117_3493286	2.5487	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_chr15_-_84388245_84388282	2.54507	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_chr1_-_192803077_192803174	2.53172	SOX2.p2	BC024141|Vash2|226841|vasohibin 2	AK163193|Vash2|226841|vasohibin 2	AK045261|Vash2|226841|vasohibin 2	AK078596|Vash2|226841|vasohibin 2
mm9_v1_chr4_-_91066674_91066674	2.52356	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_chr11_+_87881747_87881842	2.5094	SOX2.p2	AF104410|Vezf1|22344|vascular endothelial zinc finger 1	NM_016686|Vezf1|22344|vascular endothelial zinc finger 1
mm9_v1_chr7_+_89319681_89319705	2.50882	SOX2.p2	BC027096|Sh3gl3|20408|SH3-domain GRB2-like 3
mm9_v1_chr7_-_85722668_85722860	2.4861	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_chr3_+_65332306_65332400	2.47642	SOX2.p2	AK163347|Tiparp|99929|TCDD-inducible poly(ADP-ribose) polymerase	AK162094|Tiparp|99929|TCDD-inducible poly(ADP-ribose) polymerase	U55178|Tiparp|99929|TCDD-inducible poly(ADP-ribose) polymerase	AK028529|Tiparp|99929|TCDD-inducible poly(ADP-ribose) polymerase	NM_178892|Tiparp|99929|TCDD-inducible poly(ADP-ribose) polymerase	AK032453|Tiparp|99929|TCDD-inducible poly(ADP-ribose) polymerase	AK150248|Tiparp|99929|TCDD-inducible poly(ADP-ribose) polymerase	BC068173|Tiparp|99929|TCDD-inducible poly(ADP-ribose) polymerase
mm9_v1_chr16_+_52031733_52031765	2.46684	SOX2.p2	AK045005|Cblb|208650|Casitas B-lineage lymphoma b
mm9_v1_chr13_-_67162084_67162105	2.46288	SOX2.p2	AK019536|Zfp712|78251|zinc finger protein 712	NM_001166218|Zfp712|78251|zinc finger protein 712
mm9_v1_chr14_-_50403002_50403057	2.45934	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_chr7_+_29649467_29649473	2.45742	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_chr3_+_13946371_13946410	2.45734	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_chr4_+_108132602_108132646	2.45703	SOX2.p2	AF194972|Zcchc11|230594|zinc finger, CCHC domain containing 11	BC038132|Zcchc11|230594|zinc finger, CCHC domain containing 11
mm9_v1_chr19_+_40905768_40905801	2.44005	SOX2.p2	AK052506|Ccnj|240665|cyclin J	NM_172839|Ccnj|240665|cyclin J	AK157841|Ccnj|240665|cyclin J	BC120921|Ccnj|240665|cyclin J	BC120922|Ccnj|240665|cyclin J	BC117559|Ccnj|240665|cyclin J
mm9_v1_chr7_-_27980727_27980786	2.43932	SOX2.p2	NM_001046637|Snrpa|53607|small nuclear ribonucleoprotein polypeptide A
mm9_v1_chr1_+_58449940_58450019	2.43285	SOX2.p2	AK152939|Bzw1|66882|basic leucine zipper and W2 domains 1	AK168158|Bzw1|66882|basic leucine zipper and W2 domains 1	AK029030|Bzw1|66882|basic leucine zipper and W2 domains 1	AK088322|Bzw1|66882|basic leucine zipper and W2 domains 1	AK167982|Bzw1|66882|basic leucine zipper and W2 domains 1	AK166247|Bzw1|66882|basic leucine zipper and W2 domains 1	AK004784|Bzw1|66882|basic leucine zipper and W2 domains 1	AK076086|Bzw1|66882|basic leucine zipper and W2 domains 1	AK076560|Bzw1|66882|basic leucine zipper and W2 domains 1	AK133973|Bzw1|66882|basic leucine zipper and W2 domains 1	NM_025824|Bzw1|66882|basic leucine zipper and W2 domains 1	AK161192|Bzw1|66882|basic leucine zipper and W2 domains 1	AK013980|Bzw1|66882|basic leucine zipper and W2 domains 1	BC028865|Bzw1|66882|basic leucine zipper and W2 domains 1	AK087980|Bzw1|66882|basic leucine zipper and W2 domains 1	AK151919|Bzw1|66882|basic leucine zipper and W2 domains 1	AK153538|Bzw1|66882|basic leucine zipper and W2 domains 1	AK167056|Bzw1|66882|basic leucine zipper and W2 domains 1	BC005466|Bzw1|66882|basic leucine zipper and W2 domains 1	AK167074|Bzw1|66882|basic leucine zipper and W2 domains 1	AK212098|Bzw1|66882|basic leucine zipper and W2 domains 1	AK167514|Bzw1|66882|basic leucine zipper and W2 domains 1
mm9_v1_chr8_+_26629214_26629332	2.43015	SOX2.p2	NM_001079908|Fgfr1|14182|fibroblast growth factor receptor 1	NM_001079909|Fgfr1|14182|fibroblast growth factor receptor 1	NM_010206|Fgfr1|14182|fibroblast growth factor receptor 1	AK049704|Fgfr1|14182|fibroblast growth factor receptor 1	S74765|Fgfr1|14182|fibroblast growth factor receptor 1	BC010200|Fgfr1|14182|fibroblast growth factor receptor 1
mm9_v1_chr18_+_21160434_21160595	2.42755	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_+_117193738_117193767	2.42118	SOX2.p2	AK164581|Sept9|53860|septin 9	AK031757|Sept9|53860|septin 9
mm9_v1_chr9_+_122832164_122832215	2.41017	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_chr5_+_53981893_53981983	2.40063	SOX2.p2	BC051387|Rbpj|19664|recombination signal binding protein for immunoglobulin kappa J region	AK080359|Rbpj|19664|recombination signal binding protein for immunoglobulin kappa J region	AK145187|Rbpj|19664|recombination signal binding protein for immunoglobulin kappa J region	AK090006|Rbpj|19664|recombination signal binding protein for immunoglobulin kappa J region
mm9_v1_chrX_-_153929935_153930011	2.40028	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_chr19_+_3767420_3767525	2.39916	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_chr18_+_37112301_37112419	2.39343	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_chr19_+_7492081_7492131	2.38939	SOX2.p2	NM_175381|2700081O15Rik|108899|RIKEN cDNA 2700081O15 gene
mm9_v1_chr4_+_59639079_59639315	2.3856	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_chr6_+_121014481_121014613	2.38006	SOX2.p2	AK085340|Gm4651|100043793|predicted gene 4651
mm9_v1_chr5_-_138596915_138596971	2.37366	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_chr9_-_49606862_49606915	2.37018	SOX2.p2	BC011310|Ncam1|17967|neural cell adhesion molecule 1
mm9_v1_chr1_+_92100572_92100639	2.3677	SOX2.p2	AK031100|Cxcr7|12778|chemokine (C-X-C motif) receptor 7	NM_007722|Cxcr7|12778|chemokine (C-X-C motif) receptor 7	AF000236|Cxcr7|12778|chemokine (C-X-C motif) receptor 7	BC015254|Cxcr7|12778|chemokine (C-X-C motif) receptor 7
mm9_v1_chr11_+_80623859_80623939	2.36162	SOX2.p2	BC011208|Tmem98|103743|transmembrane protein 98	NM_029537|Tmem98|103743|transmembrane protein 98	AK148132|Tmem98|103743|transmembrane protein 98	AK153960|Tmem98|103743|transmembrane protein 98
mm9_v1_chr4_-_133309484_133309525	2.31801	SOX2.p2	NM_001080819|Arid1a|93760|AT rich interactive domain 1A (SWI-like)
mm9_v1_chr1_-_127808723_127808763	2.31661	SOX2.p2	BC058599|Lypd1|72585|Ly6/Plaur domain containing 1
mm9_v1_chr13_+_9275741_9275783	2.28841	SOX2.p2	NM_001081426|Dip2c|208440|DIP2 disco-interacting protein 2 homolog C (Drosophila)
mm9_v1_chr14_-_34260323_34260352	2.28447	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_chr9_-_62994774_62994817	2.28424	SOX2.p2	BC138063|Skor1|207667|SKI family transcriptional corepressor 1	AK049035|Skor1|207667|SKI family transcriptional corepressor 1	NM_172446|Skor1|207667|SKI family transcriptional corepressor 1	AK134840|Skor1|207667|SKI family transcriptional corepressor 1	AB185113|Skor1|207667|SKI family transcriptional corepressor 1	NM_001163755|Skor1|207667|SKI family transcriptional corepressor 1	NM_001163757|Skor1|207667|SKI family transcriptional corepressor 1
mm9_v1_chr2_-_60719361_60719568	2.28134	SOX2.p2	AK161102|Rbms1|56878|RNA binding motif, single stranded interacting protein 1	AK164307|Rbms1|56878|RNA binding motif, single stranded interacting protein 1	AK145897|Rbms1|56878|RNA binding motif, single stranded interacting protein 1	NM_001141931|Rbms1|56878|RNA binding motif, single stranded interacting protein 1	NM_001141932|Rbms1|56878|RNA binding motif, single stranded interacting protein 1	BC057866|Rbms1|56878|RNA binding motif, single stranded interacting protein 1
mm9_v1_chr10_-_75395207_75395224	2.27936	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_chr17_-_31992708_31992780	2.26938	SOX2.p2	U11494|Sik1|17691|salt inducible kinase 1	AK141817|Sik1|17691|salt inducible kinase 1	NM_010831|Sik1|17691|salt inducible kinase 1	AK172427|Sik1|17691|salt inducible kinase 1
mm9_v1_chr9_-_69608633_69608746	2.26831	SOX2.p2	X92592|Foxb1|64290|forkhead box B1	U04198|Foxb1|64290|forkhead box B1	U90538|Foxb1|64290|forkhead box B1	NM_022378|Foxb1|64290|forkhead box B1
mm9_v1_chr14_-_52723590_52723721	2.26813	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_chr1_-_153347884_153348127	2.26802	SOX2.p2	BC020122|Rnf2|19821|ring finger protein 2	AK090066|Rnf2|19821|ring finger protein 2	AK013124|Rnf2|19821|ring finger protein 2	AK030319|Rnf2|19821|ring finger protein 2	AK012358|Rnf2|19821|ring finger protein 2	NM_011277|Rnf2|19821|ring finger protein 2	AK145767|Rnf2|19821|ring finger protein 2
mm9_v1_chr9_-_66440640_66440842	2.26754	SOX2.p2	AK031141|Usp3|235441|ubiquitin specific peptidase 3	NM_144937|Usp3|235441|ubiquitin specific peptidase 3	AK158516|Usp3|235441|ubiquitin specific peptidase 3	AK161676|Usp3|235441|ubiquitin specific peptidase 3
mm9_v1_chr14_-_67487226_67487503	2.26634	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_chr3_+_145541951_145541971	2.25916	SOX2.p2	
mm9_v1_chr2_+_78709363_78709419	2.25442	SOX2.p2	AK168072|Ube2e3|22193|ubiquitin-conjugating enzyme E2E 3, UBC4/5 homolog (yeast)	AK048227|Ube2e3|22193|ubiquitin-conjugating enzyme E2E 3, UBC4/5 homolog (yeast)	AK076011|Ube2e3|22193|ubiquitin-conjugating enzyme E2E 3, UBC4/5 homolog (yeast)	X92664|Ube2e3|22193|ubiquitin-conjugating enzyme E2E 3, UBC4/5 homolog (yeast)
mm9_v1_chr16_-_90144013_90144100	2.24979	SOX2.p2	BC065126|Tiam1|21844|T-cell lymphoma invasion and metastasis 1	AK043966|Tiam1|21844|T-cell lymphoma invasion and metastasis 1
mm9_v1_chr8_-_4259126_4259300	2.2447	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_chr5_+_138882703_138882746	2.24364	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_chr5_+_104631633_104631713	2.24228	SOX2.p2	AK132177|Dmp1|13406|dentin matrix protein 1	AK157973|Dmp1|13406|dentin matrix protein 1	NM_016779|Dmp1|13406|dentin matrix protein 1	U65020|Dmp1|13406|dentin matrix protein 1	BC113753|Dmp1|13406|dentin matrix protein 1
mm9_v1_chr16_+_20097626_20097705	2.24117	SOX2.p2	NM_029436|Klhl24|75785|kelch-like 24 (Drosophila)	AK015239|Klhl24|75785|kelch-like 24 (Drosophila)	AK044892|Klhl24|75785|kelch-like 24 (Drosophila)
mm9_v1_chr2_-_152223710_152223930	2.23596	SOX2.p2	BC067019|Sox12|20667|SRY-box containing gene 12	NM_011438|Sox12|20667|SRY-box containing gene 12
mm9_v1_chr15_-_76487319_76487388	2.23282	SOX2.p2	BC062184|Cyhr1|54151|cysteine and histidine rich 1	BC082772|Cyhr1|54151|cysteine and histidine rich 1	AK080867|Cyhr1|54151|cysteine and histidine rich 1
mm9_v1_chr4_-_108506131_108506262	2.23103	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_chr15_-_79489373_79489385	2.23026	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_+_156246644_156246847	2.22875	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_chr7_+_133903186_133903314	2.22581	SOX2.p2	S58470|Mapk3|26417|mitogen-activated protein kinase 3	BC013754|Mapk3|26417|mitogen-activated protein kinase 3
mm9_v1_chr13_-_84204320_84204376	2.22373	SOX2.p2	AK082072|LOC553095|553095|hypothetical LOC553095
mm9_v1_chr5_-_143665305_143665346	2.2183	SOX2.p2	AK151514|Actb|11461|actin, beta
mm9_v1_chr4_+_41082993_41083094	2.21682	SOX2.p2	AK003550|Ube2r2|67615|ubiquitin-conjugating enzyme E2R 2	AK075703|Ube2r2|67615|ubiquitin-conjugating enzyme E2R 2	BC011112|Ube2r2|67615|ubiquitin-conjugating enzyme E2R 2	AK075714|Ube2r2|67615|ubiquitin-conjugating enzyme E2R 2	NM_026275|Ube2r2|67615|ubiquitin-conjugating enzyme E2R 2	AJ240086|Ube2r2|67615|ubiquitin-conjugating enzyme E2R 2
mm9_v1_chr8_+_108939247_108939300	2.20697	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_chr12_+_17999625_17999803	2.20386	SOX2.p2	BC030401|Gm4983|245297|predicted gene 4983	BC083083|Gm4983|245297|predicted gene 4983
mm9_v1_chr8_+_32222291_32222336	2.2035	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_chr12_-_84938095_84938119	2.20324	SOX2.p2	AK170954|Zfyve1|217695|zinc finger, FYVE domain containing 1	NM_183154|Zfyve1|217695|zinc finger, FYVE domain containing 1	AK139825|Zfyve1|217695|zinc finger, FYVE domain containing 1
mm9_v1_chr18_+_37133455_37133703	2.18991	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_chrX_-_71070284_71070317	2.1867	SOX2.p2	AK046101|Pdzd4|245469|PDZ domain containing 4	NM_001029868|Pdzd4|245469|PDZ domain containing 4
mm9_v1_chr5_-_99681835_99681949	2.18437	SOX2.p2	AK028756|Rasgef1b|320292|RasGEF domain family, member 1B	BC052726|Rasgef1b|320292|RasGEF domain family, member 1B	AK090085|Rasgef1b|320292|RasGEF domain family, member 1B	AK149812|Rasgef1b|320292|RasGEF domain family, member 1B	AY129963|Rasgef1b|320292|RasGEF domain family, member 1B	BC050858|Rasgef1b|320292|RasGEF domain family, member 1B	NM_145839|Rasgef1b|320292|RasGEF domain family, member 1B	NM_181318|Rasgef1b|320292|RasGEF domain family, member 1B
mm9_v1_chr2_-_153067043_153067211	2.18286	SOX2.p2	BC037664|Plagl2|54711|pleiomorphic adenoma gene-like 2	BC078453|Plagl2|54711|pleiomorphic adenoma gene-like 2	NM_018807|Plagl2|54711|pleiomorphic adenoma gene-like 2	AK040626|Plagl2|54711|pleiomorphic adenoma gene-like 2	AK133833|Plagl2|54711|pleiomorphic adenoma gene-like 2	AK141713|Plagl2|54711|pleiomorphic adenoma gene-like 2	AK150243|Plagl2|54711|pleiomorphic adenoma gene-like 2	AK129087|Plagl2|54711|pleiomorphic adenoma gene-like 2
mm9_v1_chrX_+_148451021_148451054	2.18198	SOX2.p2	AK017948|Smc1a|24061|structural maintenance of chromosomes 1A	BC036973|Smc1a|24061|structural maintenance of chromosomes 1A	BC003279|Smc1a|24061|structural maintenance of chromosomes 1A	AK088183|Smc1a|24061|structural maintenance of chromosomes 1A	AK145255|Smc1a|24061|structural maintenance of chromosomes 1A	BC025590|Smc1a|24061|structural maintenance of chromosomes 1A
mm9_v1_chr11_+_23978029_23978056	2.18083	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_chr10_+_127176590_127176697	2.17307	SOX2.p2	BC058661|Zbtb39|320080|zinc finger and BTB domain containing 39	NM_198035|Zbtb39|320080|zinc finger and BTB domain containing 39	AK135409|Zbtb39|320080|zinc finger and BTB domain containing 39	AK155700|Zbtb39|320080|zinc finger and BTB domain containing 39	BC079569|Zbtb39|320080|zinc finger and BTB domain containing 39
mm9_v1_chr2_-_179777080_179777173	2.17041	SOX2.p2	BC014752|Psma7|26444|proteasome (prosome, macropain) subunit, alpha type 7	BC008222|Psma7|26444|proteasome (prosome, macropain) subunit, alpha type 7	AF019662|Psma7|26444|proteasome (prosome, macropain) subunit, alpha type 7	NM_011969|Psma7|26444|proteasome (prosome, macropain) subunit, alpha type 7	AK088615|Psma7|26444|proteasome (prosome, macropain) subunit, alpha type 7	AK165563|Psma7|26444|proteasome (prosome, macropain) subunit, alpha type 7	AK146765|Psma7|26444|proteasome (prosome, macropain) subunit, alpha type 7	AK168234|Psma7|26444|proteasome (prosome, macropain) subunit, alpha type 7
mm9_v1_chr13_+_22036962_22036998	2.1657	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_chr7_+_74792295_74792398	2.16363	SOX2.p2	AK086049|Ttc23|67009|tetratricopeptide repeat domain 23	AK165626|Ttc23|67009|tetratricopeptide repeat domain 23	NM_001168475|Ttc23|67009|tetratricopeptide repeat domain 23	NM_001168476|Ttc23|67009|tetratricopeptide repeat domain 23	NM_001168477|Ttc23|67009|tetratricopeptide repeat domain 23	NM_025905|Ttc23|67009|tetratricopeptide repeat domain 23	AK141754|Ttc23|67009|tetratricopeptide repeat domain 23	BC038179|Ttc23|67009|tetratricopeptide repeat domain 23	AK005431|Ttc23|67009|tetratricopeptide repeat domain 23	AK084269|Ttc23|67009|tetratricopeptide repeat domain 23	AK166555|Ttc23|67009|tetratricopeptide repeat domain 23	AK166613|Ttc23|67009|tetratricopeptide repeat domain 23
mm9_v1_chr6_-_114871769_114871855	2.15944	SOX2.p2	BC048841|Vgll4|232334|vestigial like 4 (Drosophila)	NM_177683|Vgll4|232334|vestigial like 4 (Drosophila)	BC060305|Vgll4|232334|vestigial like 4 (Drosophila)	AK144447|Vgll4|232334|vestigial like 4 (Drosophila)	AK078466|Vgll4|232334|vestigial like 4 (Drosophila)
mm9_v1_chr18_-_43847193_43847252	2.15398	SOX2.p2	AK143449|Jakmip2|76217|janus kinase and microtubule interacting protein 2	AK051838|Jakmip2|76217|janus kinase and microtubule interacting protein 2
mm9_v1_chrX_-_163647088_163647149	2.15246	SOX2.p2	AK010659|Tmsb4x|19241|thymosin, beta 4, X chromosome	AK088783|Tmsb4x|19241|thymosin, beta 4, X chromosome	AK162286|Tmsb4x|19241|thymosin, beta 4, X chromosome	AK169718|Tmsb4x|19241|thymosin, beta 4, X chromosome	AK169108|Tmsb4x|19241|thymosin, beta 4, X chromosome	NM_021278|Tmsb4x|19241|thymosin, beta 4, X chromosome
mm9_v1_chr17_+_13109289_13109379	2.14583	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_chr12_-_36768992_36769002	2.14089	SOX2.p2	AK008175|Tspan13|66109|tetraspanin 13
mm9_v1_chr9_+_35075447_35075515	2.12585	SOX2.p2	AK010322|Rpusd4|71989|RNA pseudouridylate synthase domain containing 4	AK156574|Rpusd4|71989|RNA pseudouridylate synthase domain containing 4	BC061256|Rpusd4|71989|RNA pseudouridylate synthase domain containing 4	NM_028040|Rpusd4|71989|RNA pseudouridylate synthase domain containing 4
mm9_v1_chr3_+_63780058_63780135	2.12554	SOX2.p2	AK143197|Gmps|229363|guanine monophosphate synthetase	NM_001033300|Gmps|229363|guanine monophosphate synthetase	AK169701|Gmps|229363|guanine monophosphate synthetase	AK169043|Gmps|229363|guanine monophosphate synthetase	AK167857|Gmps|229363|guanine monophosphate synthetase	AK049755|Gmps|229363|guanine monophosphate synthetase	BC138411|Gmps|229363|guanine monophosphate synthetase	BC138412|Gmps|229363|guanine monophosphate synthetase	AK168239|Gmps|229363|guanine monophosphate synthetase
mm9_v1_chrX_+_93651684_93651766	2.1159	SOX2.p2	NM_001159627|Heph|15203|hephaestin	NM_181273|Heph|15203|hephaestin	AK081330|Heph|15203|hephaestin	AK129194|Heph|15203|hephaestin	AK032895|Heph|15203|hephaestin	AK086923|Heph|15203|hephaestin
mm9_v1_chr10_-_116500780_116500882	2.11127	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_chr5_-_52581705_52581765	2.11084	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_chr16_-_5013596_5013670	2.11032	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_chr3_-_146432922_146432972	2.10759	SOX2.p2	AK139419|Prkacb|18749|protein kinase, cAMP dependent, catalytic, beta
mm9_v1_chr15_-_103045710_103045798	2.09185	SOX2.p2	X99641|Cbx5|12419|chromobox homolog 5 (Drosophila HP1a)	AK018349|Cbx5|12419|chromobox homolog 5 (Drosophila HP1a)	AK030442|Cbx5|12419|chromobox homolog 5 (Drosophila HP1a)	AK032975|Cbx5|12419|chromobox homolog 5 (Drosophila HP1a)	AK030366|Cbx5|12419|chromobox homolog 5 (Drosophila HP1a)	NM_001110216|Cbx5|12419|chromobox homolog 5 (Drosophila HP1a)	NM_007626|Cbx5|12419|chromobox homolog 5 (Drosophila HP1a)
mm9_v1_chr19_-_28754566_28754608	2.07997	SOX2.p2	AK054020|Glis3|226075|GLIS family zinc finger 3	DQ871027|Glis3|226075|GLIS family zinc finger 3	NM_175459|Glis3|226075|GLIS family zinc finger 3
mm9_v1_chr2_-_174120889_174120936	2.07196	SOX2.p2	AF319945|Nespas|56802|neuroendocrine secretory protein antisense	AK153813|Nespas|56802|neuroendocrine secretory protein antisense
mm9_v1_chr17_+_33130067_33130141	2.06658	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_chrX_+_90900201_90900217	2.05239	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_chr16_-_42340613_42340763	2.05163	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_-_3166349_3166433	2.05154	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_chr3_+_34548916_34548976	2.05076	SOX2.p2	NM_011443|Sox2|20674|SRY-box containing gene 2	U31967|Sox2|20674|SRY-box containing gene 2
mm9_v1_chr2_+_160556982_160557045	2.04272	SOX2.p2	BC057161|Plcg1|18803|phospholipase C, gamma 1	BC065091|Plcg1|18803|phospholipase C, gamma 1	NM_021280|Plcg1|18803|phospholipase C, gamma 1
mm9_v1_chr5_+_125343129_125343133	2.04163	SOX2.p2	AK035022|Zfp664|269704|zinc finger protein 664
mm9_v1_chr1_+_173341438_173341535	2.03952	SOX2.p2	AK142437|Usf1|22278|upstream transcription factor 1	BC049784|Usf1|22278|upstream transcription factor 1
mm9_v1_chr3_-_116126932_116126949	2.03838	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_chr16_+_52031704_52031719	2.03622	SOX2.p2	BC150934|Cblb|208650|Casitas B-lineage lymphoma b	BC150938|Cblb|208650|Casitas B-lineage lymphoma b	AK156295|Cblb|208650|Casitas B-lineage lymphoma b	AK171350|Cblb|208650|Casitas B-lineage lymphoma b
mm9_v1_chrX_+_149932693_149932774	2.03411	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_chr6_-_88824977_88825061	2.03382	SOX2.p2	AK038943|Podxl2|319655|podocalyxin-like 2
mm9_v1_chr11_+_67090625_67090855	2.02833	SOX2.p2	NM_177369|Myh8|17885|myosin, heavy polypeptide 8, skeletal muscle, perinatal	DQ021877|Myh8|17885|myosin, heavy polypeptide 8, skeletal muscle, perinatal	DQ021876|Myh8|17885|myosin, heavy polypeptide 8, skeletal muscle, perinatal	BC150737|Myh8|17885|myosin, heavy polypeptide 8, skeletal muscle, perinatal	AK029328|Myh8|17885|myosin, heavy polypeptide 8, skeletal muscle, perinatal	AK081482|Myh8|17885|myosin, heavy polypeptide 8, skeletal muscle, perinatal	AK087387|Myh8|17885|myosin, heavy polypeptide 8, skeletal muscle, perinatal	AY963802|Myh8|17885|myosin, heavy polypeptide 8, skeletal muscle, perinatal	DQ021878|Myh8|17885|myosin, heavy polypeptide 8, skeletal muscle, perinatal
mm9_v1_chr1_-_170361525_170361683	2.02803	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_chr7_-_89079168_89079313	2.02774	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_chr5_+_93696566_93696638	2.02443	SOX2.p2	NM_007635|Ccng2|12452|cyclin G2	AK170651|Ccng2|12452|cyclin G2	AF005885|Ccng2|12452|cyclin G2
mm9_v1_chr1_+_66368571_66368671	2.0209	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_chr13_-_76081244_76081314	2.01647	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_chr9_-_96338457_96338611	2.01508	SOX2.p2	AK050822|BC043934|270185|cDNA sequence BC043934
mm9_v1_chr9_-_62828677_62828715	2.01269	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_chr8_-_87461220_87461246	2.01006	SOX2.p2	AF077818|Mast1|56527|microtubule associated serine/threonine kinase 1
mm9_v1_chr7_+_146271910_146271981	2.00912	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_+_107479719_107479841	2.00535	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_chr16_+_37777075_37777220	2.00488	SOX2.p2	BC006185|Fstl1|14314|follistatin-like 1	AK049440|Fstl1|14314|follistatin-like 1	NM_008047|Fstl1|14314|follistatin-like 1	AK147117|Fstl1|14314|follistatin-like 1	BC028921|Fstl1|14314|follistatin-like 1	M91380|Fstl1|14314|follistatin-like 1
mm9_v1_chr14_-_34260308_34260313	1.99606	SOX2.p2	BC053027|Mapk8|26419|mitogen-activated protein kinase 8
mm9_v1_chr15_-_98748371_98748661	1.98747	SOX2.p2	AY052398|Lmbr1l|74775|limb region 1 like	AK003656|Lmbr1l|74775|limb region 1 like	BC023397|Lmbr1l|74775|limb region 1 like	AK170328|Lmbr1l|74775|limb region 1 like	AK143891|Lmbr1l|74775|limb region 1 like	AK030589|Lmbr1l|74775|limb region 1 like	AK049110|Lmbr1l|74775|limb region 1 like	NM_029098|Lmbr1l|74775|limb region 1 like	AK154968|Lmbr1l|74775|limb region 1 like
mm9_v1_chr12_+_81619976_81620155	1.98425	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_chr18_+_34407238_34407352	1.98396	SOX2.p2	AK039061|Apc|11789|adenomatosis polyposis coli	L19608|Apc|11789|adenomatosis polyposis coli	AK082724|Apc|11789|adenomatosis polyposis coli
mm9_v1_chr14_-_65881225_65881304	1.96749	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_chr7_+_97535516_97535523	1.96623	SOX2.p2	AB057756|Sytl2|83671|synaptotagmin-like 2
mm9_v1_chr13_+_42804911_42805054	1.96234	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_chr7_+_88005861_88005865	1.9596	SOX2.p2	AK147779|Zscan2|22691|zinc finger and SCAN domain containing 2
mm9_v1_chr16_-_96349292_96349333	1.94465	SOX2.p2	NM_008251|Hmgn1|15312|high mobility group nucleosomal binding domain 1
mm9_v1_chr7_-_53069599_53069692	1.93674	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_chrX_+_68809163_68809181	1.9274	SOX2.p2	NM_008253|Hmgb3|15354|high mobility group box 3	AK032163|Hmgb3|15354|high mobility group box 3
mm9_v1_chr6_-_115788429_115788481	1.9173	SOX2.p2	BC060267|BC060267|212516|cDNA sequence BC060267	NM_001110506|BC060267|212516|cDNA sequence BC060267
mm9_v1_chr16_-_91044623_91044646	1.90667	SOX2.p2	NM_026110|Gcfc1|67367|GC-rich sequence DNA-binding factor 1
mm9_v1_chr7_-_52124950_52125085	1.87876	SOX2.p2	BC008543|Ptov1|84113|prostate tumor over expressed gene 1
mm9_v1_chr4_+_108507258_108507370	1.872	SOX2.p2	BC006857|Txndc12|66073|thioredoxin domain containing 12 (endoplasmic reticulum)	NM_025334|Txndc12|66073|thioredoxin domain containing 12 (endoplasmic reticulum)	AK002862|Txndc12|66073|thioredoxin domain containing 12 (endoplasmic reticulum)	AK003481|Txndc12|66073|thioredoxin domain containing 12 (endoplasmic reticulum)	AY548113|Txndc12|66073|thioredoxin domain containing 12 (endoplasmic reticulum)
mm9_v1_chr18_-_43847367_43847426	1.8719	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_chr13_-_41454358_41454379	1.87148	SOX2.p2	AK054179|Nedd9|18003|neural precursor cell expressed, developmentally down-regulated gene 9	AK033729|Nedd9|18003|neural precursor cell expressed, developmentally down-regulated gene 9	NM_017464|Nedd9|18003|neural precursor cell expressed, developmentally down-regulated gene 9
mm9_v1_chr11_+_121098532_121098610	1.86858	SOX2.p2	NM_026272|Narf|67608|nuclear prelamin A recognition factor	AK076232|Narf|67608|nuclear prelamin A recognition factor	AK081305|Narf|67608|nuclear prelamin A recognition factor	AK013432|Narf|67608|nuclear prelamin A recognition factor	BC016090|Narf|67608|nuclear prelamin A recognition factor
mm9_v1_chr12_+_53800302_53800317	1.86263	SOX2.p2	DQ233645|Akap6|238161|A kinase (PRKA) anchor protein 6
mm9_v1_chr3_-_143867852_143867939	1.8619	SOX2.p2	AK080534|Lmo4|16911|LIM domain only 4	BC010278|Lmo4|16911|LIM domain only 4	AF096996|Lmo4|16911|LIM domain only 4
mm9_v1_chr8_-_73386905_73387156	1.85778	SOX2.p2	AF303461|Kcnn1|84036|potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	AF303462|Kcnn1|84036|potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	BC090622|Kcnn1|84036|potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1
mm9_v1_chrX_+_68809128_68809157	1.83788	SOX2.p2	BC011276|Hmgb3|15354|high mobility group box 3	BC158037|Hmgb3|15354|high mobility group box 3
mm9_v1_chr17_-_48548973_48549148	1.82245	SOX2.p2	AK156487|Nfya|18044|nuclear transcription factor-Y alpha	BC029695|Nfya|18044|nuclear transcription factor-Y alpha	X55315|Nfya|18044|nuclear transcription factor-Y alpha	BC057099|Nfya|18044|nuclear transcription factor-Y alpha	AK137561|Nfya|18044|nuclear transcription factor-Y alpha	AK004729|Nfya|18044|nuclear transcription factor-Y alpha	AK143723|Nfya|18044|nuclear transcription factor-Y alpha	NM_001110832|Nfya|18044|nuclear transcription factor-Y alpha	NM_010913|Nfya|18044|nuclear transcription factor-Y alpha
mm9_v1_chr9_+_3335139_3335230	1.81984	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_chr5_+_34892224_34892336	1.81751	SOX2.p2	AK143548|Sh3bp2|24055|SH3-domain binding protein 2	NM_001145859|Sh3bp2|24055|SH3-domain binding protein 2	BC085497|Sh3bp2|24055|SH3-domain binding protein 2	NM_001136088|Sh3bp2|24055|SH3-domain binding protein 2
mm9_v1_chr9_+_70390523_70390626	1.8143	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_chr1_+_134088010_134088033	1.81216	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_chr11_+_78156930_78157077	1.80611	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_chr3_-_49561168_49561243	1.80263	SOX2.p2	AF416735|Pcdh18|73173|protocadherin 18	AK173204|Pcdh18|73173|protocadherin 18	BC052198|Pcdh18|73173|protocadherin 18	AK036560|Pcdh18|73173|protocadherin 18	AK032820|Pcdh18|73173|protocadherin 18	NM_130448|Pcdh18|73173|protocadherin 18
mm9_v1_chr1_+_19202046_19202134	1.80136	SOX2.p2	AK032045|Tcfap2b|21419|transcription factor AP-2 beta	NM_001025305|Tcfap2b|21419|transcription factor AP-2 beta
mm9_v1_chr4_-_117169519_117169656	1.79627	SOX2.p2	BC056359|Rnf220|66743|ring finger protein 220	BC058415|Rnf220|66743|ring finger protein 220	NM_025739|Rnf220|66743|ring finger protein 220	AK028975|Rnf220|66743|ring finger protein 220	AK041785|Rnf220|66743|ring finger protein 220
mm9_v1_chr10_-_80693488_80693567	1.79494	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_chr11_+_115243203_115243359	1.79331	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_chr12_+_30622876_30622919	1.79096	SOX2.p2	AK142872|Pxdn|69675|peroxidasin homolog (Drosophila)	NM_181395|Pxdn|69675|peroxidasin homolog (Drosophila)	BC150789|Pxdn|69675|peroxidasin homolog (Drosophila)	AK054255|Pxdn|69675|peroxidasin homolog (Drosophila)	AK163597|Pxdn|69675|peroxidasin homolog (Drosophila)
mm9_v1_chr12_+_41172651_41172657	1.78488	SOX2.p2	AK122353|Dock4|238130|dedicator of cytokinesis 4
mm9_v1_chr13_-_56236756_56236903	1.78204	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_chr6_-_149050067_149050107	1.77609	SOX2.p2	AK135015|Dennd5b|320560|DENN/MADD domain containing 5B	AK038858|Dennd5b|320560|DENN/MADD domain containing 5B
mm9_v1_chr7_-_107475377_107475426	1.77103	SOX2.p2	
mm9_v1_chr2_+_179777363_179777404	1.77077	SOX2.p2	BC053087|Ss18l1|269397|synovial sarcoma translocation gene on chromosome 18-like 1
mm9_v1_chr15_-_83341285_83341349	1.76601	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_chr17_+_32643402_32643407	1.76162	SOX2.p2	NM_001101445|Cyp4f17|208285|cytochrome P450, family 4, subfamily f, polypeptide 17
mm9_v1_chr12_-_113912266_113912513	1.76004	SOX2.p2	AK154936|Akt1|11651|thymoma viral proto-oncogene 1	AK040758|Akt1|11651|thymoma viral proto-oncogene 1	X65687|Akt1|11651|thymoma viral proto-oncogene 1	BC066018|Akt1|11651|thymoma viral proto-oncogene 1	NM_001165894|Akt1|11651|thymoma viral proto-oncogene 1	NM_009652|Akt1|11651|thymoma viral proto-oncogene 1
mm9_v1_chr4_-_131604821_131605088	1.76004	SOX2.p2	BC079875|Epb4.1|269587|erythrocyte protein band 4.1	AK220462|Epb4.1|269587|erythrocyte protein band 4.1	NM_001128606|Epb4.1|269587|erythrocyte protein band 4.1
mm9_v1_chr11_+_116295502_116295595	1.75914	SOX2.p2	AK050732|Fam100b|319370|family with sequence similarity 100, member B	BC119080|Fam100b|319370|family with sequence similarity 100, member B	BC116983|Fam100b|319370|family with sequence similarity 100, member B
mm9_v1_chr5_+_31191349_31191378	1.756	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_+_22319075_22319102	1.75512	SOX2.p2	AK052307|Myst4|54169|MYST histone acetyltransferase monocytic leukemia 4	NM_017479|Myst4|54169|MYST histone acetyltransferase monocytic leukemia 4	AF222800|Myst4|54169|MYST histone acetyltransferase monocytic leukemia 4
mm9_v1_chr16_+_13780778_13780842	1.75363	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_chr11_-_60727237_60727316	1.74814	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_chr11_+_32247758_32247888	1.74156	SOX2.p2	NM_177364|Sh3pxd2b|268396|SH3 and PX domains 2B	AK169978|Sh3pxd2b|268396|SH3 and PX domains 2B	AK220175|Sh3pxd2b|268396|SH3 and PX domains 2B	AK090119|Sh3pxd2b|268396|SH3 and PX domains 2B	AK042261|Sh3pxd2b|268396|SH3 and PX domains 2B	BC141306|Sh3pxd2b|268396|SH3 and PX domains 2B	AK043324|Sh3pxd2b|268396|SH3 and PX domains 2B	AK089330|Sh3pxd2b|268396|SH3 and PX domains 2B	AK163471|Sh3pxd2b|268396|SH3 and PX domains 2B	AK171384|Sh3pxd2b|268396|SH3 and PX domains 2B	BC115711|Sh3pxd2b|268396|SH3 and PX domains 2B	BC115764|Sh3pxd2b|268396|SH3 and PX domains 2B	AK154898|Sh3pxd2b|268396|SH3 and PX domains 2B	AB430861|Sh3pxd2b|268396|SH3 and PX domains 2B
mm9_v1_chr10_+_126500607_126500768	1.74102	SOX2.p2	BC046336|Cdk4|12567|cyclin-dependent kinase 4	NM_009870|Cdk4|12567|cyclin-dependent kinase 4	AK153465|Cdk4|12567|cyclin-dependent kinase 4	BC052694|Cdk4|12567|cyclin-dependent kinase 4	BC031599|Cdk4|12567|cyclin-dependent kinase 4	AK011871|Cdk4|12567|cyclin-dependent kinase 4	AK003804|Cdk4|12567|cyclin-dependent kinase 4	AK006918|Cdk4|12567|cyclin-dependent kinase 4	AK012064|Cdk4|12567|cyclin-dependent kinase 4	AK146107|Cdk4|12567|cyclin-dependent kinase 4	AK019380|Cdk4|12567|cyclin-dependent kinase 4	AK078440|Cdk4|12567|cyclin-dependent kinase 4	AK013400|Cdk4|12567|cyclin-dependent kinase 4	AK185090|Cdk4|12567|cyclin-dependent kinase 4
mm9_v1_chr18_+_37501355_37501397	1.73867	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_chr8_+_73118329_73118423	1.73148	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_chr11_+_29592946_29593072	1.72933	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_chr7_+_123236814_123237015	1.7223	SOX2.p2	AK003415|1110004F10Rik|56372|RIKEN cDNA 1110004F10 gene	AK170172|1110004F10Rik|56372|RIKEN cDNA 1110004F10 gene	BC072575|1110004F10Rik|56372|RIKEN cDNA 1110004F10 gene	AK168206|1110004F10Rik|56372|RIKEN cDNA 1110004F10 gene	AK167571|1110004F10Rik|56372|RIKEN cDNA 1110004F10 gene	AK144059|1110004F10Rik|56372|RIKEN cDNA 1110004F10 gene	AK169309|1110004F10Rik|56372|RIKEN cDNA 1110004F10 gene	AB025407|1110004F10Rik|56372|RIKEN cDNA 1110004F10 gene	NM_019772|1110004F10Rik|56372|RIKEN cDNA 1110004F10 gene	AK180958|1110004F10Rik|56372|RIKEN cDNA 1110004F10 gene	AK182617|1110004F10Rik|56372|RIKEN cDNA 1110004F10 gene
mm9_v1_chr6_-_149049906_149050060	1.71329	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_chr6_-_39370221_39370334	1.71146	SOX2.p2	AK078962|Mkrn1|54484|makorin, ring finger protein, 1
mm9_v1_chr9_+_64988960_64989018	1.71038	SOX2.p2	AK011916|Igdcc3|19289|immunoglobulin superfamily, DCC subclass, member 3	AF026465|Igdcc3|19289|immunoglobulin superfamily, DCC subclass, member 3	AK051027|Igdcc3|19289|immunoglobulin superfamily, DCC subclass, member 3	NM_008988|Igdcc3|19289|immunoglobulin superfamily, DCC subclass, member 3	BC086481|Igdcc3|19289|immunoglobulin superfamily, DCC subclass, member 3	BC053057|Igdcc3|19289|immunoglobulin superfamily, DCC subclass, member 3
mm9_v1_chr11_+_51781124_51781401	1.70193	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_chr17_+_17539908_17539941	1.69828	SOX2.p2	AF351204|Lix1|66643|limb expression 1 homolog (chicken)
mm9_v1_chr9_+_119311561_119311618	1.69739	SOX2.p2	BC106189|Acvr2b|11481|activin receptor IIB	M84120|Acvr2b|11481|activin receptor IIB	NM_007397|Acvr2b|11481|activin receptor IIB
mm9_v1_chr12_-_71212591_71212711	1.69482	SOX2.p2	AK141891|Nin|18080|ninein	AK134860|Nin|18080|ninein
mm9_v1_chr9_+_108998083_108998108	1.6934	SOX2.p2	AB072381|Plxnb1|235611|plexin B1
mm9_v1_chr14_-_55272452_55272539	1.69193	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_chr18_+_67365012_67365154	1.69044	SOX2.p2	NM_024190|Chmp1b|67064|chromatin modifying protein 1B	AK151071|Chmp1b|67064|chromatin modifying protein 1B	AK014091|Chmp1b|67064|chromatin modifying protein 1B	AK012996|Chmp1b|67064|chromatin modifying protein 1B	AK167614|Chmp1b|67064|chromatin modifying protein 1B	BC002229|Chmp1b|67064|chromatin modifying protein 1B	BC034442|Chmp1b|67064|chromatin modifying protein 1B	CT010307|Chmp1b|67064|chromatin modifying protein 1B
mm9_v1_chr4_-_12015073_12015153	1.68954	SOX2.p2	AK017238|Tmem67|329795|transmembrane protein 67	AK039177|Tmem67|329795|transmembrane protein 67	AK042835|Tmem67|329795|transmembrane protein 67	AK133059|Tmem67|329795|transmembrane protein 67	AK045429|Tmem67|329795|transmembrane protein 67	NM_177861|Tmem67|329795|transmembrane protein 67	AK077246|Tmem67|329795|transmembrane protein 67
mm9_v1_chr13_+_14156038_14156092	1.68929	SOX2.p2	AK136105|Arid4b|94246|AT rich interactive domain 4B (RBP1-like)	AK041414|Arid4b|94246|AT rich interactive domain 4B (RBP1-like)	NM_194262|Arid4b|94246|AT rich interactive domain 4B (RBP1-like)	NM_198122|Arid4b|94246|AT rich interactive domain 4B (RBP1-like)	AK161669|Arid4b|94246|AT rich interactive domain 4B (RBP1-like)	AK031062|Arid4b|94246|AT rich interactive domain 4B (RBP1-like)
mm9_v1_chr16_+_13986691_13986753	1.68875	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_chr13_-_54788995_54789018	1.68684	SOX2.p2	AK160090|Rnf44|105239|ring finger protein 44	AK160115|Rnf44|105239|ring finger protein 44
mm9_v1_chr15_+_4325490_4325644	1.68255	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_-_39156609_39156661	1.67764	SOX2.p2	AK136209|Jhdm1d|338523|jumonji C domain-containing histone demethylase 1 homolog D (S. cerevisiae)	BC145216|Jhdm1d|338523|jumonji C domain-containing histone demethylase 1 homolog D (S. cerevisiae)	BC145848|Jhdm1d|338523|jumonji C domain-containing histone demethylase 1 homolog D (S. cerevisiae)
mm9_v1_chr15_+_92427539_92427556	1.67414	SOX2.p2	NM_001164594|Pdzrn4|239618|PDZ domain containing RING finger 4	AK135524|Pdzrn4|239618|PDZ domain containing RING finger 4
mm9_v1_chr7_+_87171113_87171302	1.67353	SOX2.p2	NM_175433|Zfp710|209225|zinc finger protein 710	AK155416|Zfp710|209225|zinc finger protein 710	BC060641|Zfp710|209225|zinc finger protein 710	AK083979|Zfp710|209225|zinc finger protein 710	BC058640|Zfp710|209225|zinc finger protein 710
mm9_v1_chr9_+_21420612_21420824	1.67082	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_chr3_+_7366586_7366727	1.6706	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_chr18_+_37673305_37673473	1.65498	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_chr5_-_102498929_102498975	1.65285	SOX2.p2	AK047077|Wdfy3|72145|WD repeat and FYVE domain containing 3	AY336569|Wdfy3|72145|WD repeat and FYVE domain containing 3	NM_172882|Wdfy3|72145|WD repeat and FYVE domain containing 3
mm9_v1_chr17_+_36003000_36003072	1.6527	SOX2.p2	BC020483|2310014H01Rik|76448|RIKEN cDNA 2310014H01 gene	AK149943|2310014H01Rik|76448|RIKEN cDNA 2310014H01 gene	NM_001146710|2310014H01Rik|76448|RIKEN cDNA 2310014H01 gene
mm9_v1_chr15_+_98957150_98957201	1.63973	SOX2.p2	AK159335|Spats2|72572|spermatogenesis associated, serine-rich 2
mm9_v1_chr1_+_180249260_180249302	1.63957	SOX2.p2	NM_025511|Fam36a|66359|family with sequence similarity 36, member A	BC059717|Fam36a|66359|family with sequence similarity 36, member A	AK009178|Fam36a|66359|family with sequence similarity 36, member A	BC055277|Fam36a|66359|family with sequence similarity 36, member A
mm9_v1_chr13_+_77274778_77274859	1.6358	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_chr7_-_77511242_77511282	1.62844	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_chr4_+_8462805_8462808	1.62756	SOX2.p2	AK135421|Rab2a|59021|RAB2A, member RAS oncogene family	AK163320|Rab2a|59021|RAB2A, member RAS oncogene family	AK146179|Rab2a|59021|RAB2A, member RAS oncogene family
mm9_v1_chr16_+_30065419_30065442	1.62665	SOX2.p2	AK133538|Hes1|15205|hairy and enhancer of split 1 (Drosophila)	AK132536|Hes1|15205|hairy and enhancer of split 1 (Drosophila)	BC018375|Hes1|15205|hairy and enhancer of split 1 (Drosophila)	BC051428|Hes1|15205|hairy and enhancer of split 1 (Drosophila)	NM_008235|Hes1|15205|hairy and enhancer of split 1 (Drosophila)
mm9_v1_chr12_+_71008808_71008844	1.6246	SOX2.p2	AK140185|Atl1|73991|atlastin GTPase 1	AK046919|Atl1|73991|atlastin GTPase 1	BC050784|Atl1|73991|atlastin GTPase 1
mm9_v1_chr11_-_102226475_102226594	1.62083	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_chr3_-_89141938_89141960	1.62009	SOX2.p2	AK012195|Efna4|13639|ephrin A4	AK142604|Efna4|13639|ephrin A4	NM_007910|Efna4|13639|ephrin A4	AK144085|Efna4|13639|ephrin A4
mm9_v1_chrX_-_140261831_140261910	1.61699	SOX2.p2	BC052167|Capn6|12338|calpain 6	Y12582|Capn6|12338|calpain 6	AK048028|Capn6|12338|calpain 6
mm9_v1_chr7_+_137836279_137836292	1.61426	SOX2.p2	AK165603|Tacc2|57752|transforming, acidic coiled-coil containing protein 2
mm9_v1_chr3_+_66789621_66789657	1.61304	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_chr12_-_82881995_82882183	1.60704	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_chr5_+_54200903_54200980	1.59699	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_chr11_+_44430784_44430845	1.5838	SOX2.p2	
mm9_v1_chr17_-_71339826_71339901	1.5823	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_-_27331122_27331221	1.57942	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_chr2_+_74707394_74707441	1.57918	SOX2.p2	AK207939|Mtx2|53375|metaxin 2	AK212612|Mtx2|53375|metaxin 2	AK216047|Mtx2|53375|metaxin 2
mm9_v1_chr1_-_173957316_173957398	1.57753	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_chr16_+_23520391_23520449	1.57644	SOX2.p2	
mm9_v1_chr19_+_6363686_6363698	1.576	SOX2.p2	NM_001110791|Sf1|22668|splicing factor 1	NM_011750|Sf1|22668|splicing factor 1
mm9_v1_chrX_+_131252542_131252558	1.57505	SOX2.p2	AK019405|Armcx1|78248|armadillo repeat containing, X-linked 1	BC021410|Armcx1|78248|armadillo repeat containing, X-linked 1
mm9_v1_chr9_-_75458918_75458929	1.57297	SOX2.p2	AK018223|Tmod2|50876|tropomodulin 2
mm9_v1_chr15_-_100325669_100325697	1.57248	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_chr14_+_63456514_63456721	1.56694	SOX2.p2	AK086275|Wdfy2|268752|WD repeat and FYVE domain containing 2	NM_175546|Wdfy2|268752|WD repeat and FYVE domain containing 2	AK131958|Wdfy2|268752|WD repeat and FYVE domain containing 2	AK169499|Wdfy2|268752|WD repeat and FYVE domain containing 2	AK151817|Wdfy2|268752|WD repeat and FYVE domain containing 2	BC116632|Wdfy2|268752|WD repeat and FYVE domain containing 2	AK045072|Wdfy2|268752|WD repeat and FYVE domain containing 2
mm9_v1_chr4_+_100449375_100449436	1.55897	SOX2.p2	AK046646|Cachd1|320508|cache domain containing 1
mm9_v1_chr6_+_54545104_54545338	1.55712	SOX2.p2	AK078040|Plekha8|231999|pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8	NM_001164361|Plekha8|231999|pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8	AK170592|Plekha8|231999|pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8
mm9_v1_chr7_+_29649404_29649463	1.55384	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_chr9_-_106691395_106691543	1.55161	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_chr4_+_6118252_6118258	1.54999	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_chr3_-_38383688_38383798	1.54815	SOX2.p2	AK129484|Ankrd50|99696|ankyrin repeat domain 50	NM_001167883|Ankrd50|99696|ankyrin repeat domain 50
mm9_v1_chr13_-_76081343_76081394	1.5455	SOX2.p2	AK081381|Rhobtb3|73296|Rho-related BTB domain containing 3
mm9_v1_chr9_-_57493393_57493475	1.5445	SOX2.p2	AK136876|Csk|12988|c-src tyrosine kinase
mm9_v1_chr9_-_82869034_82869071	1.53891	SOX2.p2	BC022102|Phip|83946|pleckstrin homology domain interacting protein	BC039765|Phip|83946|pleckstrin homology domain interacting protein	AK050025|Phip|83946|pleckstrin homology domain interacting protein
mm9_v1_chr13_-_85428957_85429102	1.53833	SOX2.p2	NM_145452|Rasa1|218397|RAS p21 protein activator 1	AK046620|Rasa1|218397|RAS p21 protein activator 1
mm9_v1_chr16_+_23224955_23224980	1.538	SOX2.p2	AK084124|St6gal1|20440|beta galactoside alpha 2,6 sialyltransferase 1
mm9_v1_chr7_-_29086780_29086803	1.53234	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_chr6_+_86354212_86354404	1.5304	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_chr15_-_90880241_90880381	1.5302	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_chr4_-_88368313_88368424	1.5292	SOX2.p2	AK129338|Klhl9|242521|kelch-like 9 (Drosophila)	BC094556|Klhl9|242521|kelch-like 9 (Drosophila)	AK049803|Klhl9|242521|kelch-like 9 (Drosophila)	AK033231|Klhl9|242521|kelch-like 9 (Drosophila)	NM_172871|Klhl9|242521|kelch-like 9 (Drosophila)
mm9_v1_chr13_+_60703261_60703571	1.52366	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_chr7_+_19679892_19679978	1.51871	SOX2.p2	NM_011383|Six5|20475|sine oculis-related homeobox 5 homolog (Drosophila)
mm9_v1_chr9_-_113563906_113564041	1.51239	SOX2.p2	AK199870|Pdcd6ip|18571|programmed cell death 6 interacting protein
mm9_v1_chr4_+_128365981_128366038	1.51204	SOX2.p2	NM_018774|Phc2|54383|polyhomeotic-like 2 (Drosophila)	BC057571|Phc2|54383|polyhomeotic-like 2 (Drosophila)
mm9_v1_chrX_-_100678555_100678592	1.50919	SOX2.p2	L04961|Xist|213742|inactive X specific transcripts	AK002727|Xist|213742|inactive X specific transcripts
mm9_v1_chr4_+_135842003_135842015	1.50887	SOX2.p2	AK051031|Zfp46|22704|zinc finger protein 46
mm9_v1_chr16_-_32079420_32079468	1.50832	SOX2.p2	AK037275|Pak2|224105|p21 protein (Cdc42/Rac)-activated kinase 2
mm9_v1_chr5_+_115751128_115751148	1.50281	SOX2.p2	
mm9_v1_chr11_-_78311204_78311255	1.5018	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_chr2_+_68699498_68699613	1.50084	SOX2.p2	AK081354|Lass6|241447|LAG1 homolog, ceramide synthase 6	AK135798|Lass6|241447|LAG1 homolog, ceramide synthase 6	AK151848|Lass6|241447|LAG1 homolog, ceramide synthase 6	AK152417|Lass6|241447|LAG1 homolog, ceramide synthase 6	BC057629|Lass6|241447|LAG1 homolog, ceramide synthase 6	AK028849|Lass6|241447|LAG1 homolog, ceramide synthase 6	NM_172856|Lass6|241447|LAG1 homolog, ceramide synthase 6
mm9_v1_chr7_+_25292201_25292230	1.49833	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_chr1_-_178744138_178744216	1.49819	SOX2.p2	BC054781|Cep170|545389|centrosomal protein 170	BC057019|Cep170|545389|centrosomal protein 170
mm9_v1_chr10_+_66648458_66648510	1.48991	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_chr4_+_28740280_28740313	1.48223	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_chr18_-_34784206_34784257	1.47839	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_chr8_-_27229485_27229708	1.47314	SOX2.p2	AY223806|Hook3|320191|hook homolog 3 (Drosophila)	BC090960|Hook3|320191|hook homolog 3 (Drosophila)	AK054263|Hook3|320191|hook homolog 3 (Drosophila)	AK170858|Hook3|320191|hook homolog 3 (Drosophila)	AK080377|Hook3|320191|hook homolog 3 (Drosophila)	AK145149|Hook3|320191|hook homolog 3 (Drosophila)	NM_207659|Hook3|320191|hook homolog 3 (Drosophila)
mm9_v1_chr16_+_65815758_65815952	1.46736	SOX2.p2	NM_028572|Vgll3|73569|vestigial like 3 (Drosophila)	BC042696|Vgll3|73569|vestigial like 3 (Drosophila)
mm9_v1_chr13_-_54850954_54851046	1.45957	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_-_134409044_134409108	1.45931	SOX2.p2	AY364165|Tmem57|66146|transmembrane protein 57	BC054355|Tmem57|66146|transmembrane protein 57	BC010714|Tmem57|66146|transmembrane protein 57
mm9_v1_chr2_-_94253040_94253188	1.45138	SOX2.p2	AK208753|Api5|11800|apoptosis inhibitor 5
mm9_v1_chr12_-_99816091_99816149	1.44797	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_chr16_-_98073389_98073456	1.44626	SOX2.p2	BC072597|Prdm15|114604|PR domain containing 15	AK144820|Prdm15|114604|PR domain containing 15
mm9_v1_chr6_+_103460834_103460869	1.44533	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_chr18_-_33623400_33623430	1.43443	SOX2.p2	NM_001109989|D0H4S114|27528|DNA segment, human D4S114
mm9_v1_chr11_-_74710562_74710581	1.43314	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_chr7_+_137836057_137836069	1.4305	SOX2.p2	AB041546|Tacc2|57752|transforming, acidic coiled-coil containing protein 2	NM_021314|Tacc2|57752|transforming, acidic coiled-coil containing protein 2
mm9_v1_chr6_+_120314442_120314515	1.42808	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_chr10_-_85379640_85379767	1.42807	SOX2.p2	AK028414|Prdm4|72843|PR domain containing 4	NM_181650|Prdm4|72843|PR domain containing 4
mm9_v1_chr3_+_88336316_88336316	1.42783	SOX2.p2	NM_001029890|Mex3a|72640|mex3 homolog A (C. elegans)
mm9_v1_chr4_+_137549366_137549416	1.42517	SOX2.p2	AK019693|Eif4g3|230861|eukaryotic translation initiation factor 4 gamma, 3	AK054068|Eif4g3|230861|eukaryotic translation initiation factor 4 gamma, 3	BC072600|Eif4g3|230861|eukaryotic translation initiation factor 4 gamma, 3	NM_172703|Eif4g3|230861|eukaryotic translation initiation factor 4 gamma, 3	AK046639|Eif4g3|230861|eukaryotic translation initiation factor 4 gamma, 3	BC082549|Eif4g3|230861|eukaryotic translation initiation factor 4 gamma, 3	BC079885|Eif4g3|230861|eukaryotic translation initiation factor 4 gamma, 3
mm9_v1_chr1_+_42752608_42752622	1.4232	SOX2.p2	
mm9_v1_chr13_-_55589463_55589528	1.42265	SOX2.p2	BC006714|Dbn1|56320|drebrin 1
mm9_v1_chr9_-_10904725_10904816	1.41413	SOX2.p2	AK138164|Cntn5|244682|contactin 5	AK162856|Cntn5|244682|contactin 5	NM_001033359|Cntn5|244682|contactin 5	NM_001170787|Cntn5|244682|contactin 5
mm9_v1_chr18_+_37467108_37467135	1.41238	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_chr19_+_3768021_3768138	1.40556	SOX2.p2	AY555192|Suv420h1|225888|suppressor of variegation 4-20 homolog 1 (Drosophila)	AK082660|Suv420h1|225888|suppressor of variegation 4-20 homolog 1 (Drosophila)	AK054093|Suv420h1|225888|suppressor of variegation 4-20 homolog 1 (Drosophila)
mm9_v1_chr15_+_44259636_44259698	1.40164	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_chr14_+_117324518_117324572	1.39496	SOX2.p2	AK164668|Gpc6|23888|glypican 6	AK135442|Gpc6|23888|glypican 6	NM_001079844|Gpc6|23888|glypican 6	NM_011821|Gpc6|23888|glypican 6
mm9_v1_chr10_+_127485339_127485356	1.39486	SOX2.p2	
mm9_v1_chr5_+_117807290_117807469	1.39291	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_chr19_-_40588297_40588344	1.3929	SOX2.p2	NM_009166|Sorbs1|20411|sorbin and SH3 domain containing 1
mm9_v1_chr18_+_37633193_37633199	1.39288	SOX2.p2	BC066178|Pcdhb15|93886|protocadherin beta 15	AK038663|Pcdhb15|93886|protocadherin beta 15	NM_053140|Pcdhb15|93886|protocadherin beta 15
mm9_v1_chr14_-_34195326_34195332	1.38839	SOX2.p2	AK047936|Mapk8|26419|mitogen-activated protein kinase 8	AK053062|Mapk8|26419|mitogen-activated protein kinase 8
mm9_v1_chr3_+_60432922_60432975	1.38737	SOX2.p2	AK166145|Mbnl1|56758|muscleblind-like 1 (Drosophila)
mm9_v1_chr10_+_128242649_128242744	1.38354	SOX2.p2	AK159388|Dnajc14|74330|DnaJ (Hsp40) homolog, subfamily C, member 14	AK083878|Dnajc14|74330|DnaJ (Hsp40) homolog, subfamily C, member 14	AK032681|Dnajc14|74330|DnaJ (Hsp40) homolog, subfamily C, member 14	AK017830|Dnajc14|74330|DnaJ (Hsp40) homolog, subfamily C, member 14	AK082579|Dnajc14|74330|DnaJ (Hsp40) homolog, subfamily C, member 14	NM_028873|Dnajc14|74330|DnaJ (Hsp40) homolog, subfamily C, member 14
mm9_v1_chr3_+_63780020_63780051	1.38267	SOX2.p2	AK146654|Gmps|229363|guanine monophosphate synthetase
mm9_v1_chr18_+_37656644_37656807	1.38261	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_chr3_+_159502646_159502709	1.3806	SOX2.p2	BC075615|Wls|68151|wntless homolog (Drosophila)	NM_026582|Wls|68151|wntless homolog (Drosophila)	AK029053|Wls|68151|wntless homolog (Drosophila)	AK044810|Wls|68151|wntless homolog (Drosophila)	AK019886|Wls|68151|wntless homolog (Drosophila)	AK029104|Wls|68151|wntless homolog (Drosophila)	AK029315|Wls|68151|wntless homolog (Drosophila)	AK031444|Wls|68151|wntless homolog (Drosophila)	AK049842|Wls|68151|wntless homolog (Drosophila)	AK128912|Wls|68151|wntless homolog (Drosophila)	AK159207|Wls|68151|wntless homolog (Drosophila)	AK159977|Wls|68151|wntless homolog (Drosophila)	AK077407|Wls|68151|wntless homolog (Drosophila)
mm9_v1_chr4_+_21858472_21858503	1.37964	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_chr14_-_55196138_55196410	1.37708	SOX2.p2	BC011035|Jub|16475|ajuba	NM_010590|Jub|16475|ajuba	U79776|Jub|16475|ajuba
mm9_v1_chr9_+_59465036_59465209	1.37448	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_chr7_-_27981077_27981289	1.37433	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_chr16_+_98218479_98218528	1.37373	SOX2.p2	AK045713|B230307C23Rik|245305|RIKEN cDNA B230307C23 gene	BC056174|B230307C23Rik|245305|RIKEN cDNA B230307C23 gene
mm9_v1_chr9_+_110034489_110034583	1.37355	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_chr10_-_70747929_70748034	1.37218	SOX2.p2	AK144468|Ube2d1|216080|ubiquitin-conjugating enzyme E2D 1, UBC4/5 homolog (yeast)	AK043167|Ube2d1|216080|ubiquitin-conjugating enzyme E2D 1, UBC4/5 homolog (yeast)	BC019464|Ube2d1|216080|ubiquitin-conjugating enzyme E2D 1, UBC4/5 homolog (yeast)	AK148364|Ube2d1|216080|ubiquitin-conjugating enzyme E2D 1, UBC4/5 homolog (yeast)	NM_145420|Ube2d1|216080|ubiquitin-conjugating enzyme E2D 1, UBC4/5 homolog (yeast)
mm9_v1_chr10_-_62254998_62255005	1.36895	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_chr3_-_116671573_116671671	1.36735	SOX2.p2	AF263246|Palmd|114301|palmdelphin	AL391037|Palmd|114301|palmdelphin	AJ312215|Palmd|114301|palmdelphin	AK171869|Palmd|114301|palmdelphin	BC010193|Palmd|114301|palmdelphin	AK043695|Palmd|114301|palmdelphin	AK014531|Palmd|114301|palmdelphin
mm9_v1_chr1_-_176851949_176851953	1.36368	SOX2.p2	AB011030|Grem2|23893|gremlin 2 homolog, cysteine knot superfamily (Xenopus laevis)	NM_011825|Grem2|23893|gremlin 2 homolog, cysteine knot superfamily (Xenopus laevis)	AK142008|Grem2|23893|gremlin 2 homolog, cysteine knot superfamily (Xenopus laevis)
mm9_v1_chr3_+_80840575_80840591	1.3628	SOX2.p2	AK042767|Pdgfc|54635|platelet-derived growth factor, C polypeptide
mm9_v1_chr6_+_4853319_4853431	1.36156	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_chr13_-_47138492_47138553	1.35356	SOX2.p2	AK002335|Tpmt|22017|thiopurine methyltransferase	AF037043|Tpmt|22017|thiopurine methyltransferase	AK019205|Tpmt|22017|thiopurine methyltransferase
mm9_v1_chr8_+_87493507_87493627	1.35038	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_chr3_-_90313339_90313430	1.35014	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_chr4_+_6118247_6118251	1.34916	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_chr1_+_72871060_72871146	1.3467	SOX2.p2	AK012703|Igfbp2|16008|insulin-like growth factor binding protein 2	BC012724|Igfbp2|16008|insulin-like growth factor binding protein 2	NM_008342|Igfbp2|16008|insulin-like growth factor binding protein 2	BC054473|Igfbp2|16008|insulin-like growth factor binding protein 2	X81580|Igfbp2|16008|insulin-like growth factor binding protein 2	AK011784|Igfbp2|16008|insulin-like growth factor binding protein 2	AK011790|Igfbp2|16008|insulin-like growth factor binding protein 2
mm9_v1_chr19_-_31839462_31839522	1.34635	SOX2.p2	AK051624|Prkg1|19091|protein kinase, cGMP-dependent, type I	AK083991|Prkg1|19091|protein kinase, cGMP-dependent, type I	NM_001013833|Prkg1|19091|protein kinase, cGMP-dependent, type I
mm9_v1_chr8_+_34842304_34842440	1.34137	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_chr1_-_30920095_30920100	1.34105	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_chr9_-_44215391_44215460	1.3395	SOX2.p2	AK032168|Trappc4|60409|trafficking protein particle complex 4	AK005276|Trappc4|60409|trafficking protein particle complex 4
mm9_v1_chr11_-_86621130_86621161	1.33493	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_chr4_-_88367207_88367304	1.33265	SOX2.p2	
mm9_v1_chr12_+_41172585_41172629	1.33067	SOX2.p2	AK085002|Dock4|238130|dedicator of cytokinesis 4	AK030389|Dock4|238130|dedicator of cytokinesis 4
mm9_v1_chr1_-_145851257_145851282	1.33046	SOX2.p2	AF432916|Rgs2|19735|regulator of G-protein signaling 2	BC023001|Rgs2|19735|regulator of G-protein signaling 2	AF215668|Rgs2|19735|regulator of G-protein signaling 2	U67187|Rgs2|19735|regulator of G-protein signaling 2	AK029310|Rgs2|19735|regulator of G-protein signaling 2	AK031603|Rgs2|19735|regulator of G-protein signaling 2	AK077922|Rgs2|19735|regulator of G-protein signaling 2	AK162276|Rgs2|19735|regulator of G-protein signaling 2	NM_009061|Rgs2|19735|regulator of G-protein signaling 2
mm9_v1_chr8_+_125935470_125935482	1.32511	SOX2.p2	AF312873|Tubb3|22152|tubulin, beta 3
mm9_v1_chr15_-_91022165_91022189	1.32144	SOX2.p2	BC019187|Abcd2|26874|ATP-binding cassette, sub-family D (ALD), member 2
mm9_v1_chr5_+_53981453_53981812	1.32144	SOX2.p2	NM_009035|Rbpj|19664|recombination signal binding protein for immunoglobulin kappa J region	S63463|Rbpj|19664|recombination signal binding protein for immunoglobulin kappa J region	AK152746|Rbpj|19664|recombination signal binding protein for immunoglobulin kappa J region	X17459|Rbpj|19664|recombination signal binding protein for immunoglobulin kappa J region	AK028363|Rbpj|19664|recombination signal binding protein for immunoglobulin kappa J region	AK132145|Rbpj|19664|recombination signal binding protein for immunoglobulin kappa J region	AK139087|Rbpj|19664|recombination signal binding protein for immunoglobulin kappa J region	NM_001080927|Rbpj|19664|recombination signal binding protein for immunoglobulin kappa J region
mm9_v1_chr5_-_110771973_110772012	1.31616	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_chr1_-_16509276_16509454	1.31195	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_chr14_+_76245136_76245138	1.30509	SOX2.p2	AK149695|Tpt1|22070|tumor protein, translationally-controlled 1	AK150500|Tpt1|22070|tumor protein, translationally-controlled 1	AK151266|Tpt1|22070|tumor protein, translationally-controlled 1	AK151375|Tpt1|22070|tumor protein, translationally-controlled 1	AK151894|Tpt1|22070|tumor protein, translationally-controlled 1	AK152690|Tpt1|22070|tumor protein, translationally-controlled 1	AK159516|Tpt1|22070|tumor protein, translationally-controlled 1	AK165736|Tpt1|22070|tumor protein, translationally-controlled 1	AK167413|Tpt1|22070|tumor protein, translationally-controlled 1	AK167936|Tpt1|22070|tumor protein, translationally-controlled 1	AK168151|Tpt1|22070|tumor protein, translationally-controlled 1	AK150300|Tpt1|22070|tumor protein, translationally-controlled 1	AK150858|Tpt1|22070|tumor protein, translationally-controlled 1	AK151059|Tpt1|22070|tumor protein, translationally-controlled 1	AK152808|Tpt1|22070|tumor protein, translationally-controlled 1	AK159565|Tpt1|22070|tumor protein, translationally-controlled 1	X06407|Tpt1|22070|tumor protein, translationally-controlled 1
mm9_v1_chr17_+_74738475_74738547	1.30128	SOX2.p2	AK044900|Spast|50850|spastin	AK007793|Spast|50850|spastin
mm9_v1_chr1_+_138027943_138028013	1.29494	SOX2.p2	NM_001039472|Kif21b|16565|kinesin family member 21B
mm9_v1_chrX_+_137909951_137910122	1.29283	SOX2.p2	AK133179|Col4a5|12830|collagen, type IV, alpha 5	NM_001163155|Col4a5|12830|collagen, type IV, alpha 5	NM_007736|Col4a5|12830|collagen, type IV, alpha 5	AB041350|Col4a5|12830|collagen, type IV, alpha 5	BC082788|Col4a5|12830|collagen, type IV, alpha 5
mm9_v1_chr2_-_180689380_180689413	1.28761	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_chr14_+_59820284_59820346	1.2854	SOX2.p2	AK017287|Rcbtb1|71330|regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1
mm9_v1_chr10_+_27794625_27794662	1.28225	SOX2.p2	NM_008983|Ptprk|19272|protein tyrosine phosphatase, receptor type, K	AK078614|Ptprk|19272|protein tyrosine phosphatase, receptor type, K	BC138376|Ptprk|19272|protein tyrosine phosphatase, receptor type, K	BC145261|Ptprk|19272|protein tyrosine phosphatase, receptor type, K	AK083006|Ptprk|19272|protein tyrosine phosphatase, receptor type, K
mm9_v1_chr11_-_41814008_41814185	1.27811	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_chr5_+_120881778_120882006	1.2765	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_chr17_-_35840931_35841083	1.27385	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_chr6_-_97155541_97155640	1.2631	SOX2.p2	BC002002|Uba3|22200|ubiquitin-like modifier activating enzyme 3	BC080776|Uba3|22200|ubiquitin-like modifier activating enzyme 3	AK048148|Uba3|22200|ubiquitin-like modifier activating enzyme 3	AK032514|Uba3|22200|ubiquitin-like modifier activating enzyme 3	AK166655|Uba3|22200|ubiquitin-like modifier activating enzyme 3	AK168859|Uba3|22200|ubiquitin-like modifier activating enzyme 3	AK043801|Uba3|22200|ubiquitin-like modifier activating enzyme 3	AK014433|Uba3|22200|ubiquitin-like modifier activating enzyme 3	NM_001111106|Uba3|22200|ubiquitin-like modifier activating enzyme 3	NM_011666|Uba3|22200|ubiquitin-like modifier activating enzyme 3	AK159381|Uba3|22200|ubiquitin-like modifier activating enzyme 3
mm9_v1_chr10_+_106708886_106708980	1.25813	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_+_147415297_147415395	1.25784	SOX2.p2	AK150159|Mthfr|17769|5,10-methylenetetrahydrofolate reductase	NM_001161798|Mthfr|17769|5,10-methylenetetrahydrofolate reductase	AK149795|Mthfr|17769|5,10-methylenetetrahydrofolate reductase	BC052466|Mthfr|17769|5,10-methylenetetrahydrofolate reductase	AF404273|Mthfr|17769|5,10-methylenetetrahydrofolate reductase	BC051017|Mthfr|17769|5,10-methylenetetrahydrofolate reductase
mm9_v1_chr16_-_96349334_96349335	1.24833	SOX2.p2	AK010763|Hmgn1|15312|high mobility group nucleosomal binding domain 1
mm9_v1_chr19_-_41922577_41922621	1.24725	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_chr3_+_89019108_89019113	1.24602	SOX2.p2	NM_013691|Thbs3|21827|thrombospondin 3
mm9_v1_chr10_+_36694322_36694389	1.24524	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_chr18_+_37901716_37901894	1.24191	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_chr11_-_100259061_100259098	1.24169	SOX2.p2	AK170934|Jup|16480|junction plakoglobin	AK171501|Jup|16480|junction plakoglobin	AK145895|Jup|16480|junction plakoglobin
mm9_v1_chr11_-_72028494_72028582	1.24142	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_chr2_-_14970818_14970938	1.24094	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_chr6_+_17413930_17414106	1.23955	SOX2.p2	NM_008591|Met|17295|met proto-oncogene	AK170560|Met|17295|met proto-oncogene	AK148258|Met|17295|met proto-oncogene
mm9_v1_chr8_+_56040211_56040342	1.23785	SOX2.p2	BC043130|Gpm6a|234267|glycoprotein m6a	AK147245|Gpm6a|234267|glycoprotein m6a	AK147280|Gpm6a|234267|glycoprotein m6a
mm9_v1_chr8_-_87784612_87784676	1.23673	SOX2.p2	AK219106|Vps35|65114|vacuolar protein sorting 35
mm9_v1_chr3_-_68930928_68931049	1.2325	SOX2.p2	BC052162|Kpna4|16649|karyopherin (importin) alpha 4	NM_008467|Kpna4|16649|karyopherin (importin) alpha 4	AK147920|Kpna4|16649|karyopherin (importin) alpha 4
mm9_v1_chr3_-_122241909_122241984	1.23163	SOX2.p2	AK019185|Fnbp1l|214459|formin binding protein 1-like
mm9_v1_chr10_-_126558035_126558203	1.23078	SOX2.p2	BC006844|Os9|216440|amplified in osteosarcoma	BC031768|Os9|216440|amplified in osteosarcoma	AK028047|Os9|216440|amplified in osteosarcoma
mm9_v1_chrX_+_131252456_131252527	1.22684	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_chr10_+_44786959_44787139	1.2263	SOX2.p2	AK053816|Prep|19072|prolyl endopeptidase	AK163787|Prep|19072|prolyl endopeptidase	AK141851|Prep|19072|prolyl endopeptidase	AK170570|Prep|19072|prolyl endopeptidase	BC012869|Prep|19072|prolyl endopeptidase	NM_011156|Prep|19072|prolyl endopeptidase	AK076257|Prep|19072|prolyl endopeptidase	AK133875|Prep|19072|prolyl endopeptidase	AK161528|Prep|19072|prolyl endopeptidase	BC050830|Prep|19072|prolyl endopeptidase	AB007631|Prep|19072|prolyl endopeptidase
mm9_v1_chr8_-_8690519_8690552	1.22543	SOX2.p2	BC046971|Arglu1|234023|arginine and glutamate rich 1	NM_176849|Arglu1|234023|arginine and glutamate rich 1
mm9_v1_chr15_-_95358578_95358610	1.20836	SOX2.p2	AK048913|Nell2|54003|NEL-like 2 (chicken)
mm9_v1_chr5_+_76612903_76613006	1.2063	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_chr3_+_109143558_109143678	1.20018	SOX2.p2	AK033253|Vav3|57257|vav 3 oncogene	NM_020505|Vav3|57257|vav 3 oncogene	AK041249|Vav3|57257|vav 3 oncogene
mm9_v1_chr5_+_125343060_125343124	1.19887	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_chr2_-_136942066_136942255	1.19806	SOX2.p2	NM_013822|Jag1|16449|jagged 1	AK137092|Jag1|16449|jagged 1	AF171092|Jag1|16449|jagged 1
mm9_v1_chr19_-_25036047_25036105	1.19512	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_chr12_-_85262786_85262867	1.19452	SOX2.p2	AK004553|Numb|18222|numb gene homolog (Drosophila)	BC050108|Numb|18222|numb gene homolog (Drosophila)	BC033459|Numb|18222|numb gene homolog (Drosophila)
mm9_v1_chr13_-_8870231_8870293	1.19328	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_chr1_+_134942609_134942622	1.1921	SOX2.p2	AK049181|Pik3c2b|240752|phosphoinositide-3-kinase, class 2, beta polypeptide
mm9_v1_chr15_-_91022198_91022269	1.19155	SOX2.p2	AK082588|Abcd2|26874|ATP-binding cassette, sub-family D (ALD), member 2	AK051445|Abcd2|26874|ATP-binding cassette, sub-family D (ALD), member 2	Z48670|Abcd2|26874|ATP-binding cassette, sub-family D (ALD), member 2	NM_011994|Abcd2|26874|ATP-binding cassette, sub-family D (ALD), member 2
mm9_v1_chr18_-_84255781_84255953	1.18819	SOX2.p2	BC040215|Tshz1|110796|teashirt zinc finger family member 1	AK220545|Tshz1|110796|teashirt zinc finger family member 1	AK152140|Tshz1|110796|teashirt zinc finger family member 1	NM_001081300|Tshz1|110796|teashirt zinc finger family member 1
mm9_v1_chr3_-_130412297_130412356	1.18696	SOX2.p2	AK011085|Ostc|66357|oligosaccharyltransferase complex subunit	AK017845|Ostc|66357|oligosaccharyltransferase complex subunit	AK135332|Ostc|66357|oligosaccharyltransferase complex subunit	AK013011|Ostc|66357|oligosaccharyltransferase complex subunit	AK032969|Ostc|66357|oligosaccharyltransferase complex subunit	AK009237|Ostc|66357|oligosaccharyltransferase complex subunit	BC014799|Ostc|66357|oligosaccharyltransferase complex subunit	BC021935|Ostc|66357|oligosaccharyltransferase complex subunit
mm9_v1_chr5_-_110772051_110772230	1.18628	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_chr18_+_10325174_10325177	1.18278	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_chr14_+_47917895_47918025	1.18246	SOX2.p2	AK164183|Mapk1ip1l|218975|mitogen-activated protein kinase 1 interacting protein 1-like	AK048061|Mapk1ip1l|218975|mitogen-activated protein kinase 1 interacting protein 1-like	AK086896|Mapk1ip1l|218975|mitogen-activated protein kinase 1 interacting protein 1-like	AK168694|Mapk1ip1l|218975|mitogen-activated protein kinase 1 interacting protein 1-like	BC047201|Mapk1ip1l|218975|mitogen-activated protein kinase 1 interacting protein 1-like	AK169333|Mapk1ip1l|218975|mitogen-activated protein kinase 1 interacting protein 1-like	NM_178684|Mapk1ip1l|218975|mitogen-activated protein kinase 1 interacting protein 1-like
mm9_v1_chr8_-_89269853_89269958	1.17971	SOX2.p2	BC046317|Siah1a|20437|seven in absentia 1A	NM_009172|Siah1a|20437|seven in absentia 1A
mm9_v1_chr15_+_79489607_79489701	1.17492	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_chr3_+_102862151_102862295	1.17057	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_chr5_+_54200858_54200899	1.16537	SOX2.p2	NM_144517|Tbc1d19|67249|TBC1 domain family, member 19	AK083084|Tbc1d19|67249|TBC1 domain family, member 19
mm9_v1_chr11_+_80196766_80196898	1.16282	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_chr9_+_86916846_86916935	1.16244	SOX2.p2	AK090159|Cyb5r4|266690|cytochrome b5 reductase 4	NM_024195|Cyb5r4|266690|cytochrome b5 reductase 4	AK157312|Cyb5r4|266690|cytochrome b5 reductase 4	AK169937|Cyb5r4|266690|cytochrome b5 reductase 4	AK169995|Cyb5r4|266690|cytochrome b5 reductase 4	BC025438|Cyb5r4|266690|cytochrome b5 reductase 4	AK034878|Cyb5r4|266690|cytochrome b5 reductase 4	AK172252|Cyb5r4|266690|cytochrome b5 reductase 4
mm9_v1_chr3_+_152009474_152009480	1.16132	SOX2.p2	AK047530|Usp33|170822|ubiquitin specific peptidase 33
mm9_v1_chr11_+_106078232_106078424	1.15945	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_chr17_-_13153538_13153631	1.15895	SOX2.p2	BC004823|Acat2|110460|acetyl-Coenzyme A acetyltransferase 2	BC012496|Acat2|110460|acetyl-Coenzyme A acetyltransferase 2	AK037249|Acat2|110460|acetyl-Coenzyme A acetyltransferase 2	AK151751|Acat2|110460|acetyl-Coenzyme A acetyltransferase 2	AK167234|Acat2|110460|acetyl-Coenzyme A acetyltransferase 2	NM_009338|Acat2|110460|acetyl-Coenzyme A acetyltransferase 2	AK166813|Acat2|110460|acetyl-Coenzyme A acetyltransferase 2
mm9_v1_chr13_-_29045399_29045574	1.15625	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_chr5_-_136720706_136720731	1.15565	SOX2.p2	BC049777|Sh2b2|23921|SH2B adaptor protein 2	AK140319|Sh2b2|23921|SH2B adaptor protein 2	AK140325|Sh2b2|23921|SH2B adaptor protein 2	AK017604|Sh2b2|23921|SH2B adaptor protein 2
mm9_v1_chr5_-_23953594_23953663	1.15536	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_chr7_-_30290470_30290595	1.15438	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_chr12_-_15823536_15823550	1.14973	SOX2.p2	BC037387|Trib2|217410|tribbles homolog 2 (Drosophila)	AK044747|Trib2|217410|tribbles homolog 2 (Drosophila)
mm9_v1_chr2_+_3035692_3035956	1.14519	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_chr7_+_73254341_73254400	1.14072	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_chr13_+_8202111_8202186	1.13793	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_chr19_-_46401618_46401645	1.13735	SOX2.p2	BC057353|Psd|73728|pleckstrin and Sec7 domain containing	NM_028627|Psd|73728|pleckstrin and Sec7 domain containing
mm9_v1_chr9_-_36954842_36954852	1.13734	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_chr10_-_31410391_31410392	1.13313	SOX2.p2	AK018248|Nkain2|432450|Na+/K+ transporting ATPase interacting 2
mm9_v1_chr13_-_29044564_29044751	1.13263	SOX2.p2	U70440|Sox4|20677|SRY-box containing gene 4
mm9_v1_chr2_+_154262114_154262265	1.13246	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_chr6_-_38825815_38825951	1.12791	SOX2.p2	AF333791|Hipk2|15258|homeodomain interacting protein kinase 2	AF333792|Hipk2|15258|homeodomain interacting protein kinase 2	AF273680|Hipk2|15258|homeodomain interacting protein kinase 2	BC031904|Hipk2|15258|homeodomain interacting protein kinase 2	AF170301|Hipk2|15258|homeodomain interacting protein kinase 2	AF170302|Hipk2|15258|homeodomain interacting protein kinase 2	AF077659|Hipk2|15258|homeodomain interacting protein kinase 2
mm9_v1_chr18_+_80243633_80243827	1.12753	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_chr1_+_67169588_67169639	1.12701	SOX2.p2	BC126969|Cps1|227231|carbamoyl-phosphate synthetase 1	NM_001080809|Cps1|227231|carbamoyl-phosphate synthetase 1
mm9_v1_chr18_-_16967754_16967859	1.12572	SOX2.p2	AK146981|Cdh2|12558|cadherin 2
mm9_v1_chr12_+_33832641_33832680	1.12509	SOX2.p2	AK013145|Atxn7l1|380753|ataxin 7-like 1	BC100598|Atxn7l1|380753|ataxin 7-like 1	BC017546|Atxn7l1|380753|ataxin 7-like 1
mm9_v1_chr1_+_160292665_160292848	1.12407	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_chr12_-_99975614_99975748	1.12151	SOX2.p2	BC098500|Ptpn21|24000|protein tyrosine phosphatase, non-receptor type 21	NM_001146199|Ptpn21|24000|protein tyrosine phosphatase, non-receptor type 21
mm9_v1_chrX_+_74756540_74756586	1.11876	SOX2.p2	AK036996|Tbl1x|21372|transducin (beta)-like 1 X-linked	AK038674|Tbl1x|21372|transducin (beta)-like 1 X-linked	NM_020601|Tbl1x|21372|transducin (beta)-like 1 X-linked
mm9_v1_chr8_-_23763885_23763908	1.11806	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_chr19_+_41557168_41557205	1.11757	SOX2.p2	AK077424|Lcor|212391|ligand dependent nuclear receptor corepressor	AB076079|Lcor|212391|ligand dependent nuclear receptor corepressor
mm9_v1_chr3_-_19211000_19211321	1.1146	SOX2.p2	AY007702|Pde7a|18583|phosphodiesterase 7A	AK154521|Pde7a|18583|phosphodiesterase 7A	BC062909|Pde7a|18583|phosphodiesterase 7A	NM_001122759|Pde7a|18583|phosphodiesterase 7A
mm9_v1_chr7_+_137836116_137836140	1.114	SOX2.p2	AK165194|Tacc2|57752|transforming, acidic coiled-coil containing protein 2
mm9_v1_chr8_+_37157863_37157905	1.11028	SOX2.p2	NM_172911|D8Ertd82e|244418|DNA segment, Chr 8, ERATO Doi 82, expressed
mm9_v1_chr4_+_118081908_118082012	1.10813	SOX2.p2	AK011080|Med8|80509|mediator of RNA polymerase II transcription, subunit 8 homolog (yeast)	NM_020000|Med8|80509|mediator of RNA polymerase II transcription, subunit 8 homolog (yeast)	NM_173719|Med8|80509|mediator of RNA polymerase II transcription, subunit 8 homolog (yeast)	AK147032|Med8|80509|mediator of RNA polymerase II transcription, subunit 8 homolog (yeast)	AK005422|Med8|80509|mediator of RNA polymerase II transcription, subunit 8 homolog (yeast)	AK148025|Med8|80509|mediator of RNA polymerase II transcription, subunit 8 homolog (yeast)	BC051683|Med8|80509|mediator of RNA polymerase II transcription, subunit 8 homolog (yeast)	AK008759|Med8|80509|mediator of RNA polymerase II transcription, subunit 8 homolog (yeast)	BC021870|Med8|80509|mediator of RNA polymerase II transcription, subunit 8 homolog (yeast)	AB041805|Med8|80509|mediator of RNA polymerase II transcription, subunit 8 homolog (yeast)
mm9_v1_chr7_+_138712015_138712162	1.10034	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_chr16_-_24090166_24090201	1.09545	SOX2.p2	
mm9_v1_chr1_+_17135421_17135611	1.09516	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_chr18_-_33623668_33623692	1.09408	SOX2.p2	NM_001109988|D0H4S114|27528|DNA segment, human D4S114
mm9_v1_chr1_-_52784161_52784228	1.09274	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_chr1_-_33871261_33871282	1.09193	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_chr8_-_73223897_73223993	1.08293	SOX2.p2	AK135112|Gm11175|100303737|predicted gene 11175
mm9_v1_chr9_+_35024031_35024058	1.07821	SOX2.p2	AK219602|Srpr|67398|signal recognition particle receptor ('docking protein')
mm9_v1_chr5_+_73882264_73882364	1.07688	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_chr6_-_49214015_49214054	1.07664	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_-_111239017_111239099	1.07597	SOX2.p2	BC059835|Ulk1|22241|Unc-51 like kinase 1 (C. elegans)	AK148317|Ulk1|22241|Unc-51 like kinase 1 (C. elegans)	AK156534|Ulk1|22241|Unc-51 like kinase 1 (C. elegans)	BC057121|Ulk1|22241|Unc-51 like kinase 1 (C. elegans)	NM_009469|Ulk1|22241|Unc-51 like kinase 1 (C. elegans)
mm9_v1_chr11_-_69480763_69480942	1.07289	SOX2.p2	
mm9_v1_chr12_+_76919276_76919336	1.07113	SOX2.p2	AK078542|Syne2|319565|synaptic nuclear envelope 2	AK145252|Syne2|319565|synaptic nuclear envelope 2	NM_001005510|Syne2|319565|synaptic nuclear envelope 2	AK084811|Syne2|319565|synaptic nuclear envelope 2	AK084394|Syne2|319565|synaptic nuclear envelope 2	AF435012|Syne2|319565|synaptic nuclear envelope 2	AK052521|Syne2|319565|synaptic nuclear envelope 2
mm9_v1_chr10_+_5958432_5958574	1.07082	SOX2.p2	AK132308|Zbtb2|381990|zinc finger and BTB domain containing 2	NM_001033466|Zbtb2|381990|zinc finger and BTB domain containing 2
mm9_v1_chr12_+_8681058_8681080	1.0707	SOX2.p2	NM_001160219|Pum2|80913|pumilio 2 (Drosophila)	NM_001160220|Pum2|80913|pumilio 2 (Drosophila)	AK147617|Pum2|80913|pumilio 2 (Drosophila)
mm9_v1_chr15_+_75447114_75447188	1.07038	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_chr6_+_57652594_57652646	1.06702	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_chr17_+_78907402_78907511	1.06389	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_chr12_+_114378368_114378447	1.06097	SOX2.p2	NM_024223|Crip2|68337|cysteine rich protein 2
mm9_v1_chr3_+_103718466_103718512	1.06009	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_chr11_-_60988419_60988468	1.05756	SOX2.p2	BC080737|Usp22|216825|ubiquitin specific peptidase 22	AK160992|Usp22|216825|ubiquitin specific peptidase 22
mm9_v1_chr6_-_42643001_42643085	1.0574	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_chr2_+_32006651_32006708	1.05718	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_chr4_+_6118235_6118245	1.05509	SOX2.p2	AK049018|Ubxn2b|68053|UBX domain protein 2B
mm9_v1_chr5_+_108890247_108890362	1.05418	SOX2.p2	AK033609|Pcgf3|69587|polycomb group ring finger 3	AK085574|Pcgf3|69587|polycomb group ring finger 3	AK089091|Pcgf3|69587|polycomb group ring finger 3	NM_172716|Pcgf3|69587|polycomb group ring finger 3
mm9_v1_chr2_-_118375365_118375421	1.05135	SOX2.p2	AK040622|Bmf|171543|BCL2 modifying factor	AK169903|Bmf|171543|BCL2 modifying factor	NM_138313|Bmf|171543|BCL2 modifying factor	AK084658|Bmf|171543|BCL2 modifying factor
mm9_v1_chr2_-_17970075_17970075	1.04995	SOX2.p2	BC050860|2810030E01Rik|72668|RIKEN cDNA 2810030E01 gene	NM_028317|2810030E01Rik|72668|RIKEN cDNA 2810030E01 gene
mm9_v1_chr15_+_80453912_80453951	1.04871	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_chr9_+_107948285_107948372	1.04824	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_chr9_+_108686107_108686181	1.04757	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_chr11_-_115560691_115560842	1.04701	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_chr10_-_121484248_121484370	1.04686	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_chr16_-_76288569_76288581	1.04224	SOX2.p2	BC062260|Nrip1|268903|nuclear receptor interacting protein 1
mm9_v1_chrX_-_131343508_131343539	1.04072	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_chr13_-_67601323_67601457	1.04061	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_chr5_+_31191224_31191333	1.04027	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_chr13_+_21570775_21570839	1.03982	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_chr2_+_25127985_25128074	1.03762	SOX2.p2	NM_175300|Anapc2|99152|anaphase promoting complex subunit 2	AK033784|Anapc2|99152|anaphase promoting complex subunit 2	BC137583|Anapc2|99152|anaphase promoting complex subunit 2	AK154465|Anapc2|99152|anaphase promoting complex subunit 2	AK170676|Anapc2|99152|anaphase promoting complex subunit 2	BC096381|Anapc2|99152|anaphase promoting complex subunit 2	AK129351|Anapc2|99152|anaphase promoting complex subunit 2	BC027351|Anapc2|99152|anaphase promoting complex subunit 2
mm9_v1_chr1_+_161162285_161162568	1.03727	SOX2.p2	BC082804|Rfwd2|26374|ring finger and WD repeat domain 2	NM_011931|Rfwd2|26374|ring finger and WD repeat domain 2	BC051565|Rfwd2|26374|ring finger and WD repeat domain 2	BC158002|Rfwd2|26374|ring finger and WD repeat domain 2	AF151110|Rfwd2|26374|ring finger and WD repeat domain 2
mm9_v1_chrX_+_162782484_162782852	1.03359	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_chr5_-_144031666_144031702	1.02967	SOX2.p2	NM_017467|Zfp316|54201|zinc finger protein 316
mm9_v1_chr14_+_28435613_28435695	1.02745	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_chr12_+_91570569_91570694	1.02669	SOX2.p2	AJ006804|Nrxn3|18191|neurexin III
mm9_v1_chr4_-_109959185_109959241	1.02555	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_chr8_+_56040193_56040201	1.02444	SOX2.p2	AK081877|Gpm6a|234267|glycoprotein m6a
mm9_v1_chr3_+_121129502_121129542	1.02411	SOX2.p2	AK081672|Cnn3|71994|calponin 3, acidic
mm9_v1_chrX_+_50265390_50265552	1.02388	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_chr3_+_53267715_53267853	1.02236	SOX2.p2	AK087909|2810046L04Rik|212127|RIKEN cDNA 2810046L04 gene	AK038404|2810046L04Rik|212127|RIKEN cDNA 2810046L04 gene	NM_173382|2810046L04Rik|212127|RIKEN cDNA 2810046L04 gene	AK012908|2810046L04Rik|212127|RIKEN cDNA 2810046L04 gene	AK161440|2810046L04Rik|212127|RIKEN cDNA 2810046L04 gene
mm9_v1_chr5_+_34163324_34163431	1.01966	SOX2.p2	AK038286|Whsc1|107823|Wolf-Hirschhorn syndrome candidate 1 (human)
mm9_v1_chr9_-_60535274_60535340	1.01883	SOX2.p2	AK051325|Lrrc49|102747|leucine rich repeat containing 49	NM_001146047|Lrrc49|102747|leucine rich repeat containing 49
mm9_v1_chr7_-_99889932_99889979	1.01634	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_chr14_+_61757271_61757327	1.01616	SOX2.p2	AK160797|Sacs|50720|sacsin	NM_172809|Sacs|50720|sacsin	AK046501|Sacs|50720|sacsin
mm9_v1_chr2_-_102026486_102026616	1.01329	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_chr10_-_33344405_33344571	1.00626	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_chr19_-_56896633_56896705	1.00614	SOX2.p2	BC064039|A630007B06Rik|213993|RIKEN cDNA A630007B06 gene	AK041398|A630007B06Rik|213993|RIKEN cDNA A630007B06 gene	AK054204|A630007B06Rik|213993|RIKEN cDNA A630007B06 gene
mm9_v1_chr12_-_41172348_41172381	1.00449	SOX2.p2	AK156529|Zfp277|246196|zinc finger protein 277	BC043453|Zfp277|246196|zinc finger protein 277	AK077401|Zfp277|246196|zinc finger protein 277	AK075945|Zfp277|246196|zinc finger protein 277	AK145060|Zfp277|246196|zinc finger protein 277	NM_172575|Zfp277|246196|zinc finger protein 277	NM_178845|Zfp277|246196|zinc finger protein 277
mm9_v1_chr11_-_50105794_50105864	1.00249	SOX2.p2	AY442299|Maml1|103806|mastermind like 1 (Drosophila)	AK129088|Maml1|103806|mastermind like 1 (Drosophila)	NM_175334|Maml1|103806|mastermind like 1 (Drosophila)
mm9_v1_chr10_+_36694535_36694557	1.00136	SOX2.p2	AB221663|Hdac2|15182|histone deacetylase 2
mm9_v1_chr9_+_86360760_86360843	0.99896	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_chr11_+_72420705_72421072	0.998813	SOX2.p2	NM_025985|Ube2g1|67128|ubiquitin-conjugating enzyme E2G 1 (UBC7 homolog, C. elegans)	BC065083|Ube2g1|67128|ubiquitin-conjugating enzyme E2G 1 (UBC7 homolog, C. elegans)	AK083029|Ube2g1|67128|ubiquitin-conjugating enzyme E2G 1 (UBC7 homolog, C. elegans)	AK012539|Ube2g1|67128|ubiquitin-conjugating enzyme E2G 1 (UBC7 homolog, C. elegans)	AK013902|Ube2g1|67128|ubiquitin-conjugating enzyme E2G 1 (UBC7 homolog, C. elegans)	AK167472|Ube2g1|67128|ubiquitin-conjugating enzyme E2G 1 (UBC7 homolog, C. elegans)	AK197264|Ube2g1|67128|ubiquitin-conjugating enzyme E2G 1 (UBC7 homolog, C. elegans)
mm9_v1_chr4_-_109959366_109959438	0.998257	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_chr14_+_47896669_47896817	0.990198	SOX2.p2	BC057159|Socs4|67296|suppressor of cytokine signaling 4	AK014115|Socs4|67296|suppressor of cytokine signaling 4	NM_080843|Socs4|67296|suppressor of cytokine signaling 4
mm9_v1_chr11_-_102308910_102308956	0.989727	SOX2.p2	BC025575|Fam171a2|217219|family with sequence similarity 171, member A2	BC064455|Fam171a2|217219|family with sequence similarity 171, member A2
mm9_v1_chr12_-_71212906_71213013	0.985209	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_chr7_+_118172447_118172534	0.984835	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_chr10_+_21601968_21601989	0.98366	SOX2.p2	BC070401|Sgk1|20393|serum/glucocorticoid regulated kinase 1	NM_001161845|Sgk1|20393|serum/glucocorticoid regulated kinase 1
mm9_v1_chr14_-_20642973_20643066	0.982851	SOX2.p2	AK162433|2700060E02Rik|68045|RIKEN cDNA 2700060E02 gene	AK148686|2700060E02Rik|68045|RIKEN cDNA 2700060E02 gene	AK162070|2700060E02Rik|68045|RIKEN cDNA 2700060E02 gene	AK160555|2700060E02Rik|68045|RIKEN cDNA 2700060E02 gene	AK012451|2700060E02Rik|68045|RIKEN cDNA 2700060E02 gene	BC023932|2700060E02Rik|68045|RIKEN cDNA 2700060E02 gene	BC096571|2700060E02Rik|68045|RIKEN cDNA 2700060E02 gene	AK012460|2700060E02Rik|68045|RIKEN cDNA 2700060E02 gene	AK003732|2700060E02Rik|68045|RIKEN cDNA 2700060E02 gene	BC048357|2700060E02Rik|68045|RIKEN cDNA 2700060E02 gene	AK012486|2700060E02Rik|68045|RIKEN cDNA 2700060E02 gene	NM_026528|2700060E02Rik|68045|RIKEN cDNA 2700060E02 gene	AK160696|2700060E02Rik|68045|RIKEN cDNA 2700060E02 gene
mm9_v1_chr4_-_41670160_41670212	0.980266	SOX2.p2	AF098508|Dctn3|53598|dynactin 3	AK003255|Dctn3|53598|dynactin 3	BC061120|Dctn3|53598|dynactin 3	AK002720|Dctn3|53598|dynactin 3	AK011840|Dctn3|53598|dynactin 3	AK159344|Dctn3|53598|dynactin 3	NM_001159565|Dctn3|53598|dynactin 3	NM_016890|Dctn3|53598|dynactin 3
mm9_v1_chr9_-_110019806_110019945	0.979684	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_chr18_+_37105758_37105860	0.979533	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_chr12_+_120085663_120085788	0.979504	SOX2.p2	BC082582|Sp8|320145|trans-acting transcription factor 8
mm9_v1_chr17_-_88464582_88464624	0.979446	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_chr11_-_106993235_106993235	0.978362	SOX2.p2	NM_176850|Bptf|207165|bromodomain PHD finger transcription factor
mm9_v1_chr4_-_94223435_94223491	0.97672	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_chr15_-_13103346_13103429	0.976125	SOX2.p2	NM_007666|Cdh6|12563|cadherin 6	AK134611|Cdh6|12563|cadherin 6
mm9_v1_chr4_-_134409254_134409295	0.974595	SOX2.p2	AY846873|Tmem57|66146|transmembrane protein 57	AY846874|Tmem57|66146|transmembrane protein 57	NM_025382|Tmem57|66146|transmembrane protein 57
mm9_v1_chr7_-_34926055_34926067	0.970777	SOX2.p2	AK213025|Uba2|50995|ubiquitin-like modifier activating enzyme 2
mm9_v1_chr8_-_8690334_8690515	0.966966	SOX2.p2	AK145733|Arglu1|234023|arginine and glutamate rich 1
mm9_v1_chr15_-_39775498_39775574	0.965568	SOX2.p2	BC058345|Lrp12|239393|low density lipoprotein-related protein 12
mm9_v1_chr14_+_68701838_68701963	0.963845	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_chr11_+_101414168_101414211	0.959879	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_chr8_-_41720091_41720170	0.959767	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_chr4_-_45024999_45025283	0.959302	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_chr16_-_91728816_91728882	0.956981	SOX2.p2	BC019387|Cryzl1|66609|crystallin, zeta (quinone reductase)-like 1	AK008846|Cryzl1|66609|crystallin, zeta (quinone reductase)-like 1	BC010479|Cryzl1|66609|crystallin, zeta (quinone reductase)-like 1	NM_133679|Cryzl1|66609|crystallin, zeta (quinone reductase)-like 1	AK010433|Cryzl1|66609|crystallin, zeta (quinone reductase)-like 1	AK145827|Cryzl1|66609|crystallin, zeta (quinone reductase)-like 1
mm9_v1_chr4_+_118293403_118293498	0.956867	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_chr10_-_82996846_82996884	0.95677	SOX2.p2	AK141954|Aldh1l2|216188|aldehyde dehydrogenase 1 family, member L2	NM_153543|Aldh1l2|216188|aldehyde dehydrogenase 1 family, member L2
mm9_v1_chrX_-_161765324_161765332	0.953984	SOX2.p2	AK139335|Glra2|237213|glycine receptor, alpha 2 subunit
mm9_v1_chr11_-_69229653_69229709	0.952228	SOX2.p2	BC075632|Kdm6b|216850|KDM1 lysine (K)-specific demethylase 6B
mm9_v1_chr2_-_93174606_93174694	0.949943	SOX2.p2	BC052169|Tspan18|241556|tetraspanin 18	AK042573|Tspan18|241556|tetraspanin 18	NM_183180|Tspan18|241556|tetraspanin 18	AK011742|Tspan18|241556|tetraspanin 18
mm9_v1_chr8_+_3587675_3587681	0.949335	SOX2.p2	AK081728|2310057J16Rik|69697|RIKEN cDNA 2310057J16 gene
mm9_v1_chr11_+_87574041_87574047	0.946633	SOX2.p2	AK043747|Bzrap1|207777|benzodiazepine receptor associated protein 1	NM_172449|Bzrap1|207777|benzodiazepine receptor associated protein 1
mm9_v1_chr1_+_87961184_87961303	0.945484	SOX2.p2	AK153386|Psmd1|70247|proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	NM_027357|Psmd1|70247|proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	AK159123|Psmd1|70247|proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	AK159750|Psmd1|70247|proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	BC039937|Psmd1|70247|proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	BC138526|Psmd1|70247|proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	BC138527|Psmd1|70247|proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	AK087947|Psmd1|70247|proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	BC089028|Psmd1|70247|proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	BC029319|Psmd1|70247|proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	BC031587|Psmd1|70247|proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	BC032068|Psmd1|70247|proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	BC025802|Psmd1|70247|proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	BC022955|Psmd1|70247|proteasome (prosome, macropain) 26S subunit, non-ATPase, 1
mm9_v1_chr11_+_45869473_45869501	0.944171	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_chr6_-_119494295_119494364	0.9386	SOX2.p2	BC051406|Wnt5b|22419|wingless-related MMTV integration site 5B	AK013218|Wnt5b|22419|wingless-related MMTV integration site 5B	NM_009525|Wnt5b|22419|wingless-related MMTV integration site 5B
mm9_v1_chr8_+_96334452_96334737	0.938429	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_chrX_+_17739762_17739792	0.937065	SOX2.p2	AK164941|Kdm6a|22289|4lysine (K)-specific demethylase 6A	AK144654|Kdm6a|22289|4lysine (K)-specific demethylase 6A	AK080370|Kdm6a|22289|4lysine (K)-specific demethylase 6A	BC053433|Kdm6a|22289|4lysine (K)-specific demethylase 6A	NM_009483|Kdm6a|22289|4lysine (K)-specific demethylase 6A
mm9_v1_chr18_-_43597890_43597947	0.933682	SOX2.p2	AF501324|Dpysl3|22240|dihydropyrimidinase-like 3
mm9_v1_chr3_-_92289795_92289819	0.932731	SOX2.p2	X91824|Sprr1a|20753|small proline-rich protein 1A	BC027534|Sprr1a|20753|small proline-rich protein 1A	NM_009264|Sprr1a|20753|small proline-rich protein 1A	AK144782|Sprr1a|20753|small proline-rich protein 1A
mm9_v1_chr2_-_160934743_160934810	0.930429	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_chr2_+_104430617_104430708	0.930315	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_chr11_-_76577056_76577075	0.92934	SOX2.p2	BC008542|Gosr1|53334|golgi SNAP receptor complex member 1	NM_016810|Gosr1|53334|golgi SNAP receptor complex member 1	AK134515|Gosr1|53334|golgi SNAP receptor complex member 1	AK133836|Gosr1|53334|golgi SNAP receptor complex member 1	AK161386|Gosr1|53334|golgi SNAP receptor complex member 1	AF079901|Gosr1|53334|golgi SNAP receptor complex member 1	BC051661|Gosr1|53334|golgi SNAP receptor complex member 1
mm9_v1_chr14_+_22318991_22319040	0.928432	SOX2.p2	AK147509|Myst4|54169|MYST histone acetyltransferase monocytic leukemia 4
mm9_v1_chr17_+_85025803_85025818	0.927871	SOX2.p2	AK160259|Dync2li1|213575|dynein cytoplasmic 2 light intermediate chain 1
mm9_v1_chr16_+_27388907_27389196	0.927688	SOX2.p2	BC144895|Ccdc50|67501|coiled-coil domain containing 50	BC144898|Ccdc50|67501|coiled-coil domain containing 50	BC145933|Ccdc50|67501|coiled-coil domain containing 50	BC145935|Ccdc50|67501|coiled-coil domain containing 50	NM_001025615|Ccdc50|67501|coiled-coil domain containing 50	NM_026202|Ccdc50|67501|coiled-coil domain containing 50	AK162434|Ccdc50|67501|coiled-coil domain containing 50	AK016827|Ccdc50|67501|coiled-coil domain containing 50	AK151672|Ccdc50|67501|coiled-coil domain containing 50	AK147820|Ccdc50|67501|coiled-coil domain containing 50	AK077557|Ccdc50|67501|coiled-coil domain containing 50	AK165214|Ccdc50|67501|coiled-coil domain containing 50	AK012190|Ccdc50|67501|coiled-coil domain containing 50	AJ534985|Ccdc50|67501|coiled-coil domain containing 50
mm9_v1_chr4_+_135842023_135842037	0.927593	SOX2.p2	AK148255|Zfp46|22704|zinc finger protein 46
mm9_v1_chr4_+_155186568_155186886	0.926031	SOX2.p2	NM_207678|Ccnl2|56036|cyclin L2	AK007552|Ccnl2|56036|cyclin L2	BC132295|Ccnl2|56036|cyclin L2	AK048244|Ccnl2|56036|cyclin L2	AK156037|Ccnl2|56036|cyclin L2	AB041605|Ccnl2|56036|cyclin L2	AY337018|Ccnl2|56036|cyclin L2	AK169857|Ccnl2|56036|cyclin L2	BC023747|Ccnl2|56036|cyclin L2	AF211859|Ccnl2|56036|cyclin L2	AK044204|Ccnl2|56036|cyclin L2	AK008585|Ccnl2|56036|cyclin L2	AK138938|Ccnl2|56036|cyclin L2
mm9_v1_chr5_+_34678976_34679138	0.924914	SOX2.p2	AK133924|Rnf4|19822|ring finger protein 4	AK159949|Rnf4|19822|ring finger protein 4	AK090162|Rnf4|19822|ring finger protein 4	NM_011278|Rnf4|19822|ring finger protein 4	AK147057|Rnf4|19822|ring finger protein 4	AK158987|Rnf4|19822|ring finger protein 4	AK019171|Rnf4|19822|ring finger protein 4	AK159296|Rnf4|19822|ring finger protein 4	AK151116|Rnf4|19822|ring finger protein 4	AK159778|Rnf4|19822|ring finger protein 4	AF169300|Rnf4|19822|ring finger protein 4	BC003282|Rnf4|19822|ring finger protein 4	AK145596|Rnf4|19822|ring finger protein 4	AK179891|Rnf4|19822|ring finger protein 4	AK207872|Rnf4|19822|ring finger protein 4	AK219295|Rnf4|19822|ring finger protein 4
mm9_v1_chr5_-_122804200_122804240	0.923683	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_chr5_-_66089061_66089225	0.922142	SOX2.p2	NM_001081321|Pds5a|71521|PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)
mm9_v1_chr1_-_42751652_42751673	0.921917	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_chr12_-_52930506_52930535	0.917953	SOX2.p2	AK172326|Hectd1|207304|HECT domain containing 1	NM_144788|Hectd1|207304|HECT domain containing 1
mm9_v1_chr1_+_64579559_64579575	0.917487	SOX2.p2	AK044992|Creb1|12912|cAMP responsive element binding protein 1	AK044993|Creb1|12912|cAMP responsive element binding protein 1
mm9_v1_chr2_+_48669628_48669670	0.913881	SOX2.p2	NM_007396|Acvr2a|11480|activin receptor IIA	AK081022|Acvr2a|11480|activin receptor IIA
mm9_v1_chr9_+_77602337_77602341	0.912036	SOX2.p2	AK143228|Gclc|14629|glutamate-cysteine ligase, catalytic subunit	AK144339|Gclc|14629|glutamate-cysteine ligase, catalytic subunit
mm9_v1_chr6_-_71858736_71858760	0.90555	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_chr4_-_33010429_33010479	0.904812	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_chr9_-_96918641_96918773	0.901169	SOX2.p2	BC055705|Spsb4|211949|splA/ryanodine receptor domain and SOCS box containing 4	AK142195|Spsb4|211949|splA/ryanodine receptor domain and SOCS box containing 4	AF403039|Spsb4|211949|splA/ryanodine receptor domain and SOCS box containing 4	NM_145134|Spsb4|211949|splA/ryanodine receptor domain and SOCS box containing 4
mm9_v1_chr19_+_36484237_36484340	0.899221	SOX2.p2	AK146133|Pcgf5|76073|polycomb group ring finger 5
mm9_v1_chr4_-_151235758_151235857	0.891822	SOX2.p2	AK076589|Camta1|100072|calmodulin binding transcription activator 1	BC150740|Camta1|100072|calmodulin binding transcription activator 1	AK034038|Camta1|100072|calmodulin binding transcription activator 1	AK144150|Camta1|100072|calmodulin binding transcription activator 1	AK009988|Camta1|100072|calmodulin binding transcription activator 1
mm9_v1_chrX_+_97689629_97689706	0.890444	SOX2.p2	NM_008784|Igbp1|18518|immunoglobulin (CD79A) binding protein 1	AK032709|Igbp1|18518|immunoglobulin (CD79A) binding protein 1	AK141470|Igbp1|18518|immunoglobulin (CD79A) binding protein 1	BC089567|Igbp1|18518|immunoglobulin (CD79A) binding protein 1	AK017166|Igbp1|18518|immunoglobulin (CD79A) binding protein 1	L31652|Igbp1|18518|immunoglobulin (CD79A) binding protein 1
mm9_v1_chr7_+_89319717_89319836	0.890195	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_chr10_-_102698899_102698955	0.889884	SOX2.p2	AK158531|Lrriq1|74978|leucine-rich repeats and IQ motif containing 1	BC051400|Lrriq1|74978|leucine-rich repeats and IQ motif containing 1	AK015687|Lrriq1|74978|leucine-rich repeats and IQ motif containing 1	NM_001163559|Lrriq1|74978|leucine-rich repeats and IQ motif containing 1	NM_029134|Lrriq1|74978|leucine-rich repeats and IQ motif containing 1
mm9_v1_chr11_+_76015590_76015598	0.886112	SOX2.p2	AK160183|Fam57a|116972|family with sequence similarity 57, member A	AK077374|Fam57a|116972|family with sequence similarity 57, member A
mm9_v1_chr17_+_36053855_36053941	0.885366	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_chr14_-_19164241_19164397	0.884476	SOX2.p2	BC003781|Ube2e1|22194|ubiquitin-conjugating enzyme E2E 1, UBC4/5 homolog (yeast)	AK148266|Ube2e1|22194|ubiquitin-conjugating enzyme E2E 1, UBC4/5 homolog (yeast)	X92665|Ube2e1|22194|ubiquitin-conjugating enzyme E2E 1, UBC4/5 homolog (yeast)	AK090177|Ube2e1|22194|ubiquitin-conjugating enzyme E2E 1, UBC4/5 homolog (yeast)	NM_009455|Ube2e1|22194|ubiquitin-conjugating enzyme E2E 1, UBC4/5 homolog (yeast)
mm9_v1_chr19_+_53385022_53385154	0.884329	SOX2.p2	D31824|Mxi1|17859|Max interacting protein 1
mm9_v1_chr17_-_63230665_63230665	0.883985	SOX2.p2	BC040218|Efna5|13640|ephrin A5	NM_010109|Efna5|13640|ephrin A5	NM_207654|Efna5|13640|ephrin A5
mm9_v1_chr12_-_100631260_100631297	0.882176	SOX2.p2	AK046748|Foxn3|71375|forkhead box N3
mm9_v1_chrX_+_7476460_7476569	0.877297	SOX2.p2	AK151396|Timm17b|21855|translocase of inner mitochondrial membrane 17b	AK150836|Timm17b|21855|translocase of inner mitochondrial membrane 17b	AK009164|Timm17b|21855|translocase of inner mitochondrial membrane 17b	AK011830|Timm17b|21855|translocase of inner mitochondrial membrane 17b	AK049584|Timm17b|21855|translocase of inner mitochondrial membrane 17b	AK153097|Timm17b|21855|translocase of inner mitochondrial membrane 17b	NM_011591|Timm17b|21855|translocase of inner mitochondrial membrane 17b	AK184288|Timm17b|21855|translocase of inner mitochondrial membrane 17b	BC008275|Timm17b|21855|translocase of inner mitochondrial membrane 17b	AK003204|Timm17b|21855|translocase of inner mitochondrial membrane 17b	AF106621|Timm17b|21855|translocase of inner mitochondrial membrane 17b
mm9_v1_chr1_-_55084217_55084256	0.876311	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_chr15_-_79272478_79272599	0.874221	SOX2.p2	NM_013767|Csnk1e|27373|casein kinase 1, epsilon
mm9_v1_chr6_-_119305193_119305208	0.872076	SOX2.p2	BC030936|Adipor2|68465|adiponectin receptor 2
mm9_v1_chr2_+_180921963_180922240	0.871072	SOX2.p2	AK002602|Ppdpf|66496|pancreatic progenitor cell differentiation and proliferation factor homolog (zebrafish)RIKEN cDNA 2700038C09 gene	BC058516|Ppdpf|66496|pancreatic progenitor cell differentiation and proliferation factor homolog (zebrafish)RIKEN cDNA 2700038C09 gene	AK154758|Ppdpf|66496|pancreatic progenitor cell differentiation and proliferation factor homolog (zebrafish)RIKEN cDNA 2700038C09 gene	AK166314|Ppdpf|66496|pancreatic progenitor cell differentiation and proliferation factor homolog (zebrafish)RIKEN cDNA 2700038C09 gene	BC100439|Ppdpf|66496|pancreatic progenitor cell differentiation and proliferation factor homolog (zebrafish)RIKEN cDNA 2700038C09 gene	AK003282|Ppdpf|66496|pancreatic progenitor cell differentiation and proliferation factor homolog (zebrafish)RIKEN cDNA 2700038C09 gene	NM_025598|Ppdpf|66496|pancreatic progenitor cell differentiation and proliferation factor homolog (zebrafish)RIKEN cDNA 2700038C09 gene	AK012327|Ppdpf|66496|pancreatic progenitor cell differentiation and proliferation factor homolog (zebrafish)RIKEN cDNA 2700038C09 gene	AK012037|Ppdpf|66496|pancreatic progenitor cell differentiation and proliferation factor homolog (zebrafish)RIKEN cDNA 2700038C09 gene	AK014211|Ppdpf|66496|pancreatic progenitor cell differentiation and proliferation factor homolog (zebrafish)RIKEN cDNA 2700038C09 gene	BC029225|Ppdpf|66496|pancreatic progenitor cell differentiation and proliferation factor homolog (zebrafish)RIKEN cDNA 2700038C09 gene	BC091753|Ppdpf|66496|pancreatic progenitor cell differentiation and proliferation factor homolog (zebrafish)RIKEN cDNA 2700038C09 gene	AK012545|Ppdpf|66496|pancreatic progenitor cell differentiation and proliferation factor homolog (zebrafish)RIKEN cDNA 2700038C09 gene
mm9_v1_chr3_+_13471643_13471656	0.869644	SOX2.p2	NM_001163328|Ralyl|76897|RALY RNA binding protein-like	NM_178631|Ralyl|76897|RALY RNA binding protein-like
mm9_v1_chr5_+_27231234_27231317	0.868828	SOX2.p2	AK051708|Dpp6|13483|dipeptidylpeptidase 6	BC085154|Dpp6|13483|dipeptidylpeptidase 6	NM_001198886|Dpp6|13483|dipeptidylpeptidase 6
mm9_v1_chr16_-_85862579_85862641	0.867302	SOX2.p2	AK046558|Adamts5|23794|a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)	AK164560|Adamts5|23794|a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)
mm9_v1_chr1_+_19093102_19093153	0.861975	SOX2.p2	AK132112|Tcfap2d|226896|transcription factor AP-2, delta	NM_153154|Tcfap2d|226896|transcription factor AP-2, delta	BC152324|Tcfap2d|226896|transcription factor AP-2, delta	BC152325|Tcfap2d|226896|transcription factor AP-2, delta
mm9_v1_chr2_+_31805751_31805822	0.861848	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_chr1_+_193541845_193542002	0.857033	SOX2.p2	AK133814|Lpgat1|226856|lysophosphatidylglycerol acyltransferase 1	NM_172266|Lpgat1|226856|lysophosphatidylglycerol acyltransferase 1
mm9_v1_chr11_-_4999029_4999066	0.856819	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_chr5_+_129106980_129107017	0.853046	SOX2.p2	AY509002|Fzd10|93897|frizzled homolog 10 (Drosophila)	NM_175284|Fzd10|93897|frizzled homolog 10 (Drosophila)	BC117759|Fzd10|93897|frizzled homolog 10 (Drosophila)
mm9_v1_chr1_+_40082070_40082114	0.848039	SOX2.p2	AK159799|Map4k4|26921|mitogen-activated protein kinase kinase kinase kinase 4
mm9_v1_chr18_+_73732352_73732560	0.847	SOX2.p2	NM_001039214|Mex3c|240396|mex3 homolog C (C. elegans)	AK133686|Mex3c|240396|mex3 homolog C (C. elegans)
mm9_v1_chr9_+_85736444_85736534	0.845394	SOX2.p2	NM_001164792|Tpbg|21983|trophoblast glycoprotein	AK165553|Tpbg|21983|trophoblast glycoprotein	BC058198|Tpbg|21983|trophoblast glycoprotein	AK143519|Tpbg|21983|trophoblast glycoprotein
mm9_v1_chr15_-_84388113_84388233	0.841844	SOX2.p2	AK083881|Ldoc1l|223732|leucine zipper, down-regulated in cancer 1-like
mm9_v1_chr7_-_17199935_17200012	0.841656	SOX2.p2	AK161796|Grlf1|232906|glucocorticoid receptor DNA binding factor 1
mm9_v1_chr9_+_44412931_44412987	0.841192	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_chr9_-_59334393_59334511	0.837328	SOX2.p2	BC057680|Arih1|23806|ariadne ubiquitin-conjugating enzyme E2 binding protein homolog 1 (Drosophila)
mm9_v1_chr9_+_21172314_21172446	0.836608	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_chr5_-_8622882_8622951	0.830842	SOX2.p2	BC058808|Rundc3b|242819|RUN domain containing 3B	NM_198620|Rundc3b|242819|RUN domain containing 3B
mm9_v1_chrX_+_20265093_20265121	0.830359	SOX2.p2	AK166188|Cdk16|18555|cyclin-dependent kinase 16
mm9_v1_chr13_+_78337168_78337277	0.829313	SOX2.p2	AK082108|A830082K12Rik|320174|RIKEN cDNA A830082K12 gene
mm9_v1_chr2_+_14525932_14526000	0.827532	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_chr19_+_26822892_26822948	0.826592	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_chr12_-_81861527_81861701	0.821126	SOX2.p2	AK147473|Gm1568|380768|predicted gene 1568	BC067044|Gm1568|380768|predicted gene 1568	NM_001008423|Gm1568|380768|predicted gene 1568
mm9_v1_chr1_+_158769044_158769153	0.819415	SOX2.p2	AK142319|Angptl1|72713|angiopoietin-like 1	AK012888|Angptl1|72713|angiopoietin-like 1	BC082563|Angptl1|72713|angiopoietin-like 1	NM_028333|Angptl1|72713|angiopoietin-like 1
mm9_v1_chr13_-_60278723_60278734	0.819271	SOX2.p2	X65128|Gas1|14451|growth arrest specific 1
mm9_v1_chr10_-_87937335_87937390	0.818774	SOX2.p2	AK080245|Chpt1|212862|choline phosphotransferase 1
mm9_v1_chr2_+_25036524_25036678	0.818501	SOX2.p2	BC069891|Nrarp|67122|Notch-regulated ankyrin repeat protein	AK012426|Nrarp|67122|Notch-regulated ankyrin repeat protein
mm9_v1_chr11_+_67779939_67779975	0.818464	SOX2.p2	AK003297|Stx8|55943|syntaxin 8	BC048479|Stx8|55943|syntaxin 8	BC061118|Stx8|55943|syntaxin 8	AK016271|Stx8|55943|syntaxin 8	AK011376|Stx8|55943|syntaxin 8
mm9_v1_chr5_-_97540568_97540637	0.818235	SOX2.p2	AK172689|Paqr3|231474|progestin and adipoQ receptor family member III	BC096380|Paqr3|231474|progestin and adipoQ receptor family member III	AK149213|Paqr3|231474|progestin and adipoQ receptor family member III	BC120853|Paqr3|231474|progestin and adipoQ receptor family member III	BC120855|Paqr3|231474|progestin and adipoQ receptor family member III	AY424292|Paqr3|231474|progestin and adipoQ receptor family member III	BC050248|Paqr3|231474|progestin and adipoQ receptor family member III	BC051173|Paqr3|231474|progestin and adipoQ receptor family member III	NM_198422|Paqr3|231474|progestin and adipoQ receptor family member III
mm9_v1_chr7_+_52151432_52151509	0.817985	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_chr1_+_129702056_129702170	0.817683	SOX2.p2	AK033697|Ccnt2|72949|cyclin T2
mm9_v1_chr2_-_39046224_39046253	0.815716	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_chr2_+_157250020_157250043	0.815571	SOX2.p2	NM_001025395|Src|20779|Rous sarcoma oncogene	NM_009271|Src|20779|Rous sarcoma oncogene	BC039953|Src|20779|Rous sarcoma oncogene
mm9_v1_chr6_+_142723841_142723893	0.815227	SOX2.p2	AK213220|Cmas|12764|cytidine monophospho-N-acetylneuraminic acid synthetase
mm9_v1_chr7_+_128177958_128178339	0.814376	SOX2.p2	AJ278576|Mettl9|59052|methyltransferase like 9	NM_021554|Mettl9|59052|methyltransferase like 9	BC068124|Mettl9|59052|methyltransferase like 9	AB041664|Mettl9|59052|methyltransferase like 9	AK075586|Mettl9|59052|methyltransferase like 9
mm9_v1_chr11_-_87800799_87801034	0.80989	SOX2.p2	AK028319|Dynll2|68097|dynein light chain LC8-type 2	BC011289|Dynll2|68097|dynein light chain LC8-type 2	BC058797|Dynll2|68097|dynein light chain LC8-type 2	BC040822|Dynll2|68097|dynein light chain LC8-type 2	AK011284|Dynll2|68097|dynein light chain LC8-type 2	AK160114|Dynll2|68097|dynein light chain LC8-type 2	AK049645|Dynll2|68097|dynein light chain LC8-type 2	AK078434|Dynll2|68097|dynein light chain LC8-type 2	AK169212|Dynll2|68097|dynein light chain LC8-type 2	NM_026556|Dynll2|68097|dynein light chain LC8-type 2
mm9_v1_chr17_+_44090222_44090252	0.809654	SOX2.p2	AK160865|Rcan2|53901|regulator of calcineurin 2
mm9_v1_chr15_-_57702643_57702752	0.801564	SOX2.p2	AK200586|Derl1|67819|Der1-like domain family, member 1	AK216985|Derl1|67819|Der1-like domain family, member 1	AK220009|Derl1|67819|Der1-like domain family, member 1
mm9_v1_chr11_-_109159357_109159494	0.800482	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_chr4_+_8462823_8462831	0.7987	SOX2.p2	AK042862|Rab2a|59021|RAB2A, member RAS oncogene family
mm9_v1_chr2_+_35516774_35517011	0.798677	SOX2.p2	AY305656|Dab2ip|69601|disabled homolog 2 (Drosophila) interacting protein
mm9_v1_chr1_+_97230610_97230736	0.798612	SOX2.p2	AK152164|Fam174a|67698|family with sequence similarity 174, member A
mm9_v1_chr1_+_162836582_162836617	0.797713	SOX2.p2	AK173335|Rc3h1|381305|RING CCCH (C3H) domains 1	AY948287|Rc3h1|381305|RING CCCH (C3H) domains 1
mm9_v1_chr19_+_53384990_53385011	0.797599	SOX2.p2	NM_001008542|Mxi1|17859|Max interacting protein 1	AK154538|Mxi1|17859|Max interacting protein 1	BC064453|Mxi1|17859|Max interacting protein 1
mm9_v1_chr2_-_89247233_89247234	0.790384	SOX2.p2	NM_146790|Olfr1238|258786|olfactory receptor 1238	BC128571|Olfr1238|258786|olfactory receptor 1238
mm9_v1_chrX_-_101176574_101176590	0.786049	SOX2.p2	AF069992|Rlim|19820|ring finger protein, LIM domain interacting
mm9_v1_chr11_+_72609717_72609729	0.785203	SOX2.p2	AK158924|Zzef1|195018|zinc finger, ZZ-type with EF hand domain 1	NM_001045536|Zzef1|195018|zinc finger, ZZ-type with EF hand domain 1
mm9_v1_chr9_+_20447739_20447785	0.785121	SOX2.p2	AK051149|Ubl5|66177|ubiquitin-like 5	NM_025401|Ubl5|66177|ubiquitin-like 5	AK040449|Ubl5|66177|ubiquitin-like 5
mm9_v1_chr7_+_73834774_73834871	0.783934	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_chr5_+_81449776_81449780	0.783202	SOX2.p2	AK155931|Lphn3|319387|latrophilin 3
mm9_v1_chr18_-_89063689_89063737	0.782637	SOX2.p2	AK142069|Socs6|54607|suppressor of cytokine signaling 6	AK053803|Socs6|54607|suppressor of cytokine signaling 6	AK156591|Socs6|54607|suppressor of cytokine signaling 6
mm9_v1_chr11_-_120434075_120434180	0.779043	SOX2.p2	BC093512|P4hb|18453|prolyl 4-hydroxylase, beta polypeptide	AK168336|P4hb|18453|prolyl 4-hydroxylase, beta polypeptide	AK150755|P4hb|18453|prolyl 4-hydroxylase, beta polypeptide	BC008549|P4hb|18453|prolyl 4-hydroxylase, beta polypeptide	AK151351|P4hb|18453|prolyl 4-hydroxylase, beta polypeptide
mm9_v1_chr15_+_80629020_80629144	0.777399	SOX2.p2	NM_177124|Tnrc6b|213988|trinucleotide repeat containing 6b	AK051922|Tnrc6b|213988|trinucleotide repeat containing 6b	BC068158|Tnrc6b|213988|trinucleotide repeat containing 6b
mm9_v1_chr11_+_115626816_115626845	0.776583	SOX2.p2	BC053088|2310067B10Rik|71947|RIKEN cDNA 2310067B10 gene
mm9_v1_chr13_+_54676356_54676474	0.776487	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_chr5_-_136720740_136720830	0.776451	SOX2.p2	AF234838|Sh2b2|23921|SH2B adaptor protein 2	BC057334|Sh2b2|23921|SH2B adaptor protein 2	NM_018825|Sh2b2|23921|SH2B adaptor protein 2
mm9_v1_chr3_+_80841086_80841191	0.775424	SOX2.p2	AK052947|Pdgfc|54635|platelet-derived growth factor, C polypeptide	BC029099|Pdgfc|54635|platelet-derived growth factor, C polypeptide	AF117608|Pdgfc|54635|platelet-derived growth factor, C polypeptide	BC037696|Pdgfc|54635|platelet-derived growth factor, C polypeptide
mm9_v1_chr1_+_57831651_57831771	0.775109	SOX2.p2	NM_144882|Spats2l|67198|spermatogenesis associated, serine-rich 2-like	AK012791|Spats2l|67198|spermatogenesis associated, serine-rich 2-like	AK019292|Spats2l|67198|spermatogenesis associated, serine-rich 2-like	AK161988|Spats2l|67198|spermatogenesis associated, serine-rich 2-like	AK031266|Spats2l|67198|spermatogenesis associated, serine-rich 2-like	BC021879|Spats2l|67198|spermatogenesis associated, serine-rich 2-like	AK032169|Spats2l|67198|spermatogenesis associated, serine-rich 2-like
mm9_v1_chr8_+_87604829_87604904	0.771113	SOX2.p2	AK010893|BC056474|414077|cDNA sequence BC056474	BC089623|BC056474|414077|cDNA sequence BC056474	NM_001001493|BC056474|414077|cDNA sequence BC056474	BC024937|BC056474|414077|cDNA sequence BC056474	BC091742|BC056474|414077|cDNA sequence BC056474	BC056474|BC056474|414077|cDNA sequence BC056474
mm9_v1_chr7_+_140829357_140829384	0.770238	SOX2.p2	NM_178115|2700050L05Rik|214764|RIKEN cDNA 2700050L05 gene	AK052387|2700050L05Rik|214764|RIKEN cDNA 2700050L05 gene
mm9_v1_chr6_-_86683191_86683319	0.763189	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_chr1_-_152840432_152840584	0.763062	SOX2.p2	BC147549|Hmcn1|545370|hemicentin 1	BC147568|Hmcn1|545370|hemicentin 1	AK052713|Hmcn1|545370|hemicentin 1	NM_001024720|Hmcn1|545370|hemicentin 1
mm9_v1_chr2_+_44966657_44966746	0.762571	SOX2.p2	BC031611|Gm13476|433424|predicted gene 13476	NM_001177394|Gm13476|433424|predicted gene 13476
mm9_v1_chr10_-_62255007_62255115	0.761755	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_chr16_-_14159346_14159388	0.761504	SOX2.p2	AK158881|4921513D23Rik|223989|RIKEN cDNA 4921513D23 gene	NM_001081154|4921513D23Rik|223989|RIKEN cDNA 4921513D23 gene
mm9_v1_chr18_-_33623069_33623089	0.75915	SOX2.p2	BC054762|D0H4S114|27528|DNA segment, human D4S114	NM_001109990|D0H4S114|27528|DNA segment, human D4S114	X70398|D0H4S114|27528|DNA segment, human D4S114	AK048361|D0H4S114|27528|DNA segment, human D4S114	AK081502|D0H4S114|27528|DNA segment, human D4S114	AK133769|D0H4S114|27528|DNA segment, human D4S114
mm9_v1_chr9_-_57612906_57612972	0.757503	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_chr15_-_85412250_85412299	0.755444	SOX2.p2	BC058398|Wnt7b|22422|wingless-related MMTV integration site 7B	NM_009528|Wnt7b|22422|wingless-related MMTV integration site 7B
mm9_v1_chr5_-_100465086_100465197	0.755049	SOX2.p2	AK011143|Hnrpdl|50926|heterogeneous nuclear ribonucleoprotein D-like
mm9_v1_chr9_+_108997946_108997990	0.754925	SOX2.p2	NM_172775|Plxnb1|235611|plexin B1
mm9_v1_chr6_+_82984190_82984300	0.752655	SOX2.p2	AF053368|Loxl3|16950|lysyl oxidase-like 3	AK145189|Loxl3|16950|lysyl oxidase-like 3	AK030548|Loxl3|16950|lysyl oxidase-like 3	NM_013586|Loxl3|16950|lysyl oxidase-like 3	BC011298|Loxl3|16950|lysyl oxidase-like 3
mm9_v1_chr9_-_57613666_57613666	0.748426	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_chr15_+_83610459_83610521	0.747246	SOX2.p2	AK165755|Mpped1|223726|metallophosphoesterase domain containing 1
mm9_v1_chr2_+_92025639_92025639	0.744126	SOX2.p2	AK037174|Phf21a|192285|PHD finger protein 21A	NM_001109691|Phf21a|192285|PHD finger protein 21A
mm9_v1_chr12_+_72149332_72149349	0.744062	SOX2.p2	AK149171|Arid4a|238247|AT rich interactive domain 4A (RBP1-like)
mm9_v1_chr3_-_130412360_130412367	0.741574	SOX2.p2	NM_025509|Ostc|66357|oligosaccharyltransferase complex subunit
mm9_v1_chr3_+_137806411_137806513	0.740716	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_chr1_+_34636537_34636571	0.738409	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_chr11_+_59120429_59120467	0.736801	SOX2.p2	AK087490|Wnt9a|216795|wingless-type MMTV integration site 9A	NM_139298|Wnt9a|216795|wingless-type MMTV integration site 9A	BC066165|Wnt9a|216795|wingless-type MMTV integration site 9A	AB072311|Wnt9a|216795|wingless-type MMTV integration site 9A
mm9_v1_chr17_+_26012421_26012476	0.734277	SOX2.p2	AK151352|0610011F06Rik|68347|RIKEN cDNA 0610011F06 gene	NM_026686|0610011F06Rik|68347|RIKEN cDNA 0610011F06 gene	AK170337|0610011F06Rik|68347|RIKEN cDNA 0610011F06 gene	AK002535|0610011F06Rik|68347|RIKEN cDNA 0610011F06 gene	BC069266|0610011F06Rik|68347|RIKEN cDNA 0610011F06 gene
mm9_v1_chr1_+_154613763_154613962	0.733059	SOX2.p2	AK166335|Arpc5|67771|actin related protein 2/3 complex, subunit 5	BC060143|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK166284|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK166725|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK166919|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK008097|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK151656|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK152281|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK159738|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK011348|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK011911|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK017669|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK019149|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK150443|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK150703|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK153262|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK149756|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK151654|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK168264|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK087427|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK151490|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK159438|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK167916|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK168986|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK191774|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK181325|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK187022|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK189385|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK208127|Arpc5|67771|actin related protein 2/3 complex, subunit 5	AK209531|Arpc5|67771|actin related protein 2/3 complex, subunit 5
mm9_v1_chr6_-_128380651_128380781	0.732121	SOX2.p2	
mm9_v1_chr9_-_79825502_79825688	0.730773	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_chr4_+_101927346_101927346	0.728544	SOX2.p2	BC049864|Pde4b|18578|phosphodiesterase 4B, cAMP specific	NM_001177983|Pde4b|18578|phosphodiesterase 4B, cAMP specific
mm9_v1_chr1_+_169528492_169528646	0.728049	SOX2.p2	NM_009107|Rxrg|20183|retinoid X receptor gamma	BC058401|Rxrg|20183|retinoid X receptor gamma	S62948|Rxrg|20183|retinoid X receptor gamma
mm9_v1_chr18_+_65857921_65857924	0.727557	SOX2.p2	AK030604|5330437I02Rik|319888|RIKEN cDNA 5330437I02 gene	NM_177028|5330437I02Rik|319888|RIKEN cDNA 5330437I02 gene	AK030615|5330437I02Rik|319888|RIKEN cDNA 5330437I02 gene	BC141265|5330437I02Rik|319888|RIKEN cDNA 5330437I02 gene
mm9_v1_chrX_+_103222548_103222685	0.725101	SOX2.p2	AK017506|Atp7a|11977|ATPase, Cu++ transporting, alpha polypeptide	AK033254|Atp7a|11977|ATPase, Cu++ transporting, alpha polypeptide	NM_001109757|Atp7a|11977|ATPase, Cu++ transporting, alpha polypeptide	NM_009726|Atp7a|11977|ATPase, Cu++ transporting, alpha polypeptide	AK155643|Atp7a|11977|ATPase, Cu++ transporting, alpha polypeptide	AK171563|Atp7a|11977|ATPase, Cu++ transporting, alpha polypeptide	AK172209|Atp7a|11977|ATPase, Cu++ transporting, alpha polypeptide	U03434|Atp7a|11977|ATPase, Cu++ transporting, alpha polypeptide	U71091|Atp7a|11977|ATPase, Cu++ transporting, alpha polypeptide	BC141395|Atp7a|11977|ATPase, Cu++ transporting, alpha polypeptide
mm9_v1_chr11_+_108781661_108781720	0.724603	SOX2.p2	AK142333|Axin2|12006|axin2	NM_015732|Axin2|12006|axin2	BC057338|Axin2|12006|axin2	AK049192|Axin2|12006|axin2
mm9_v1_chr9_-_102256962_102257026	0.722363	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_chr9_-_121825422_121825428	0.72037	SOX2.p2	NM_010012|Cyp8b1|13124|cytochrome P450, family 8, subfamily b, polypeptide 1
mm9_v1_chr7_+_13466525_13466568	0.720256	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_chr1_+_55188086_55188145	0.719921	SOX2.p2	NM_025283|Mobkl3|19070|MOB1, Mps One Binder kinase activator-like 3 (yeast)	AK162327|Mobkl3|19070|MOB1, Mps One Binder kinase activator-like 3 (yeast)	AK147857|Mobkl3|19070|MOB1, Mps One Binder kinase activator-like 3 (yeast)	AK020446|Mobkl3|19070|MOB1, Mps One Binder kinase activator-like 3 (yeast)	BC028500|Mobkl3|19070|MOB1, Mps One Binder kinase activator-like 3 (yeast)	BC037499|Mobkl3|19070|MOB1, Mps One Binder kinase activator-like 3 (yeast)	BC058168|Mobkl3|19070|MOB1, Mps One Binder kinase activator-like 3 (yeast)	BC052475|Mobkl3|19070|MOB1, Mps One Binder kinase activator-like 3 (yeast)	U01138|Mobkl3|19070|MOB1, Mps One Binder kinase activator-like 3 (yeast)
mm9_v1_chr5_-_92483744_92484066	0.718291	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_chr9_-_76171352_76171416	0.712012	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_chr4_+_8462766_8462804	0.711325	SOX2.p2	AK159607|Rab2a|59021|RAB2A, member RAS oncogene family	AK079071|Rab2a|59021|RAB2A, member RAS oncogene family	AK160333|Rab2a|59021|RAB2A, member RAS oncogene family	NM_021518|Rab2a|59021|RAB2A, member RAS oncogene family	BC058382|Rab2a|59021|RAB2A, member RAS oncogene family	X95403|Rab2a|59021|RAB2A, member RAS oncogene family
mm9_v1_chr14_-_57190668_57190714	0.710516	SOX2.p2	BC092399|Cenpj|219103|centromere protein J	AK077045|Cenpj|219103|centromere protein J	NM_001014996|Cenpj|219103|centromere protein J
mm9_v1_chr1_-_136131981_136132033	0.709636	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_chr3_-_127540408_127540409	0.709296	SOX2.p2	NM_145964|Ap1ar|211556|adaptor-related protein complex 1 associated regulatory protein
mm9_v1_chr5_-_137748860_137748870	0.708305	SOX2.p2	BC066831|Srrt|83701|serrate RNA effector molecule homolog (Arabidopsis)
mm9_v1_chr17_+_53618542_53618596	0.704149	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_-_99470989_99471155	0.703426	SOX2.p2	
mm9_v1_chr15_-_88564636_88564674	0.703322	SOX2.p2	NM_001033274|Brd1|223770|bromodomain containing 1	AK149714|Brd1|223770|bromodomain containing 1
mm9_v1_chr1_-_136131963_136131973	0.703315	SOX2.p2	AK043954|Adora1|11539|adenosine A1 receptor
mm9_v1_chr18_+_37595274_37595294	0.703004	SOX2.p2	NM_053137|Pcdhb12|93883|protocadherin beta 12
mm9_v1_chr14_+_79915429_79915530	0.70223	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_chr19_+_8963366_8963411	0.701795	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_chrX_-_16488889_16488889	0.701697	SOX2.p2	BC090623|Ndp|17986|Norrie disease (pseudoglioma) (human)	NM_010883|Ndp|17986|Norrie disease (pseudoglioma) (human)
mm9_v1_chr18_+_37890662_37890807	0.700116	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_chr11_+_32646291_32646504	0.698245	SOX2.p2	AK207541|Fbxw11|103583|F-box and WD-40 domain protein 11	AK219433|Fbxw11|103583|F-box and WD-40 domain protein 11	AK216067|Fbxw11|103583|F-box and WD-40 domain protein 11	AK210303|Fbxw11|103583|F-box and WD-40 domain protein 11	AK213659|Fbxw11|103583|F-box and WD-40 domain protein 11	AK215208|Fbxw11|103583|F-box and WD-40 domain protein 11
mm9_v1_chr4_+_130219299_130219334	0.697857	SOX2.p2	BC050747|Pum1|80912|pumilio 1 (Drosophila)	AK147185|Pum1|80912|pumilio 1 (Drosophila)	AF321909|Pum1|80912|pumilio 1 (Drosophila)	BC048174|Pum1|80912|pumilio 1 (Drosophila)
mm9_v1_chr11_-_106576380_106576409	0.697355	SOX2.p2	BC085502|Pecam1|18613|platelet/endothelial cell adhesion molecule 1
mm9_v1_chr10_-_25798407_25798455	0.691641	SOX2.p2	AK032569|Tmem200a|77220|transmembrane protein 200A	AK163932|Tmem200a|77220|transmembrane protein 200A
mm9_v1_chr16_+_72663393_72663448	0.691243	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_chr15_+_30102710_30102805	0.691185	SOX2.p2	BC138260|Ctnnd2|18163|catenin (cadherin associated protein), delta 2	BC138261|Ctnnd2|18163|catenin (cadherin associated protein), delta 2	BC145217|Ctnnd2|18163|catenin (cadherin associated protein), delta 2
mm9_v1_chr6_+_37820779_37820898	0.69099	SOX2.p2	AK080890|Trim24|21848|tripartite motif-containing 24	NM_145076|Trim24|21848|tripartite motif-containing 24	S78219|Trim24|21848|tripartite motif-containing 24	S78221|Trim24|21848|tripartite motif-containing 24	AK084870|Trim24|21848|tripartite motif-containing 24	BC056959|Trim24|21848|tripartite motif-containing 24
mm9_v1_chr7_-_54175214_54175352	0.690522	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_chr14_+_55506625_55506792	0.689027	SOX2.p2	AK020321|Bcl2l2|12050|BCL2-like 2	AK020923|Bcl2l2|12050|BCL2-like 2
mm9_v1_chr19_-_4943037_4943091	0.688151	SOX2.p2	AK044418|Peli3|240518|pellino 3	BC028931|Peli3|240518|pellino 3	AK135575|Peli3|240518|pellino 3	NM_172835|Peli3|240518|pellino 3
mm9_v1_chr2_+_90780646_90780662	0.687938	SOX2.p2	AK143698|Celf1|13046|CUGBP, Elav-like family member 1
mm9_v1_chr3_-_94937886_94937954	0.687568	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_-_67738689_67738740	0.685455	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_chr7_+_82600419_82600490	0.680396	SOX2.p2	NM_029332|Akap13|75547|A kinase (PRKA) anchor protein 13	AK157986|Akap13|75547|A kinase (PRKA) anchor protein 13	AK172125|Akap13|75547|A kinase (PRKA) anchor protein 13
mm9_v1_chr17_-_28046158_28046190	0.67606	SOX2.p2	AK133851|Taf11|68776|TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor
mm9_v1_chr3_-_153388047_153388152	0.67212	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_chr3_+_51297898_51297938	0.67112	SOX2.p2	
mm9_v1_chr18_+_60963495_60963509	0.66961	SOX2.p2	AK002232|Cd74|16149|CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)	AK020607|Cd74|16149|CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)	NM_001042605|Cd74|16149|CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)	NM_010545|Cd74|16149|CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)	BC003476|Cd74|16149|CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)	BC096435|Cd74|16149|CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)	X07129|Cd74|16149|CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)
mm9_v1_chr13_-_106084378_106084564	0.667912	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_chr3_-_119486136_119486235	0.666077	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_chr10_-_116786025_116786098	0.665515	SOX2.p2	AK018657|Cpsf6|432508|cleavage and polyadenylation specific factor 6
mm9_v1_chr18_+_35278553_35278581	0.665339	SOX2.p2	NM_009818|Ctnna1|12385|catenin (cadherin associated protein), alpha 1	X59990|Ctnna1|12385|catenin (cadherin associated protein), alpha 1	AK148496|Ctnna1|12385|catenin (cadherin associated protein), alpha 1	BC060174|Ctnna1|12385|catenin (cadherin associated protein), alpha 1	BC068316|Ctnna1|12385|catenin (cadherin associated protein), alpha 1	D90362|Ctnna1|12385|catenin (cadherin associated protein), alpha 1	BC048163|Ctnna1|12385|catenin (cadherin associated protein), alpha 1
mm9_v1_chr7_-_129164546_129164728	0.66296	SOX2.p2	AK187372|Gga2|74105|golgi associated, gamma adaptin ear containing, ARF binding protein 2	AK129280|Gga2|74105|golgi associated, gamma adaptin ear containing, ARF binding protein 2	BC062933|Gga2|74105|golgi associated, gamma adaptin ear containing, ARF binding protein 2	AK004632|Gga2|74105|golgi associated, gamma adaptin ear containing, ARF binding protein 2	AK154904|Gga2|74105|golgi associated, gamma adaptin ear containing, ARF binding protein 2	AK143691|Gga2|74105|golgi associated, gamma adaptin ear containing, ARF binding protein 2	AK159953|Gga2|74105|golgi associated, gamma adaptin ear containing, ARF binding protein 2	AK149798|Gga2|74105|golgi associated, gamma adaptin ear containing, ARF binding protein 2	NM_028758|Gga2|74105|golgi associated, gamma adaptin ear containing, ARF binding protein 2
mm9_v1_chr5_+_144309573_144309659	0.661988	SOX2.p2	NM_026050|2810453I06Rik|67238|RIKEN cDNA 2810453I06 gene	NM_133703|2810453I06Rik|67238|RIKEN cDNA 2810453I06 gene	AK075875|2810453I06Rik|67238|RIKEN cDNA 2810453I06 gene	AK076127|2810453I06Rik|67238|RIKEN cDNA 2810453I06 gene	BC012231|2810453I06Rik|67238|RIKEN cDNA 2810453I06 gene	AK156614|2810453I06Rik|67238|RIKEN cDNA 2810453I06 gene	BC100440|2810453I06Rik|67238|RIKEN cDNA 2810453I06 gene	AK165304|2810453I06Rik|67238|RIKEN cDNA 2810453I06 gene	AK014805|2810453I06Rik|67238|RIKEN cDNA 2810453I06 gene	AK005298|2810453I06Rik|67238|RIKEN cDNA 2810453I06 gene
mm9_v1_chr18_+_34919205_34919226	0.661845	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_chr16_+_5086296_5086328	0.661406	SOX2.p2	
mm9_v1_chr16_-_96304116_96304132	0.660926	SOX2.p2	BC056618|Brwd1|93871|bromodomain and WD repeat domain containing 1
mm9_v1_chr8_+_74743620_74743671	0.660431	SOX2.p2	AK075976|Fam32a|67922|family with sequence similarity 32, member A	NM_026455|Fam32a|67922|family with sequence similarity 32, member A	AB041658|Fam32a|67922|family with sequence similarity 32, member A	AK007524|Fam32a|67922|family with sequence similarity 32, member A	AK011922|Fam32a|67922|family with sequence similarity 32, member A	AK008285|Fam32a|67922|family with sequence similarity 32, member A	AK008336|Fam32a|67922|family with sequence similarity 32, member A	AK082792|Fam32a|67922|family with sequence similarity 32, member A	AK150416|Fam32a|67922|family with sequence similarity 32, member A	BC085487|Fam32a|67922|family with sequence similarity 32, member A
mm9_v1_chr6_-_99470949_99470986	0.659952	SOX2.p2	AB594192|Foxp1|108655|forkhead box P1
mm9_v1_chr3_-_8964045_8964059	0.659823	SOX2.p2	AY048852|Tpd52|21985|tumor protein D52	NM_001025261|Tpd52|21985|tumor protein D52	NM_001025262|Tpd52|21985|tumor protein D52
mm9_v1_chr2_-_37558794_37558806	0.659561	SOX2.p2	BC014710|Strbp|20744|spermatid perinuclear RNA binding protein
mm9_v1_chr4_+_132194931_132195032	0.658731	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_chr4_-_70195952_70195978	0.657596	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_chr11_-_115560620_115560673	0.657052	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_chr8_-_119502780_119502858	0.655118	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_chr7_+_128061257_128061281	0.655012	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_chr8_+_3587791_3587801	0.648441	SOX2.p2	BC043081|2310057J16Rik|69697|RIKEN cDNA 2310057J16 gene	BC048787|2310057J16Rik|69697|RIKEN cDNA 2310057J16 gene
mm9_v1_chr10_+_3366075_3366075	0.647896	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_chrX_-_43809499_43809524	0.647465	SOX2.p2	NM_001085510|Gm4987|245405|predicted gene 4987
mm9_v1_chr16_+_20672854_20672888	0.646417	SOX2.p2	AK053144|Eif4g1|208643|eukaryotic translation initiation factor 4, gamma 1	AK142399|Eif4g1|208643|eukaryotic translation initiation factor 4, gamma 1	AK133903|Eif4g1|208643|eukaryotic translation initiation factor 4, gamma 1	AK139371|Eif4g1|208643|eukaryotic translation initiation factor 4, gamma 1	AK162698|Eif4g1|208643|eukaryotic translation initiation factor 4, gamma 1	BC066038|Eif4g1|208643|eukaryotic translation initiation factor 4, gamma 1
mm9_v1_chr10_+_26492282_26492396	0.644514	SOX2.p2	BC030858|Arhgap18|73910|Rho GTPase activating protein 18	NM_176837|Arhgap18|73910|Rho GTPase activating protein 18	AK087800|Arhgap18|73910|Rho GTPase activating protein 18	AK014728|Arhgap18|73910|Rho GTPase activating protein 18
mm9_v1_chr2_+_146838735_146838857	0.642213	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_-_77511607_77511666	0.641317	SOX2.p2	BC094360|Nr2f2|11819|nuclear receptor subfamily 2, group F, member 2	NM_183261|Nr2f2|11819|nuclear receptor subfamily 2, group F, member 2
mm9_v1_chr16_-_98072833_98072833	0.639315	SOX2.p2	NM_144789|Prdm15|114604|PR domain containing 15
mm9_v1_chr3_+_121160714_121160815	0.638812	SOX2.p2	AK181356|Cnn3|71994|calponin 3, acidic
mm9_v1_chr12_+_106923552_106923650	0.638071	SOX2.p2	NM_178613|4933433P14Rik|66787|RIKEN cDNA 4933433P14 gene	AK171097|4933433P14Rik|66787|RIKEN cDNA 4933433P14 gene	BC031494|4933433P14Rik|66787|RIKEN cDNA 4933433P14 gene	AK168962|4933433P14Rik|66787|RIKEN cDNA 4933433P14 gene	AK042664|4933433P14Rik|66787|RIKEN cDNA 4933433P14 gene	AK079775|4933433P14Rik|66787|RIKEN cDNA 4933433P14 gene	AK020785|4933433P14Rik|66787|RIKEN cDNA 4933433P14 gene	AK029484|4933433P14Rik|66787|RIKEN cDNA 4933433P14 gene
mm9_v1_chr2_+_31101302_31101442	0.63602	SOX2.p2	BC059825|Ncs1|14299|neuronal calcium sensor 1	NM_019681|Ncs1|14299|neuronal calcium sensor 1
mm9_v1_chr18_+_35758269_35758376	0.634615	SOX2.p2	AK146327|Paip2|67869|polyadenylate-binding protein-interacting protein 2	AK167545|Paip2|67869|polyadenylate-binding protein-interacting protein 2	AK169207|Paip2|67869|polyadenylate-binding protein-interacting protein 2	AK169411|Paip2|67869|polyadenylate-binding protein-interacting protein 2	AK154453|Paip2|67869|polyadenylate-binding protein-interacting protein 2	BC010190|Paip2|67869|polyadenylate-binding protein-interacting protein 2	AK150957|Paip2|67869|polyadenylate-binding protein-interacting protein 2	AK005462|Paip2|67869|polyadenylate-binding protein-interacting protein 2	AK009909|Paip2|67869|polyadenylate-binding protein-interacting protein 2	NM_026420|Paip2|67869|polyadenylate-binding protein-interacting protein 2
mm9_v1_chr4_-_129012489_129012496	0.6343	SOX2.p2	AK141176|Rbbp4|19646|retinoblastoma binding protein 4
mm9_v1_chrX_+_156146532_156146595	0.631555	SOX2.p2	AK030839|Sh3kbp1|58194|SH3-domain kinase binding protein 1	NM_021389|Sh3kbp1|58194|SH3-domain kinase binding protein 1	AK004636|Sh3kbp1|58194|SH3-domain kinase binding protein 1	AK020782|Sh3kbp1|58194|SH3-domain kinase binding protein 1	BC052863|Sh3kbp1|58194|SH3-domain kinase binding protein 1
mm9_v1_chr11_-_50729643_50729683	0.629965	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_chr8_-_72149070_72149075	0.628953	SOX2.p2	AK139223|Zfp868|234362|zinc finger protein 868	NM_001045553|Zfp868|234362|zinc finger protein 868
mm9_v1_chr4_-_141155782_141155838	0.626389	SOX2.p2	X66903|Fblim1|74202|filamin binding LIM protein 1	NM_001163256|Fblim1|74202|filamin binding LIM protein 1
mm9_v1_chr2_-_60801248_60801283	0.626191	SOX2.p2	BC016501|Rbms1|56878|RNA binding motif, single stranded interacting protein 1	AK147109|Rbms1|56878|RNA binding motif, single stranded interacting protein 1	NM_020296|Rbms1|56878|RNA binding motif, single stranded interacting protein 1
mm9_v1_chr14_+_66963139_66963219	0.625942	SOX2.p2	BC014707|Stmn4|56471|stathmin-like 4	BC046752|Stmn4|56471|stathmin-like 4	NM_019675|Stmn4|56471|stathmin-like 4
mm9_v1_chr9_-_44215589_44215630	0.624947	SOX2.p2	AF233340|Trappc4|60409|trafficking protein particle complex 4	BC038898|Trappc4|60409|trafficking protein particle complex 4	NM_021789|Trappc4|60409|trafficking protein particle complex 4
mm9_v1_chr15_+_30102306_30102347	0.624227	SOX2.p2	NM_008729|Ctnnd2|18163|catenin (cadherin associated protein), delta 2	U90331|Ctnnd2|18163|catenin (cadherin associated protein), delta 2
mm9_v1_chr6_-_98292747_98292747	0.622903	SOX2.p2	BC147266|Gm765|330390|predicted gene 765	BC147267|Gm765|330390|predicted gene 765	NM_001128092|Gm765|330390|predicted gene 765
mm9_v1_chr12_-_11157178_11157178	0.622299	SOX2.p2	AK046054|Kcns3|238076|potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3	NM_173417|Kcns3|238076|potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3
mm9_v1_chr4_-_40649942_40649948	0.620829	SOX2.p2	AY040780|Aptx|66408|aprataxin	AY208844|Aptx|66408|aprataxin	AK077351|Aptx|66408|aprataxin	NM_025545|Aptx|66408|aprataxin
mm9_v1_chr3_+_19857375_19857397	0.619461	SOX2.p2	AK033842|Cp|12870|ceruloplasmin
mm9_v1_chr2_+_60047917_60048030	0.619101	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_chr14_+_120830603_120830641	0.618724	SOX2.p2	AK003316|Mbnl2|105559|muscleblind-like 2
mm9_v1_chr5_-_123632567_123632737	0.618553	SOX2.p2	X59530|Hpd|15445|4-hydroxyphenylpyruvic acid dioxygenase	NM_008277|Hpd|15445|4-hydroxyphenylpyruvic acid dioxygenase	BC013343|Hpd|15445|4-hydroxyphenylpyruvic acid dioxygenase	AK149416|Hpd|15445|4-hydroxyphenylpyruvic acid dioxygenase	D29987|Hpd|15445|4-hydroxyphenylpyruvic acid dioxygenase
mm9_v1_chr6_-_55631039_55631067	0.616202	SOX2.p2	AK144303|Neurod6|11922|neurogenic differentiation 6	BC087831|Neurod6|11922|neurogenic differentiation 6	U29086|Neurod6|11922|neurogenic differentiation 6
mm9_v1_chr12_+_45412878_45412942	0.614655	SOX2.p2	AK033938|Pnpla8|67452|patatin-like phospholipase domain containing 8
mm9_v1_chr3_+_55586431_55586482	0.614279	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_chr4_+_94281210_94281261	0.613605	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_chr14_-_52935887_52935914	0.612837	SOX2.p2	AK077601|Sall2|50524|sal-like 2 (Drosophila)
mm9_v1_chr11_+_29592897_29592944	0.611151	SOX2.p2	NM_194052|Rtn4|68585|reticulon 4	NM_194053|Rtn4|68585|reticulon 4	NM_194054|Rtn4|68585|reticulon 4
mm9_v1_chr16_-_96303958_96304070	0.610116	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_chr6_+_121195885_121196041	0.609991	SOX2.p2	AK151011|Usp18|24110|ubiquitin specific peptidase 18	AK151260|Usp18|24110|ubiquitin specific peptidase 18	AK151722|Usp18|24110|ubiquitin specific peptidase 18	NM_011909|Usp18|24110|ubiquitin specific peptidase 18	AK149772|Usp18|24110|ubiquitin specific peptidase 18	AK004296|Usp18|24110|ubiquitin specific peptidase 18	AK153312|Usp18|24110|ubiquitin specific peptidase 18	AK152034|Usp18|24110|ubiquitin specific peptidase 18	AK152574|Usp18|24110|ubiquitin specific peptidase 18	AF069502|Usp18|24110|ubiquitin specific peptidase 18	BC138562|Usp18|24110|ubiquitin specific peptidase 18	BC138577|Usp18|24110|ubiquitin specific peptidase 18
mm9_v1_chr18_+_35278538_35278551	0.60941	SOX2.p2	AK168635|Ctnna1|12385|catenin (cadherin associated protein), alpha 1	AK036752|Ctnna1|12385|catenin (cadherin associated protein), alpha 1	AK149721|Ctnna1|12385|catenin (cadherin associated protein), alpha 1	AK149738|Ctnna1|12385|catenin (cadherin associated protein), alpha 1	AK159339|Ctnna1|12385|catenin (cadherin associated protein), alpha 1
mm9_v1_chr12_-_119474010_119474093	0.608723	SOX2.p2	AK017738|Sp4|20688|trans-acting transcription factor 4
mm9_v1_chr11_+_87895626_87895848	0.607936	SOX2.p2	AK079148|Vezf1|22344|vascular endothelial zinc finger 1	AK018086|Vezf1|22344|vascular endothelial zinc finger 1
mm9_v1_chr17_-_24278482_24278583	0.607006	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_chr15_+_83610434_83610456	0.606852	SOX2.p2	AK048421|Mpped1|223726|metallophosphoesterase domain containing 1	NM_172610|Mpped1|223726|metallophosphoesterase domain containing 1
mm9_v1_chrX_+_12648604_12648673	0.605945	SOX2.p2	AK049283|Usp9x|22284|ubiquitin specific peptidase 9, X chromosome	NM_009481|Usp9x|22284|ubiquitin specific peptidase 9, X chromosome	AK028443|Usp9x|22284|ubiquitin specific peptidase 9, X chromosome	DQ086491|Usp9x|22284|ubiquitin specific peptidase 9, X chromosome	U67874|Usp9x|22284|ubiquitin specific peptidase 9, X chromosome
mm9_v1_chr12_-_85559793_85559836	0.603764	SOX2.p2	AK155768|C130039O16Rik|238317|RIKEN cDNA C130039O16 gene	NM_001163501|C130039O16Rik|238317|RIKEN cDNA C130039O16 gene
mm9_v1_chr14_-_66211842_66211926	0.603739	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_chr4_-_133801438_133801522	0.603044	SOX2.p2	AK156931|Zfp593|68040|zinc finger protein 593	BC003465|Zfp593|68040|zinc finger protein 593	AK014081|Zfp593|68040|zinc finger protein 593	AK133585|Zfp593|68040|zinc finger protein 593	AK005247|Zfp593|68040|zinc finger protein 593	NM_024215|Zfp593|68040|zinc finger protein 593
mm9_v1_chr7_+_117205194_117205269	0.602801	SOX2.p2	NM_009281|Zfp143|20841|zinc finger protein 143	AK028056|Zfp143|20841|zinc finger protein 143	AK029078|Zfp143|20841|zinc finger protein 143	BC037658|Zfp143|20841|zinc finger protein 143	AF011758|Zfp143|20841|zinc finger protein 143
mm9_v1_chr5_-_52581615_52581700	0.601622	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_chr8_-_34858230_34858241	0.599885	SOX2.p2	AK012595|2700090O03Rik|72632|RIKEN cDNA 2700090O03 gene
mm9_v1_chr15_-_77801154_77801262	0.599629	SOX2.p2	BC089020|Eif3d|55944|eukaryotic translation initiation factor 3, subunit D	AB012580|Eif3d|55944|eukaryotic translation initiation factor 3, subunit D	BC018598|Eif3d|55944|eukaryotic translation initiation factor 3, subunit D	AK049767|Eif3d|55944|eukaryotic translation initiation factor 3, subunit D	AK045228|Eif3d|55944|eukaryotic translation initiation factor 3, subunit D	AK145689|Eif3d|55944|eukaryotic translation initiation factor 3, subunit D	AK158344|Eif3d|55944|eukaryotic translation initiation factor 3, subunit D	AK168256|Eif3d|55944|eukaryotic translation initiation factor 3, subunit D	NM_018749|Eif3d|55944|eukaryotic translation initiation factor 3, subunit D
mm9_v1_chr2_+_22477837_22477846	0.599332	SOX2.p2	D42051|Gad2|14417|glutamic acid decarboxylase 2	NM_008078|Gad2|14417|glutamic acid decarboxylase 2
mm9_v1_chr18_-_46887869_46888063	0.598477	SOX2.p2	BC013638|Cdo1|12583|cysteine dioxygenase 1, cytosolic	BC020375|Cdo1|12583|cysteine dioxygenase 1, cytosolic	NM_033037|Cdo1|12583|cysteine dioxygenase 1, cytosolic	AK004249|Cdo1|12583|cysteine dioxygenase 1, cytosolic	AK011032|Cdo1|12583|cysteine dioxygenase 1, cytosolic	AK149582|Cdo1|12583|cysteine dioxygenase 1, cytosolic
mm9_v1_chr6_-_47763309_47763428	0.598431	SOX2.p2	AK168447|Pdia4|12304|protein disulfide isomerase associated 4	AK161534|Pdia4|12304|protein disulfide isomerase associated 4	AK146288|Pdia4|12304|protein disulfide isomerase associated 4	AK169387|Pdia4|12304|protein disulfide isomerase associated 4	AK028292|Pdia4|12304|protein disulfide isomerase associated 4	AK150566|Pdia4|12304|protein disulfide isomerase associated 4	J05186|Pdia4|12304|protein disulfide isomerase associated 4	BC141078|Pdia4|12304|protein disulfide isomerase associated 4	AK148801|Pdia4|12304|protein disulfide isomerase associated 4
mm9_v1_chr18_-_23197156_23197163	0.598081	SOX2.p2	BC056377|Nol4|319211|nucleolar protein 4	NM_001161483|Nol4|319211|nucleolar protein 4
mm9_v1_chr7_+_31514580_31514656	0.596039	SOX2.p2	AK049951|C630016N16Rik|791088|RIKEN cDNA C630016N16 gene
mm9_v1_chr1_-_176851918_176851937	0.595949	SOX2.p2	AK161827|Grem2|23893|gremlin 2 homolog, cysteine knot superfamily (Xenopus laevis)	BC079905|Grem2|23893|gremlin 2 homolog, cysteine knot superfamily (Xenopus laevis)
mm9_v1_chr2_-_6805937_6806041	0.594567	SOX2.p2	AK042749|Celf2|14007|CUGBP, Elav-like family member 2	AK164112|Celf2|14007|CUGBP, Elav-like family member 2	AK052102|Celf2|14007|CUGBP, Elav-like family member 2	AK135166|Celf2|14007|CUGBP, Elav-like family member 2	BC026856|Celf2|14007|CUGBP, Elav-like family member 2	AF090697|Celf2|14007|CUGBP, Elav-like family member 2	NM_001110228|Celf2|14007|CUGBP, Elav-like family member 2	NM_001160293|Celf2|14007|CUGBP, Elav-like family member 2	NM_010160|Celf2|14007|CUGBP, Elav-like family member 2
mm9_v1_chr19_-_28838026_28838038	0.594496	SOX2.p2	NM_001177391|Gm6788|627788|predicted gene 6788
mm9_v1_chr2_-_155984800_155984951	0.594107	SOX2.p2	AK134091|Rbm39|170791|RNA binding motif protein 39
mm9_v1_chrX_-_110299092_110299131	0.593311	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_chr8_+_72332573_72332679	0.592708	SOX2.p2	AK043883|Gmip|78816|Gem-interacting protein	BC057037|Gmip|78816|Gem-interacting protein	NM_198101|Gmip|78816|Gem-interacting protein	AK082337|Gmip|78816|Gem-interacting protein	AK172438|Gmip|78816|Gem-interacting protein	BC060628|Gmip|78816|Gem-interacting protein	AK137177|Gmip|78816|Gem-interacting protein	AK052221|Gmip|78816|Gem-interacting protein
mm9_v1_chr1_-_182743632_182743738	0.592214	SOX2.p2	BC106177|H3f3a|15078|H3 histone, family 3A	BC088835|H3f3a|15078|H3 histone, family 3A	BC012687|H3f3a|15078|H3 histone, family 3A	BC083353|H3f3a|15078|H3 histone, family 3A	BC002268|H3f3a|15078|H3 histone, family 3A	Z85979|H3f3a|15078|H3 histone, family 3A	AK152293|H3f3a|15078|H3 histone, family 3A	AK150591|H3f3a|15078|H3 histone, family 3A	AK150928|H3f3a|15078|H3 histone, family 3A	AK160635|H3f3a|15078|H3 histone, family 3A	AK169608|H3f3a|15078|H3 histone, family 3A	AK162040|H3f3a|15078|H3 histone, family 3A	AK153034|H3f3a|15078|H3 histone, family 3A	AK160677|H3f3a|15078|H3 histone, family 3A	AK167879|H3f3a|15078|H3 histone, family 3A	AK168197|H3f3a|15078|H3 histone, family 3A	AK150467|H3f3a|15078|H3 histone, family 3A	AK150468|H3f3a|15078|H3 histone, family 3A	AK151634|H3f3a|15078|H3 histone, family 3A	AK037900|H3f3a|15078|H3 histone, family 3A	NM_008210|H3f3a|15078|H3 histone, family 3A
mm9_v1_chr5_+_33206352_33206425	0.592041	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_chr11_-_99997241_99997264	0.58936	SOX2.p2	BC057934|Krt15|16665|keratin 15	NM_008469|Krt15|16665|keratin 15
mm9_v1_chr11_-_33743416_33743626	0.585639	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_+_126800830_126800906	0.585245	SOX2.p2	BC060297|Zmym6|100177|zinc finger, MYM-type 6
mm9_v1_chr16_+_18392675_18392746	0.585	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_+_20378816_20378944	0.584928	SOX2.p2	
mm9_v1_chr4_-_142718290_142718420	0.582942	SOX2.p2	AK136099|Prdm2|110593|PR domain containing 2, with ZNF domain
mm9_v1_chr18_-_7626805_7626890	0.579828	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_chr3_+_40439675_40439741	0.579707	SOX2.p2	NM_175515|Intu|380614|inturned planar cell polarity effector homolog (Drosophila)	AK035092|Intu|380614|inturned planar cell polarity effector homolog (Drosophila)	BC125523|Intu|380614|inturned planar cell polarity effector homolog (Drosophila)	BC132387|Intu|380614|inturned planar cell polarity effector homolog (Drosophila)
mm9_v1_chrX_-_18744357_18744370	0.576902	SOX2.p2	AK170409|Gm14636|100038616|predicted gene 14636
mm9_v1_chr12_-_112951379_112951467	0.576161	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_-_121825407_121825416	0.575653	SOX2.p2	BC049969|Cyp8b1|13124|cytochrome P450, family 8, subfamily b, polypeptide 1	AF090317|Cyp8b1|13124|cytochrome P450, family 8, subfamily b, polypeptide 1	BC010973|Cyp8b1|13124|cytochrome P450, family 8, subfamily b, polypeptide 1	BC010974|Cyp8b1|13124|cytochrome P450, family 8, subfamily b, polypeptide 1
mm9_v1_chr18_+_37460452_37460636	0.575091	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_chr2_+_71050002_71050098	0.574848	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_chr3_+_90280032_90280140	0.574304	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_chr10_+_127799210_127799343	0.574071	SOX2.p2	AK004297|Cs|12974|citrate synthase
mm9_v1_chr9_-_88417710_88417730	0.570543	SOX2.p2	BC032970|Snhg5|72655|small nucleolar RNA host gene 5	AK012825|Snhg5|72655|small nucleolar RNA host gene 5
mm9_v1_chrX_+_54307050_54307082	0.57001	SOX2.p2	AK011234|Htatsf1|72459|HIV TAT specific factor 1	AK005527|Htatsf1|72459|HIV TAT specific factor 1	AK139853|Htatsf1|72459|HIV TAT specific factor 1	AK049495|Htatsf1|72459|HIV TAT specific factor 1
mm9_v1_chr11_-_106781995_106782028	0.566589	SOX2.p2	AK012060|Smurf2|66313|SMAD specific E3 ubiquitin protein ligase 2	NM_025481|Smurf2|66313|SMAD specific E3 ubiquitin protein ligase 2
mm9_v1_chr14_+_76815627_76815627	0.561765	SOX2.p2	BC058660|Tsc22d1|21807|TSC22 domain family, member 1	NM_207652|Tsc22d1|21807|TSC22 domain family, member 1
mm9_v1_chr8_+_108404773_108404850	0.560271	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_chr1_+_173259513_173259641	0.559132	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_chr10_-_75227029_75227101	0.558535	SOX2.p2	BC057551|Cabin1|104248|calcineurin binding protein 1	AK168811|Cabin1|104248|calcineurin binding protein 1	AK162479|Cabin1|104248|calcineurin binding protein 1	AK078480|Cabin1|104248|calcineurin binding protein 1	NM_172549|Cabin1|104248|calcineurin binding protein 1
mm9_v1_chr6_+_108733075_108733279	0.557734	SOX2.p2	AK152798|Arl8b|67166|ADP-ribosylation factor-like 8B	AK144177|Arl8b|67166|ADP-ribosylation factor-like 8B	AK076292|Arl8b|67166|ADP-ribosylation factor-like 8B	AK146307|Arl8b|67166|ADP-ribosylation factor-like 8B	AK159348|Arl8b|67166|ADP-ribosylation factor-like 8B	AK170645|Arl8b|67166|ADP-ribosylation factor-like 8B	AK012024|Arl8b|67166|ADP-ribosylation factor-like 8B	AK075941|Arl8b|67166|ADP-ribosylation factor-like 8B	AK151036|Arl8b|67166|ADP-ribosylation factor-like 8B	AK149822|Arl8b|67166|ADP-ribosylation factor-like 8B	BC013719|Arl8b|67166|ADP-ribosylation factor-like 8B	AK009279|Arl8b|67166|ADP-ribosylation factor-like 8B	AK169929|Arl8b|67166|ADP-ribosylation factor-like 8B	AK005999|Arl8b|67166|ADP-ribosylation factor-like 8B	AK195129|Arl8b|67166|ADP-ribosylation factor-like 8B	AB185206|Arl8b|67166|ADP-ribosylation factor-like 8B	CT010337|Arl8b|67166|ADP-ribosylation factor-like 8B	AK203754|Arl8b|67166|ADP-ribosylation factor-like 8B
mm9_v1_chr10_+_50312445_50312544	0.556997	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_chr15_-_79272424_79272474	0.556039	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_chr5_+_53174293_53174344	0.555753	SOX2.p2	AK138997|Zcchc4|78796|zinc finger, CCHC domain containing 4	AK049511|Zcchc4|78796|zinc finger, CCHC domain containing 4	NM_030185|Zcchc4|78796|zinc finger, CCHC domain containing 4	AK019621|Zcchc4|78796|zinc finger, CCHC domain containing 4	AK143805|Zcchc4|78796|zinc finger, CCHC domain containing 4
mm9_v1_chr3_+_145784635_145784876	0.555584	SOX2.p2	AK030819|Mcoln3|171166|mucolipin 3	AK035029|Mcoln3|171166|mucolipin 3	AK033008|Mcoln3|171166|mucolipin 3	AF475086|Mcoln3|171166|mucolipin 3	BC106856|Mcoln3|171166|mucolipin 3	BC106857|Mcoln3|171166|mucolipin 3	NM_134160|Mcoln3|171166|mucolipin 3	AY083531|Mcoln3|171166|mucolipin 3	AK191060|Mcoln3|171166|mucolipin 3	AK202150|Mcoln3|171166|mucolipin 3
mm9_v1_chr10_-_82996799_82996825	0.553508	SOX2.p2	AK046198|Aldh1l2|216188|aldehyde dehydrogenase 1 family, member L2	BC034531|Aldh1l2|216188|aldehyde dehydrogenase 1 family, member L2	AK086413|Aldh1l2|216188|aldehyde dehydrogenase 1 family, member L2
mm9_v1_chr10_+_21698470_21698479	0.552921	SOX2.p2	NM_001161847|Sgk1|20393|serum/glucocorticoid regulated kinase 1
mm9_v1_chr3_-_10208575_10208582	0.552587	SOX2.p2	AK003143|Fabp4|11770|fatty acid binding protein 4, adipocyte	AK088535|Fabp4|11770|fatty acid binding protein 4, adipocyte	NM_024406|Fabp4|11770|fatty acid binding protein 4, adipocyte
mm9_v1_chr12_-_81537525_81537603	0.550854	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_chr11_+_77303247_77303355	0.549253	SOX2.p2	AK008669|2210008F06Rik|70057|RIKEN cDNA 2210008F06 gene
mm9_v1_chr17_-_46169322_46169332	0.548971	SOX2.p2	NM_001025250|Vegfa|22339|vascular endothelial growth factor A	NM_001025257|Vegfa|22339|vascular endothelial growth factor A	NM_009505|Vegfa|22339|vascular endothelial growth factor A
mm9_v1_chr4_-_135429471_135429602	0.546638	SOX2.p2	AK218125|Pnrc2|52830|proline-rich nuclear receptor coactivator 2	AK077403|Pnrc2|52830|proline-rich nuclear receptor coactivator 2
mm9_v1_chr9_-_29219382_29219527	0.544623	SOX2.p2	AK158752|Ntm|235106|neurotrimin
mm9_v1_chrX_+_132779615_132779721	0.543081	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_chr18_-_58369579_58369752	0.542603	SOX2.p2	AK132163|Fbn2|14119|fibrillin 2	NM_010181|Fbn2|14119|fibrillin 2
mm9_v1_chr8_+_35217685_35217743	0.542575	SOX2.p2	AK007787|Tmem66|67887|transmembrane protein 66	AK075744|Tmem66|67887|transmembrane protein 66	AK088728|Tmem66|67887|transmembrane protein 66
mm9_v1_chr11_+_16157685_16157805	0.540685	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_chr5_-_138721164_138721212	0.540549	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_chr7_+_77509969_77510044	0.537641	SOX2.p2	BC070425|B130024G19Rik|434198|RIKEN cDNA B130024G19 gene
mm9_v1_chr7_-_118226515_118226580	0.537261	SOX2.p2	AK150745|Eif4g2|13690|eukaryotic translation initiation factor 4, gamma 2	AK151637|Eif4g2|13690|eukaryotic translation initiation factor 4, gamma 2	AK144309|Eif4g2|13690|eukaryotic translation initiation factor 4, gamma 2	U76112|Eif4g2|13690|eukaryotic translation initiation factor 4, gamma 2	BC057673|Eif4g2|13690|eukaryotic translation initiation factor 4, gamma 2	BC127064|Eif4g2|13690|eukaryotic translation initiation factor 4, gamma 2	NM_001040131|Eif4g2|13690|eukaryotic translation initiation factor 4, gamma 2	NM_013507|Eif4g2|13690|eukaryotic translation initiation factor 4, gamma 2
mm9_v1_chr9_+_86910371_86910467	0.534193	SOX2.p2	AB212223|Ripply2|382089|ripply2 homolog (zebrafish)	NM_001037907|Ripply2|382089|ripply2 homolog (zebrafish)	AK081203|Ripply2|382089|ripply2 homolog (zebrafish)
mm9_v1_chr14_+_29318658_29318741	0.529273	SOX2.p2	NM_009524|Wnt5a|22418|wingless-related MMTV integration site 5A	AK031597|Wnt5a|22418|wingless-related MMTV integration site 5A	M89798|Wnt5a|22418|wingless-related MMTV integration site 5A
mm9_v1_chr17_-_74715708_74715816	0.52731	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_chr7_-_86877026_86877059	0.525979	SOX2.p2	AY161165|Plin1|103968|perilipin 1	AK031445|Plin1|103968|perilipin 1
mm9_v1_chr11_+_57917469_57917691	0.524374	SOX2.p2	AK150757|Cnot8|69125|CCR4-NOT transcription complex, subunit 8	AK153907|Cnot8|69125|CCR4-NOT transcription complex, subunit 8	BC004040|Cnot8|69125|CCR4-NOT transcription complex, subunit 8	NM_026949|Cnot8|69125|CCR4-NOT transcription complex, subunit 8	AK075727|Cnot8|69125|CCR4-NOT transcription complex, subunit 8	AY515608|Cnot8|69125|CCR4-NOT transcription complex, subunit 8
mm9_v1_chr11_+_3190334_3190510	0.523039	SOX2.p2	AK166189|Patz1|56218|POZ (BTB) and AT hook containing zinc finger 1	BC043035|Patz1|56218|POZ (BTB) and AT hook containing zinc finger 1	AB029397|Patz1|56218|POZ (BTB) and AT hook containing zinc finger 1	NM_019574|Patz1|56218|POZ (BTB) and AT hook containing zinc finger 1
mm9_v1_chr2_-_164860303_164860336	0.522383	SOX2.p2	AK173226|Ncoa5|228869|nuclear receptor coactivator 5
mm9_v1_chr2_+_145686377_145686454	0.51978	SOX2.p2	AK014548|Rin2|74030|Ras and Rab interactor 2	AK040763|Rin2|74030|Ras and Rab interactor 2	AK152025|Rin2|74030|Ras and Rab interactor 2	BC005529|Rin2|74030|Ras and Rab interactor 2	AK154421|Rin2|74030|Ras and Rab interactor 2
mm9_v1_chr3_+_95392855_95392908	0.518522	SOX2.p2	NM_001177669|Golph3l|229593|golgi phosphoprotein 3-like	NM_001177670|Golph3l|229593|golgi phosphoprotein 3-like	NM_146133|Golph3l|229593|golgi phosphoprotein 3-like	BC047147|Golph3l|229593|golgi phosphoprotein 3-like	AK008434|Golph3l|229593|golgi phosphoprotein 3-like	AK089547|Golph3l|229593|golgi phosphoprotein 3-like	AK160454|Golph3l|229593|golgi phosphoprotein 3-like	AK169724|Golph3l|229593|golgi phosphoprotein 3-like	AK167675|Golph3l|229593|golgi phosphoprotein 3-like
mm9_v1_chr4_+_58298833_58298983	0.517817	SOX2.p2	NM_001037127|Musk|18198|muscle, skeletal, receptor tyrosine kinase	NM_001037128|Musk|18198|muscle, skeletal, receptor tyrosine kinase	NM_001037129|Musk|18198|muscle, skeletal, receptor tyrosine kinase	NM_001037130|Musk|18198|muscle, skeletal, receptor tyrosine kinase	NM_001165996|Musk|18198|muscle, skeletal, receptor tyrosine kinase	NM_010944|Musk|18198|muscle, skeletal, receptor tyrosine kinase	U37708|Musk|18198|muscle, skeletal, receptor tyrosine kinase	U37709|Musk|18198|muscle, skeletal, receptor tyrosine kinase	BC100342|Musk|18198|muscle, skeletal, receptor tyrosine kinase	AY360453|Musk|18198|muscle, skeletal, receptor tyrosine kinase	X86444|Musk|18198|muscle, skeletal, receptor tyrosine kinase	AY955296|Musk|18198|muscle, skeletal, receptor tyrosine kinase	AY955297|Musk|18198|muscle, skeletal, receptor tyrosine kinase	AY955298|Musk|18198|muscle, skeletal, receptor tyrosine kinase	AY956403|Musk|18198|muscle, skeletal, receptor tyrosine kinase	AY956404|Musk|18198|muscle, skeletal, receptor tyrosine kinase
mm9_v1_chr7_+_130337876_130337891	0.516962	SOX2.p2	AK014218|Tnrc6a|233833|trinucleotide repeat containing 6a
mm9_v1_chr12_+_109843975_109843976	0.515926	SOX2.p2	AK134563|Evl|14026|Ena-vasodilator stimulated phosphoprotein	NM_001163395|Evl|14026|Ena-vasodilator stimulated phosphoprotein
mm9_v1_chr12_+_83717883_83718024	0.514156	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_chr4_+_73659506_73659598	0.512998	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_chr12_-_88225714_88225776	0.512939	SOX2.p2	AK155373|6430527G18Rik|238330|RIKEN cDNA 6430527G18 gene	AK171043|6430527G18Rik|238330|RIKEN cDNA 6430527G18 gene	AK160059|6430527G18Rik|238330|RIKEN cDNA 6430527G18 gene	AK140441|6430527G18Rik|238330|RIKEN cDNA 6430527G18 gene	AK082791|6430527G18Rik|238330|RIKEN cDNA 6430527G18 gene	AF525300|6430527G18Rik|238330|RIKEN cDNA 6430527G18 gene	AK084782|6430527G18Rik|238330|RIKEN cDNA 6430527G18 gene	AK173282|6430527G18Rik|238330|RIKEN cDNA 6430527G18 gene	NM_145836|6430527G18Rik|238330|RIKEN cDNA 6430527G18 gene	AK032622|6430527G18Rik|238330|RIKEN cDNA 6430527G18 gene	AK032366|6430527G18Rik|238330|RIKEN cDNA 6430527G18 gene
mm9_v1_chr8_-_69010394_69010447	0.512877	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_chr8_-_55606109_55606134	0.511767	SOX2.p2	AK051731|Spcs3|76687|signal peptidase complex subunit 3 homolog (S. cerevisiae)
mm9_v1_chr3_+_41368801_41368825	0.511597	SOX2.p2	NM_001130186|Phf17|269424|PHD finger protein 17
mm9_v1_chr6_-_142271469_142271500	0.511572	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_chr11_-_74403603_74403659	0.509985	SOX2.p2	NM_001015046|Rap1gap2|380711|RAP1 GTPase activating protein 2
mm9_v1_chr4_+_155266340_155266446	0.509169	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_chrX_-_101609169_101609195	0.50832	SOX2.p2	AK151967|Abcb7|11306|ATP-binding cassette, sub-family B (MDR/TAP), member 7	AK152535|Abcb7|11306|ATP-binding cassette, sub-family B (MDR/TAP), member 7	AK152816|Abcb7|11306|ATP-binding cassette, sub-family B (MDR/TAP), member 7	AK152946|Abcb7|11306|ATP-binding cassette, sub-family B (MDR/TAP), member 7	AK084853|Abcb7|11306|ATP-binding cassette, sub-family B (MDR/TAP), member 7	AK040069|Abcb7|11306|ATP-binding cassette, sub-family B (MDR/TAP), member 7	BC151037|Abcb7|11306|ATP-binding cassette, sub-family B (MDR/TAP), member 7	NM_009592|Abcb7|11306|ATP-binding cassette, sub-family B (MDR/TAP), member 7	BC080769|Abcb7|11306|ATP-binding cassette, sub-family B (MDR/TAP), member 7
mm9_v1_chr7_-_74367343_74367421	0.507628	SOX2.p2	AK038598|1700112J16Rik|76628|RIKEN cDNA 1700112J16 gene
mm9_v1_chr9_+_51894422_51894502	0.507456	SOX2.p2	
mm9_v1_chr2_+_3035629_3035684	0.506945	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_chr4_+_104438905_104438999	0.505829	SOX2.p2	AK050313|C8b|110382|complement component 8, beta polypeptide	NM_133882|C8b|110382|complement component 8, beta polypeptide	BC096382|C8b|110382|complement component 8, beta polypeptide	AB077304|C8b|110382|complement component 8, beta polypeptide	AB077305|C8b|110382|complement component 8, beta polypeptide	AB077306|C8b|110382|complement component 8, beta polypeptide
mm9_v1_chr11_+_101594342_101594372	0.505497	SOX2.p2	AK170616|Dhx8|217207|DEAH (Asp-Glu-Ala-His) box polypeptide 8
mm9_v1_chr11_-_106992869_106992950	0.50485	SOX2.p2	BC037661|Bptf|207165|bromodomain PHD finger transcription factor	BC046973|Bptf|207165|bromodomain PHD finger transcription factor
mm9_v1_chr1_-_173218049_173218105	0.503018	SOX2.p2	BC021903|Usp21|30941|ubiquitin specific peptidase 21	AK013252|Usp21|30941|ubiquitin specific peptidase 21	AK011148|Usp21|30941|ubiquitin specific peptidase 21	NM_013919|Usp21|30941|ubiquitin specific peptidase 21
mm9_v1_chr2_+_71049762_71049900	0.502301	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_chr2_+_26865431_26865598	0.502075	SOX2.p2	AK020041|5930434B04Rik|381356|RIKEN cDNA 5930434B04 gene	AK034046|5930434B04Rik|381356|RIKEN cDNA 5930434B04 gene	AK039867|5930434B04Rik|381356|RIKEN cDNA 5930434B04 gene	AK083582|5930434B04Rik|381356|RIKEN cDNA 5930434B04 gene	AK052562|5930434B04Rik|381356|RIKEN cDNA 5930434B04 gene	NM_029862|5930434B04Rik|381356|RIKEN cDNA 5930434B04 gene	AK038728|5930434B04Rik|381356|RIKEN cDNA 5930434B04 gene	AK043562|5930434B04Rik|381356|RIKEN cDNA 5930434B04 gene	AK040379|5930434B04Rik|381356|RIKEN cDNA 5930434B04 gene	AK169470|5930434B04Rik|381356|RIKEN cDNA 5930434B04 gene
mm9_v1_chr5_+_130384409_130384452	0.501641	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_chr19_-_8963245_8963262	0.499443	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_chr11_-_96691198_96691257	0.499262	SOX2.p2	AK131183|Nfe2l1|18023|nuclear factor, erythroid derived 2,-like 1	BC099895|Nfe2l1|18023|nuclear factor, erythroid derived 2,-like 1
mm9_v1_chr12_-_47919695_47919761	0.498796	SOX2.p2	AF232828|Nova1|664883|neuro-oncological ventral antigen 1	NM_021361|Nova1|664883|neuro-oncological ventral antigen 1
mm9_v1_chr14_+_27457610_27457865	0.498726	SOX2.p2	AK013892|Arf4|11843|ADP-ribosylation factor 4	AK002302|Arf4|11843|ADP-ribosylation factor 4	AK168793|Arf4|11843|ADP-ribosylation factor 4	NM_007479|Arf4|11843|ADP-ribosylation factor 4	AK081686|Arf4|11843|ADP-ribosylation factor 4	AK153011|Arf4|11843|ADP-ribosylation factor 4	BC115650|Arf4|11843|ADP-ribosylation factor 4	BC115651|Arf4|11843|ADP-ribosylation factor 4	D87901|Arf4|11843|ADP-ribosylation factor 4
mm9_v1_chr5_-_141124884_141125029	0.497706	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_chr11_-_76577079_76577091	0.497694	SOX2.p2	AK147799|Gosr1|53334|golgi SNAP receptor complex member 1	AK154972|Gosr1|53334|golgi SNAP receptor complex member 1
mm9_v1_chr12_+_77471506_77471590	0.497366	SOX2.p2	AK029762|Zbtb1|268564|zinc finger and BTB domain containing 1	AK131985|Zbtb1|268564|zinc finger and BTB domain containing 1	BC012239|Zbtb1|268564|zinc finger and BTB domain containing 1
mm9_v1_chr1_+_39957733_39957796	0.496534	SOX2.p2	NM_008696|Map4k4|26921|mitogen-activated protein kinase kinase kinase kinase 4
mm9_v1_chr2_+_69485227_69485311	0.495479	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_chr9_+_70390659_70390695	0.493541	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_chr13_+_118009379_118009441	0.493346	SOX2.p2	NM_010330|Emb|13723|embigin	AK138271|Emb|13723|embigin	AK079570|Emb|13723|embigin
mm9_v1_chr4_+_21775172_21775224	0.492228	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_chr4_-_117852224_117852281	0.491787	SOX2.p2	AK129187|Kdm4a|230674|lysine (K)-specific demethylase 4A
mm9_v1_chr3_+_28596824_28596914	0.491132	SOX2.p2	AK005068|Slc2a2|20526|solute carrier family 2 (facilitated glucose transporter), member 2	NM_031197|Slc2a2|20526|solute carrier family 2 (facilitated glucose transporter), member 2	AK165430|Slc2a2|20526|solute carrier family 2 (facilitated glucose transporter), member 2	X15684|Slc2a2|20526|solute carrier family 2 (facilitated glucose transporter), member 2	BC034675|Slc2a2|20526|solute carrier family 2 (facilitated glucose transporter), member 2
mm9_v1_chr8_-_85966340_85966438	0.489292	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_chr8_-_112217133_112217143	0.48897	SOX2.p2	BC039052|2400003C14Rik|71955|RIKEN cDNA 2400003C14 gene
mm9_v1_chr15_-_10643273_10643318	0.488795	SOX2.p2	AF274866|Rai14|75646|retinoic acid induced 14	BC052458|Rai14|75646|retinoic acid induced 14	NM_030690|Rai14|75646|retinoic acid induced 14	AK006172|Rai14|75646|retinoic acid induced 14
mm9_v1_chrX_+_20281028_20281089	0.488096	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_chr18_+_37880036_37880207	0.48802	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_chr10_+_80643263_80643395	0.486917	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_chr5_+_135526788_135526925	0.486907	SOX2.p2	
mm9_v1_chr12_-_70458134_70458151	0.486273	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_chr16_+_23321498_23321643	0.484707	SOX2.p2	AB027197|St6gal1|20440|beta galactoside alpha 2,6 sialyltransferase 1
mm9_v1_chr17_-_15963016_15963102	0.481888	SOX2.p2	AK004310|Rgmb|68799|RGM domain family, member B
mm9_v1_chr13_+_42776161_42776182	0.481273	SOX2.p2	AK047654|Phactr1|218194|phosphatase and actin regulator 1	AY993932|Phactr1|218194|phosphatase and actin regulator 1
mm9_v1_chr15_-_95358306_95358472	0.480649	SOX2.p2	BC051968|Nell2|54003|NEL-like 2 (chicken)
mm9_v1_chr8_-_8667108_8667134	0.480588	SOX2.p2	AK034581|Arglu1|234023|arginine and glutamate rich 1
mm9_v1_chr4_+_62280692_62280740	0.480277	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_chr6_-_18464737_18464763	0.477945	SOX2.p2	BC068156|Cttnbp2|30785|cortactin binding protein 2	AK021092|Cttnbp2|30785|cortactin binding protein 2
mm9_v1_chr14_-_64162744_64162804	0.477933	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_chr18_-_34784463_34784463	0.476015	SOX2.p2	NM_030147|Brd8|78656|bromodomain containing 8
mm9_v1_chr7_+_29649474_29649487	0.475114	SOX2.p2	AF038562|Lgals7|16858|lectin, galactose binding, soluble 7
mm9_v1_chr15_-_76476688_76476767	0.473651	SOX2.p2	AK028994|Cyhr1|54151|cysteine and histidine rich 1
mm9_v1_chr11_-_121090513_121090656	0.47288	SOX2.p2	BC026616|BC017643|217370|cDNA sequence BC017643	AK158402|BC017643|217370|cDNA sequence BC017643	AK170767|BC017643|217370|cDNA sequence BC017643	BC017643|BC017643|217370|cDNA sequence BC017643	NM_144832|BC017643|217370|cDNA sequence BC017643	AK159453|BC017643|217370|cDNA sequence BC017643	AK168104|BC017643|217370|cDNA sequence BC017643	BC027406|BC017643|217370|cDNA sequence BC017643	AK145884|BC017643|217370|cDNA sequence BC017643
mm9_v1_chr2_-_94252368_94252477	0.471755	SOX2.p2	AK212083|Api5|11800|apoptosis inhibitor 5
mm9_v1_chr14_-_76186746_76186784	0.471498	SOX2.p2	BC022676|Slc25a30|67554|solute carrier family 25, member 30	AK090086|Slc25a30|67554|solute carrier family 25, member 30	AK151420|Slc25a30|67554|solute carrier family 25, member 30
mm9_v1_chr7_-_54387915_54388047	0.469981	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_chr3_+_95392919_95392945	0.469795	SOX2.p2	BC027194|Golph3l|229593|golgi phosphoprotein 3-like
mm9_v1_chr6_+_113102884_113103027	0.469692	SOX2.p2	AK088328|Setd5|72895|SET domain containing 5
mm9_v1_chr10_+_122701051_122701245	0.469633	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_chr18_-_3337505_3337586	0.467988	SOX2.p2	AK009841|Crem|12916|cAMP responsive element modulator	AK161366|Crem|12916|cAMP responsive element modulator	AK010806|Crem|12916|cAMP responsive element modulator	NM_001110850|Crem|12916|cAMP responsive element modulator	NM_001110851|Crem|12916|cAMP responsive element modulator	NM_001110852|Crem|12916|cAMP responsive element modulator	NM_001110856|Crem|12916|cAMP responsive element modulator	NM_001110857|Crem|12916|cAMP responsive element modulator	NM_001110858|Crem|12916|cAMP responsive element modulator	NM_001110859|Crem|12916|cAMP responsive element modulator	NM_013498|Crem|12916|cAMP responsive element modulator
mm9_v1_chr10_+_60938535_60938600	0.466679	SOX2.p2	AK139384|Lrrc20|216011|leucine rich repeat containing 20	AK136380|Lrrc20|216011|leucine rich repeat containing 20	AK145920|Lrrc20|216011|leucine rich repeat containing 20	AK150142|Lrrc20|216011|leucine rich repeat containing 20	BC036304|Lrrc20|216011|leucine rich repeat containing 20	NM_153542|Lrrc20|216011|leucine rich repeat containing 20	AK150246|Lrrc20|216011|leucine rich repeat containing 20
mm9_v1_chr3_+_37538808_37538883	0.466096	SOX2.p2	BC053428|Spry1|24063|sprouty homolog 1 (Drosophila)	NM_011896|Spry1|24063|sprouty homolog 1 (Drosophila)	AK014578|Spry1|24063|sprouty homolog 1 (Drosophila)	AK140405|Spry1|24063|sprouty homolog 1 (Drosophila)	BC039139|Spry1|24063|sprouty homolog 1 (Drosophila)
mm9_v1_chr9_-_29219306_29219337	0.4649	SOX2.p2	AF282980|Ntm|235106|neurotrimin	BC023307|Ntm|235106|neurotrimin
mm9_v1_chr8_-_109417431_109417531	0.464656	SOX2.p2	AK030924|Chtf8|214987|CTF8, chromosome transmission fidelity factor 8 homolog (S. cerevisiae)	AK165993|Chtf8|214987|CTF8, chromosome transmission fidelity factor 8 homolog (S. cerevisiae)	NM_145412|Chtf8|214987|CTF8, chromosome transmission fidelity factor 8 homolog (S. cerevisiae)	AK087721|Chtf8|214987|CTF8, chromosome transmission fidelity factor 8 homolog (S. cerevisiae)	AK088257|Chtf8|214987|CTF8, chromosome transmission fidelity factor 8 homolog (S. cerevisiae)
mm9_v1_chr3_+_80840609_80840648	0.463419	SOX2.p2	AK033734|Pdgfc|54635|platelet-derived growth factor, C polypeptide
mm9_v1_chr3_+_13471681_13471721	0.463217	SOX2.p2	AK079659|Ralyl|76897|RALY RNA binding protein-like	AK032086|Ralyl|76897|RALY RNA binding protein-like
mm9_v1_chr10_-_75322941_75323054	0.463133	SOX2.p2	AK010691|Mif|17319|macrophage migration inhibitory factor	BC086928|Mif|17319|macrophage migration inhibitory factor	BC100605|Mif|17319|macrophage migration inhibitory factor	L02913|Mif|17319|macrophage migration inhibitory factor	AK152211|Mif|17319|macrophage migration inhibitory factor	BC024895|Mif|17319|macrophage migration inhibitory factor	L10613|Mif|17319|macrophage migration inhibitory factor	AK008939|Mif|17319|macrophage migration inhibitory factor	AK013328|Mif|17319|macrophage migration inhibitory factor	NM_010798|Mif|17319|macrophage migration inhibitory factor
mm9_v1_chr5_-_75440586_75440675	0.462786	SOX2.p2	BC048435|Chic2|74277|cysteine-rich hydrophobic domain 2	AK172289|Chic2|74277|cysteine-rich hydrophobic domain 2	AK006962|Chic2|74277|cysteine-rich hydrophobic domain 2	NM_028850|Chic2|74277|cysteine-rich hydrophobic domain 2
mm9_v1_chr14_-_37911383_37911496	0.461506	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_chr5_-_93611701_93611836	0.461497	SOX2.p2	
mm9_v1_chr10_+_74523775_74523878	0.461162	SOX2.p2	BC131682|Bcr|110279|breakpoint cluster region
mm9_v1_chrX_-_48371127_48371236	0.460622	SOX2.p2	AK087971|Rap2c|72065|RAP2C, member of RAS oncogene family	BC050056|Rap2c|72065|RAP2C, member of RAS oncogene family	BC027363|Rap2c|72065|RAP2C, member of RAS oncogene family	AK146057|Rap2c|72065|RAP2C, member of RAS oncogene family	BC064814|Rap2c|72065|RAP2C, member of RAS oncogene family	BC094890|Rap2c|72065|RAP2C, member of RAS oncogene family	NM_172413|Rap2c|72065|RAP2C, member of RAS oncogene family	AK146956|Rap2c|72065|RAP2C, member of RAS oncogene family	AK147015|Rap2c|72065|RAP2C, member of RAS oncogene family
mm9_v1_chrX_+_9829439_9829558	0.460508	SOX2.p2	AK050930|Otc|18416|ornithine transcarbamylase	NM_008769|Otc|18416|ornithine transcarbamylase	BC024893|Otc|18416|ornithine transcarbamylase	M17030|Otc|18416|ornithine transcarbamylase
mm9_v1_chr18_-_24761954_24762029	0.4605	SOX2.p2	BC055012|Slc39a6|106957|solute carrier family 39 (metal ion transporter), member 6
mm9_v1_chr1_-_127808790_127808807	0.460242	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_chr19_+_10978153_10978193	0.459427	SOX2.p2	AK206563|Prpf19|28000|PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae)	AK214592|Prpf19|28000|PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae)
mm9_v1_chr7_-_150734970_150735032	0.458278	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_chr6_+_127837728_127837797	0.457814	SOX2.p2	AK028808|Tspan11|68498|tetraspanin 11	AK003691|Tspan11|68498|tetraspanin 11	BC057639|Tspan11|68498|tetraspanin 11
mm9_v1_chr9_-_63869857_63869865	0.456581	SOX2.p2	AK046602|Smad6|17130|MAD homolog 6 (Drosophila)	NM_008542|Smad6|17130|MAD homolog 6 (Drosophila)
mm9_v1_chr2_+_30093236_30093288	0.455626	SOX2.p2	NM_177725|Lrrc8a|241296|leucine rich repeat containing 8A
mm9_v1_chr8_-_71708077_71708126	0.45557	SOX2.p2	
mm9_v1_chr17_+_44090192_44090211	0.454901	SOX2.p2	AB061524|Rcan2|53901|regulator of calcineurin 2	AK049006|Rcan2|53901|regulator of calcineurin 2
mm9_v1_chr2_-_119613164_119613274	0.453909	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_chr2_+_155890933_155891049	0.453476	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_chr5_-_135422795_135422804	0.451676	SOX2.p2	AK162721|Cldn4|12740|claudin 4	AK145152|Cldn4|12740|claudin 4	NM_009903|Cldn4|12740|claudin 4
mm9_v1_chr4_+_144482979_144483095	0.451079	SOX2.p2	AK032958|Dhrs3|20148|dehydrogenase/reductase (SDR family) member 3	X95281|Dhrs3|20148|dehydrogenase/reductase (SDR family) member 3	AK151419|Dhrs3|20148|dehydrogenase/reductase (SDR family) member 3	NM_011303|Dhrs3|20148|dehydrogenase/reductase (SDR family) member 3	BC013540|Dhrs3|20148|dehydrogenase/reductase (SDR family) member 3
mm9_v1_chr12_-_92828018_92828088	0.44822	SOX2.p2	AF250834|Gtf2a1|83602|general transcription factor II A, 1	BC079909|Gtf2a1|83602|general transcription factor II A, 1	AK139996|Gtf2a1|83602|general transcription factor II A, 1	NM_031391|Gtf2a1|83602|general transcription factor II A, 1
mm9_v1_chrX_+_133242520_133242603	0.447385	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_+_21069727_21069776	0.446367	SOX2.p2	AK154130|Atg4d|235040|autophagy-related 4D (yeast)	AK087258|Atg4d|235040|autophagy-related 4D (yeast)	AK036282|Atg4d|235040|autophagy-related 4D (yeast)	AK036571|Atg4d|235040|autophagy-related 4D (yeast)	AK081002|Atg4d|235040|autophagy-related 4D (yeast)	NM_153583|Atg4d|235040|autophagy-related 4D (yeast)	AK080353|Atg4d|235040|autophagy-related 4D (yeast)	AK044798|Atg4d|235040|autophagy-related 4D (yeast)	AK081605|Atg4d|235040|autophagy-related 4D (yeast)	BC030861|Atg4d|235040|autophagy-related 4D (yeast)	BC069851|Atg4d|235040|autophagy-related 4D (yeast)
mm9_v1_chr5_-_115263896_115263992	0.439719	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_chr6_-_71773747_71773805	0.437402	SOX2.p2	AK039187|Mrpl35|66223|mitochondrial ribosomal protein L35	AK010369|Mrpl35|66223|mitochondrial ribosomal protein L35	AK012807|Mrpl35|66223|mitochondrial ribosomal protein L35	AK004385|Mrpl35|66223|mitochondrial ribosomal protein L35	AK010223|Mrpl35|66223|mitochondrial ribosomal protein L35	BC028750|Mrpl35|66223|mitochondrial ribosomal protein L35	NM_025430|Mrpl35|66223|mitochondrial ribosomal protein L35
mm9_v1_chr2_+_157386313_157386316	0.437315	SOX2.p2	AK046462|Nnat|18111|neuronatin
mm9_v1_chr14_+_17197678_17197719	0.437202	SOX2.p2	AK087535|Top2b|21974|topoisomerase (DNA) II beta	AK163043|Top2b|21974|topoisomerase (DNA) II beta	AK041054|Top2b|21974|topoisomerase (DNA) II beta	BC041106|Top2b|21974|topoisomerase (DNA) II beta	BC054541|Top2b|21974|topoisomerase (DNA) II beta	NM_009409|Top2b|21974|topoisomerase (DNA) II beta
mm9_v1_chr11_-_6171302_6171325	0.436738	SOX2.p2	AK184055|Tmed4|103694|transmembrane emp24 protein transport domain containing 4
mm9_v1_chr9_+_72961223_72961298	0.436145	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_chr5_+_138613248_138613363	0.434096	SOX2.p2	AK031638|Ap4m1|11781|adaptor-related protein complex AP-4, mu 1	NM_021392|Ap4m1|11781|adaptor-related protein complex AP-4, mu 1	AK165187|Ap4m1|11781|adaptor-related protein complex AP-4, mu 1	BC011174|Ap4m1|11781|adaptor-related protein complex AP-4, mu 1
mm9_v1_chr19_-_7280741_7280794	0.432977	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_chr4_-_148500769_148500849	0.432141	SOX2.p2	AF013253|Cort|12854|cortistatin	AK013496|Cort|12854|cortistatin	NM_007745|Cort|12854|cortistatin
mm9_v1_chr19_-_41289045_41289143	0.431596	SOX2.p2	AK004050|Tm9sf3|107358|transmembrane 9 superfamily member 3
mm9_v1_chr19_+_45122281_45122364	0.431073	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_chr16_-_11137100_11137212	0.430605	SOX2.p2	AK218593|Zc3h7a|106205|zinc finger CCCH type containing 7 A
mm9_v1_chrX_+_74756332_74756489	0.429605	SOX2.p2	AK030547|Tbl1x|21372|transducin (beta)-like 1 X-linked	BC043105|Tbl1x|21372|transducin (beta)-like 1 X-linked
mm9_v1_chr9_+_58671214_58671318	0.428921	SOX2.p2	BC158106|Hcn4|330953|hyperpolarization-activated, cyclic nucleotide-gated K+ 4	BC158108|Hcn4|330953|hyperpolarization-activated, cyclic nucleotide-gated K+ 4	NM_001081192|Hcn4|330953|hyperpolarization-activated, cyclic nucleotide-gated K+ 4
mm9_v1_chr12_-_4344470_4344503	0.427525	SOX2.p2	U64606|Ncoa1|17977|nuclear receptor coactivator 1	BC068177|Ncoa1|17977|nuclear receptor coactivator 1
mm9_v1_chr18_+_35278585_35278617	0.427195	SOX2.p2	BC105576|Ctnna1|12385|catenin (cadherin associated protein), alpha 1	AK004623|Ctnna1|12385|catenin (cadherin associated protein), alpha 1
mm9_v1_chr8_+_88224886_88224972	0.427038	SOX2.p2	AK005119|1500002J14Rik|68945|RIKEN cDNA 1500002J14 gene
mm9_v1_chr5_-_23122181_23122418	0.426855	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_chr11_+_98629709_98629729	0.426713	SOX2.p2	
mm9_v1_chr10_-_114799212_114799324	0.425673	SOX2.p2	AK136778|Tmem19|67226|transmembrane protein 19	AK170143|Tmem19|67226|transmembrane protein 19	AK171087|Tmem19|67226|transmembrane protein 19	AK018383|Tmem19|67226|transmembrane protein 19	AK155275|Tmem19|67226|transmembrane protein 19	AK042426|Tmem19|67226|transmembrane protein 19	AK079735|Tmem19|67226|transmembrane protein 19	BC016895|Tmem19|67226|transmembrane protein 19	AK036228|Tmem19|67226|transmembrane protein 19	AK138931|Tmem19|67226|transmembrane protein 19	NM_133683|Tmem19|67226|transmembrane protein 19	AK034298|Tmem19|67226|transmembrane protein 19
mm9_v1_chr2_-_25127860_25127956	0.423728	SOX2.p2	AK088418|Ssna1|68475|Sjogren's syndrome nuclear autoantigen 1	AK158412|Ssna1|68475|Sjogren's syndrome nuclear autoantigen 1	BC037081|Ssna1|68475|Sjogren's syndrome nuclear autoantigen 1	BC023033|Ssna1|68475|Sjogren's syndrome nuclear autoantigen 1	BC048360|Ssna1|68475|Sjogren's syndrome nuclear autoantigen 1	AB041656|Ssna1|68475|Sjogren's syndrome nuclear autoantigen 1	AK003356|Ssna1|68475|Sjogren's syndrome nuclear autoantigen 1	NM_023464|Ssna1|68475|Sjogren's syndrome nuclear autoantigen 1
mm9_v1_chr7_+_87331726_87331785	0.423251	SOX2.p2	AK145570|Sema4b|20352|sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	NM_013659|Sema4b|20352|sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	AK028896|Sema4b|20352|sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	AK173249|Sema4b|20352|sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B
mm9_v1_chr11_-_118216591_118216621	0.422541	SOX2.p2	M82858|Timp2|21858|tissue inhibitor of metalloproteinase 2	X62622|Timp2|21858|tissue inhibitor of metalloproteinase 2	BC049126|Timp2|21858|tissue inhibitor of metalloproteinase 2
mm9_v1_chr1_-_44175585_44175667	0.422192	SOX2.p2	BC023141|Kdelc1|72050|KDEL (Lys-Asp-Glu-Leu) containing 1	AK079701|Kdelc1|72050|KDEL (Lys-Asp-Glu-Leu) containing 1	AK007835|Kdelc1|72050|KDEL (Lys-Asp-Glu-Leu) containing 1	AK035391|Kdelc1|72050|KDEL (Lys-Asp-Glu-Leu) containing 1	AK053315|Kdelc1|72050|KDEL (Lys-Asp-Glu-Leu) containing 1	AK035899|Kdelc1|72050|KDEL (Lys-Asp-Glu-Leu) containing 1	NM_023645|Kdelc1|72050|KDEL (Lys-Asp-Glu-Leu) containing 1	AK077468|Kdelc1|72050|KDEL (Lys-Asp-Glu-Leu) containing 1	AK170300|Kdelc1|72050|KDEL (Lys-Asp-Glu-Leu) containing 1
mm9_v1_chr15_+_95621222_95621461	0.421799	SOX2.p2	BC060732|Ano6|105722|anoctamin 6	NM_175344|Ano6|105722|anoctamin 6	AK159411|Ano6|105722|anoctamin 6	AK089300|Ano6|105722|anoctamin 6
mm9_v1_chr7_-_31319977_31320096	0.421717	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_chr17_-_24747469_24747516	0.421625	SOX2.p2	AK191520|Tsc2|22084|tuberous sclerosis 2	AK202101|Tsc2|22084|tuberous sclerosis 2	AK204110|Tsc2|22084|tuberous sclerosis 2
mm9_v1_chr7_+_98239230_98239295	0.421035	SOX2.p2	NM_011807|Dlg2|23859|discs, large homolog 2 (Drosophila)
mm9_v1_chr11_-_89280247_89280261	0.420592	SOX2.p2	BC140961|4932411E22Rik|214604|RIKEN cDNA 4932411E22 gene	AK029964|4932411E22Rik|214604|RIKEN cDNA 4932411E22 gene	NM_172534|4932411E22Rik|214604|RIKEN cDNA 4932411E22 gene
mm9_v1_chr2_+_74663857_74664073	0.420556	SOX2.p2	NM_016804|Mtx2|53375|metaxin 2	AK169048|Mtx2|53375|metaxin 2	AB041562|Mtx2|53375|metaxin 2	AK168000|Mtx2|53375|metaxin 2	AK168045|Mtx2|53375|metaxin 2	AK087933|Mtx2|53375|metaxin 2	AF053550|Mtx2|53375|metaxin 2	AK168021|Mtx2|53375|metaxin 2	AK083055|Mtx2|53375|metaxin 2	BC006641|Mtx2|53375|metaxin 2	AK005233|Mtx2|53375|metaxin 2	AK179720|Mtx2|53375|metaxin 2	AK179764|Mtx2|53375|metaxin 2	AK219408|Mtx2|53375|metaxin 2
mm9_v1_chr4_+_8533630_8533662	0.419995	SOX2.p2	AK213817|Rab2a|59021|RAB2A, member RAS oncogene family	AK218701|Rab2a|59021|RAB2A, member RAS oncogene family
mm9_v1_chr16_-_16829386_16829548	0.41974	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_chr16_+_34995000_34995001	0.418861	SOX2.p2	BC038902|Mylk|107589|myosin, light polypeptide kinase
mm9_v1_chr11_+_44431601_44431727	0.417906	SOX2.p2	AK141175|Ebf1|13591|early B-cell factor 1	AK051438|Ebf1|13591|early B-cell factor 1	AK139021|Ebf1|13591|early B-cell factor 1	AK031239|Ebf1|13591|early B-cell factor 1	L12147|Ebf1|13591|early B-cell factor 1	NM_007897|Ebf1|13591|early B-cell factor 1	BC139362|Ebf1|13591|early B-cell factor 1	BC139364|Ebf1|13591|early B-cell factor 1	AK137389|Ebf1|13591|early B-cell factor 1	AK035781|Ebf1|13591|early B-cell factor 1
mm9_v1_chr6_-_94233855_94233910	0.417451	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_chr11_-_113613040_113613139	0.415745	SOX2.p2	AF165114|Cdc42ep4|56699|CDC42 effector protein (Rho GTPase binding) 4	BC003857|Cdc42ep4|56699|CDC42 effector protein (Rho GTPase binding) 4	AK075739|Cdc42ep4|56699|CDC42 effector protein (Rho GTPase binding) 4	AK165318|Cdc42ep4|56699|CDC42 effector protein (Rho GTPase binding) 4	NM_001163346|Cdc42ep4|56699|CDC42 effector protein (Rho GTPase binding) 4
mm9_v1_chr12_+_85029101_85029215	0.415569	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_chr9_+_51894884_51895031	0.414388	SOX2.p2	AK216134|Rdx|19684|radixin
mm9_v1_chr12_+_82049290_82049329	0.413702	SOX2.p2	AK135336|Srsf5|20384|serine/arginine-rich splicing factor 5
mm9_v1_chr10_+_89280918_89280988	0.413089	SOX2.p2	AK079985|Uhrf1bp1l|75089|UHRF1 (ICBP90) binding protein 1-like	AK046432|Uhrf1bp1l|75089|UHRF1 (ICBP90) binding protein 1-like	AK008586|Uhrf1bp1l|75089|UHRF1 (ICBP90) binding protein 1-like
mm9_v1_chr13_+_24895094_24895151	0.412905	SOX2.p2	BC002217|BC005537|79555|cDNA sequence BC005537
mm9_v1_chr3_+_102877936_102877949	0.412275	SOX2.p2	NM_001033303|Ampd1|229665|adenosine monophosphate deaminase 1	AK137549|Ampd1|229665|adenosine monophosphate deaminase 1	AK132524|Ampd1|229665|adenosine monophosphate deaminase 1
mm9_v1_chr1_+_182571464_182571502	0.410869	SOX2.p2	AF190325|Lin9|72568|lin-9 homolog (C. elegans)	NM_001103182|Lin9|72568|lin-9 homolog (C. elegans)	NM_175186|Lin9|72568|lin-9 homolog (C. elegans)	AK052618|Lin9|72568|lin-9 homolog (C. elegans)	BC088992|Lin9|72568|lin-9 homolog (C. elegans)	BC099695|Lin9|72568|lin-9 homolog (C. elegans)	AK042357|Lin9|72568|lin-9 homolog (C. elegans)
mm9_v1_chr16_-_78576898_78576912	0.409947	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_chr4_-_40650194_40650231	0.407029	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_chr17_+_5343877_5344040	0.406822	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_chr13_+_9276178_9276284	0.405765	SOX2.p2	BC137787|Dip2c|208440|DIP2 disco-interacting protein 2 homolog C (Drosophila)	BC144909|Dip2c|208440|DIP2 disco-interacting protein 2 homolog C (Drosophila)	BC144910|Dip2c|208440|DIP2 disco-interacting protein 2 homolog C (Drosophila)
mm9_v1_chr9_+_100544186_100544228	0.404863	SOX2.p2	BC069841|Stag1|20842|stromal antigen 1
mm9_v1_chr2_+_29202327_29202356	0.404779	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_chr10_-_17742931_17743059	0.402584	SOX2.p2	BC039801|3110003A17Rik|73112|RIKEN cDNA 3110003A17 gene	AK171138|3110003A17Rik|73112|RIKEN cDNA 3110003A17 gene	BC098509|3110003A17Rik|73112|RIKEN cDNA 3110003A17 gene	AK013984|3110003A17Rik|73112|RIKEN cDNA 3110003A17 gene	NM_028440|3110003A17Rik|73112|RIKEN cDNA 3110003A17 gene
mm9_v1_chrX_-_148450731_148450837	0.401838	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_chr9_+_20447321_20447371	0.40173	SOX2.p2	AK154036|Ubl5|66177|ubiquitin-like 5
mm9_v1_chr6_-_122287014_122287032	0.400576	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_chr1_-_153317422_153317565	0.399455	SOX2.p2	AK211660|Rnf2|19821|ring finger protein 2
mm9_v1_chr4_-_115742546_115742551	0.396338	SOX2.p2	AK028137|Uqcrh|66576|ubiquinol-cytochrome c reductase hinge protein
mm9_v1_chr11_-_100355280_100355392	0.396233	SOX2.p2	AK136812|Acly|104112|ATP citrate lyase	AK043434|Acly|104112|ATP citrate lyase
mm9_v1_chr5_+_89194037_89194113	0.395957	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_chr9_+_107483009_107483202	0.395955	SOX2.p2	AK137391|Nat6|56441|N-acetyltransferase 6	AF172275|Nat6|56441|N-acetyltransferase 6
mm9_v1_chr16_-_20426357_20426468	0.395874	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_chr11_-_50700944_50701002	0.395869	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_chr2_-_104334276_104334479	0.395833	SOX2.p2	BC131663|Hipk3|15259|homeodomain interacting protein kinase 3	BC131664|Hipk3|15259|homeodomain interacting protein kinase 3	AF077660|Hipk3|15259|homeodomain interacting protein kinase 3
mm9_v1_chr17_+_35258394_35258523	0.395571	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_chr5_-_72978788_72978788	0.394793	SOX2.p2	AK084047|Gm5868|545758|predicted gene 5868	NM_001024147|Gm5868|545758|predicted gene 5868
mm9_v1_chr8_-_72149357_72149431	0.394185	SOX2.p2	AK083009|Zfp868|234362|zinc finger protein 868
mm9_v1_chr13_+_16106279_16106315	0.393285	SOX2.p2	NM_008380|Inhba|16323|inhibin beta-A	X69619|Inhba|16323|inhibin beta-A	BC053527|Inhba|16323|inhibin beta-A
mm9_v1_chr1_-_51972771_51972812	0.392725	SOX2.p2	BC054786|Myo1b|17912|myosin IB	AK161062|Myo1b|17912|myosin IB	AK141207|Myo1b|17912|myosin IB
mm9_v1_chr10_+_18127443_18127504	0.391754	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_chr5_+_110425526_110425559	0.39127	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_chrX_-_57657081_57657155	0.390641	SOX2.p2	AK143860|Atp11c|320940|ATPase, class VI, type 11C	BC106087|Atp11c|320940|ATPase, class VI, type 11C	AK079479|Atp11c|320940|ATPase, class VI, type 11C	AK043065|Atp11c|320940|ATPase, class VI, type 11C	AK039243|Atp11c|320940|ATPase, class VI, type 11C	NM_001001798|Atp11c|320940|ATPase, class VI, type 11C	NM_001037863|Atp11c|320940|ATPase, class VI, type 11C
mm9_v1_chr8_-_90483124_90483239	0.389835	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_chr10_-_88996314_88996370	0.388882	SOX2.p2	U09417|Nr1h4|20186|nuclear receptor subfamily 1, group H, member 4	NM_001163504|Nr1h4|20186|nuclear receptor subfamily 1, group H, member 4
mm9_v1_chr4_+_135728188_135728308	0.388736	SOX2.p2	AK087452|E2f2|242705|E2F transcription factor 2	NM_177733|E2f2|242705|E2F transcription factor 2
mm9_v1_chr18_+_35966147_35966251	0.388707	SOX2.p2	AK075844|Ube2d2|56550|ubiquitin-conjugating enzyme E2D 2
mm9_v1_chr4_+_126469146_126469183	0.387275	SOX2.p2	AK177499|AU040320|100317|expressed sequence AU040320
mm9_v1_chr7_-_80686630_80686631	0.387012	SOX2.p2	AK133596|Chd2|244059|chromodomain helicase DNA binding protein 2	AK040559|Chd2|244059|chromodomain helicase DNA binding protein 2	AK132638|Chd2|244059|chromodomain helicase DNA binding protein 2	AK136686|Chd2|244059|chromodomain helicase DNA binding protein 2	NM_001081345|Chd2|244059|chromodomain helicase DNA binding protein 2
mm9_v1_chr5_-_137043082_137043316	0.386901	SOX2.p2	BC054370|Cux1|13047|cut-like homeobox 1	AK220173|Cux1|13047|cut-like homeobox 1	BC014289|Cux1|13047|cut-like homeobox 1	AK133543|Cux1|13047|cut-like homeobox 1	AK098096|Cux1|13047|cut-like homeobox 1	BC090847|Cux1|13047|cut-like homeobox 1	U68542|Cux1|13047|cut-like homeobox 1	NM_198602|Cux1|13047|cut-like homeobox 1	NM_009986|Cux1|13047|cut-like homeobox 1
mm9_v1_chr3_-_94846454_94846515	0.386081	SOX2.p2	AB029146|Psmd4|19185|proteasome (prosome, macropain) 26S subunit, non-ATPase, 4	BC009005|Psmd4|19185|proteasome (prosome, macropain) 26S subunit, non-ATPase, 4	AB029144|Psmd4|19185|proteasome (prosome, macropain) 26S subunit, non-ATPase, 4	AK010969|Psmd4|19185|proteasome (prosome, macropain) 26S subunit, non-ATPase, 4	AB029142|Psmd4|19185|proteasome (prosome, macropain) 26S subunit, non-ATPase, 4	AB029143|Psmd4|19185|proteasome (prosome, macropain) 26S subunit, non-ATPase, 4	AB029145|Psmd4|19185|proteasome (prosome, macropain) 26S subunit, non-ATPase, 4	AF013099|Psmd4|19185|proteasome (prosome, macropain) 26S subunit, non-ATPase, 4	AF175574|Psmd4|19185|proteasome (prosome, macropain) 26S subunit, non-ATPase, 4	NM_008951|Psmd4|19185|proteasome (prosome, macropain) 26S subunit, non-ATPase, 4	BC016433|Psmd4|19185|proteasome (prosome, macropain) 26S subunit, non-ATPase, 4	AK145524|Psmd4|19185|proteasome (prosome, macropain) 26S subunit, non-ATPase, 4
mm9_v1_chr6_-_56312803_56312803	0.385896	SOX2.p2	AK050499|Pde1c|18575|phosphodiesterase 1C	NM_001159960|Pde1c|18575|phosphodiesterase 1C
mm9_v1_chr6_+_88051917_88051985	0.384809	SOX2.p2	AK216914|Rpn1|103963|ribophorin I
mm9_v1_chr9_-_65972570_65972698	0.383901	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_chr7_+_104100014_104100062	0.383791	SOX2.p2	AK046799|Nars2|244141|asparaginyl-tRNA synthetase 2 (mitochondrial)(putative)	AK046801|Nars2|244141|asparaginyl-tRNA synthetase 2 (mitochondrial)(putative)	NM_153591|Nars2|244141|asparaginyl-tRNA synthetase 2 (mitochondrial)(putative)	AK138260|Nars2|244141|asparaginyl-tRNA synthetase 2 (mitochondrial)(putative)
mm9_v1_chr4_+_33397279_33397404	0.383195	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_chr14_+_76245144_76245241	0.383145	SOX2.p2	BC092381|Tpt1|22070|tumor protein, translationally-controlled 1
mm9_v1_chr4_-_136158570_136158663	0.383066	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_chr4_-_147533696_147533703	0.382483	SOX2.p2	NM_001161851|Fbxo44|230903|F-box protein 44
mm9_v1_chr13_+_43880475_43880582	0.382373	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_chr2_-_152656236_152656402	0.381017	SOX2.p2	L35049|Bcl2l1|12048|BCL2-like 1	U51279|Bcl2l1|12048|BCL2-like 1	AK172250|Bcl2l1|12048|BCL2-like 1	U51277|Bcl2l1|12048|BCL2-like 1	AK146461|Bcl2l1|12048|BCL2-like 1
mm9_v1_chr18_+_37854011_37854154	0.38017	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_chr10_+_41249215_41249327	0.37989	SOX2.p2	
mm9_v1_chr3_-_104855832_104856063	0.378217	SOX2.p2	BC003236|Cttnbp2nl|80281|CTTNBP2 N-terminal like	AK145085|Cttnbp2nl|80281|CTTNBP2 N-terminal like	AK051259|Cttnbp2nl|80281|CTTNBP2 N-terminal like	AK030438|Cttnbp2nl|80281|CTTNBP2 N-terminal like	AK129359|Cttnbp2nl|80281|CTTNBP2 N-terminal like	NM_001163332|Cttnbp2nl|80281|CTTNBP2 N-terminal like	NM_001163333|Cttnbp2nl|80281|CTTNBP2 N-terminal like	AK029901|Cttnbp2nl|80281|CTTNBP2 N-terminal like	NM_030249|Cttnbp2nl|80281|CTTNBP2 N-terminal like
mm9_v1_chr11_-_115884885_115885030	0.377874	SOX2.p2	
mm9_v1_chr17_-_85463965_85464074	0.377624	SOX2.p2	
mm9_v1_chr14_+_76245115_76245135	0.376595	SOX2.p2	AK166584|Tpt1|22070|tumor protein, translationally-controlled 1	AK169730|Tpt1|22070|tumor protein, translationally-controlled 1
mm9_v1_chr6_+_104443037_104443047	0.375534	SOX2.p2	BC076594|Cntn6|53870|contactin 6	NM_017383|Cntn6|53870|contactin 6
mm9_v1_chr11_+_59953583_59953674	0.374243	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_chr11_-_102152310_102152512	0.372943	SOX2.p2	AK218190|Atxn7l3|217218|ataxin 7-like 3	AK053165|Atxn7l3|217218|ataxin 7-like 3
mm9_v1_chr5_-_110225299_110225316	0.372604	SOX2.p2	AK138792|A430073D23Rik|100310753|RIKEN cDNA A430073D23 gene
mm9_v1_chr6_+_105627738_105627848	0.372032	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_chr11_-_59850365_59850382	0.371372	SOX2.p2	AY334571|Pemt|18618|phosphatidylethanolamine N-methyltransferase
mm9_v1_chr1_+_137043277_137043554	0.370715	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_chr3_-_132754703_132754778	0.369169	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_chr8_-_112217144_112217225	0.368992	SOX2.p2	AK161899|2400003C14Rik|71955|RIKEN cDNA 2400003C14 gene	AK088192|2400003C14Rik|71955|RIKEN cDNA 2400003C14 gene	AK050468|2400003C14Rik|71955|RIKEN cDNA 2400003C14 gene	AK152830|2400003C14Rik|71955|RIKEN cDNA 2400003C14 gene	BC017605|2400003C14Rik|71955|RIKEN cDNA 2400003C14 gene	AK010262|2400003C14Rik|71955|RIKEN cDNA 2400003C14 gene	NM_028018|2400003C14Rik|71955|RIKEN cDNA 2400003C14 gene
mm9_v1_chr8_+_74432504_74432561	0.367995	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_chr14_-_50940507_50940542	0.367578	SOX2.p2	NM_146664|Olfr734|258658|olfactory receptor 734	BC141029|Olfr734|258658|olfactory receptor 734
mm9_v1_chr7_-_137663020_137663074	0.366651	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_chr3_+_89883564_89883639	0.366192	SOX2.p2	AK169821|Tpm3|59069|tropomyosin 3, gamma	AK167534|Tpm3|59069|tropomyosin 3, gamma	AK145238|Tpm3|59069|tropomyosin 3, gamma	AK145243|Tpm3|59069|tropomyosin 3, gamma	AK145804|Tpm3|59069|tropomyosin 3, gamma	AK151500|Tpm3|59069|tropomyosin 3, gamma	AK151571|Tpm3|59069|tropomyosin 3, gamma	AK151602|Tpm3|59069|tropomyosin 3, gamma	AK164086|Tpm3|59069|tropomyosin 3, gamma	AK165428|Tpm3|59069|tropomyosin 3, gamma	AK167581|Tpm3|59069|tropomyosin 3, gamma	X53753|Tpm3|59069|tropomyosin 3, gamma	AK088111|Tpm3|59069|tropomyosin 3, gamma	AK088902|Tpm3|59069|tropomyosin 3, gamma	AK151578|Tpm3|59069|tropomyosin 3, gamma	AK151991|Tpm3|59069|tropomyosin 3, gamma	AK152260|Tpm3|59069|tropomyosin 3, gamma	AK050665|Tpm3|59069|tropomyosin 3, gamma	AK166836|Tpm3|59069|tropomyosin 3, gamma	AK167268|Tpm3|59069|tropomyosin 3, gamma	AK169245|Tpm3|59069|tropomyosin 3, gamma	BC092045|Tpm3|59069|tropomyosin 3, gamma	AK146349|Tpm3|59069|tropomyosin 3, gamma	AK153031|Tpm3|59069|tropomyosin 3, gamma	AK169102|Tpm3|59069|tropomyosin 3, gamma	AK151595|Tpm3|59069|tropomyosin 3, gamma	AK152659|Tpm3|59069|tropomyosin 3, gamma	AK168843|Tpm3|59069|tropomyosin 3, gamma
mm9_v1_chr9_-_122220036_122220045	0.366025	SOX2.p2	
mm9_v1_chr1_-_69154627_69154642	0.365237	SOX2.p2	AK144050|Erbb4|13869|v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)	NM_010154|Erbb4|13869|v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)
mm9_v1_chr4_-_134470813_134470953	0.364026	SOX2.p2	BC094256|Tmem50a|71817|transmembrane protein 50A	NM_027935|Tmem50a|71817|transmembrane protein 50A	AK147069|Tmem50a|71817|transmembrane protein 50A	AK165636|Tmem50a|71817|transmembrane protein 50A	AK152654|Tmem50a|71817|transmembrane protein 50A	AK164989|Tmem50a|71817|transmembrane protein 50A	AK014282|Tmem50a|71817|transmembrane protein 50A	AK157214|Tmem50a|71817|transmembrane protein 50A	AK152630|Tmem50a|71817|transmembrane protein 50A
mm9_v1_chr8_-_106772390_106772476	0.363942	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_chr18_+_37089837_37089938	0.362983	SOX2.p2	BC082326|Pcdha1|116731|protocadherin alpha 1	AY013756|Pcdha1|116731|protocadherin alpha 1	NM_054072|Pcdha1|116731|protocadherin alpha 1
mm9_v1_chr1_-_141755209_141755302	0.362448	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_chr18_+_25224729_25224737	0.361564	SOX2.p2	BC060607|Fhod3|225288|formin homology 2 domain containing 3
mm9_v1_chr11_-_88579392_88579430	0.361447	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_chr11_-_97883924_97884006	0.361323	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_chr7_-_50745358_50745392	0.361125	SOX2.p2	AK039193|Iglon5|210094|IgLON family member 5	NM_001164518|Iglon5|210094|IgLON family member 5
mm9_v1_chr10_+_101621712_101621712	0.361102	SOX2.p2	AK032009|Mgat4c|67569|mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)	NM_001162369|Mgat4c|67569|mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)
mm9_v1_chr10_-_127444563_127444662	0.360702	SOX2.p2	BC021836|Hsd17b6|27400|hydroxysteroid (17-beta) dehydrogenase 6	NM_013786|Hsd17b6|27400|hydroxysteroid (17-beta) dehydrogenase 6	AK008212|Hsd17b6|27400|hydroxysteroid (17-beta) dehydrogenase 6
mm9_v1_chr5_+_35292092_35292155	0.360392	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_chr7_+_128061297_128061331	0.360267	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_chr2_-_26332482_26332729	0.359846	SOX2.p2	L02613|Notch1|18128|Notch gene homolog 1 (Drosophila)	AB101624|Notch1|18128|Notch gene homolog 1 (Drosophila)
mm9_v1_chr6_-_87716204_87716225	0.359369	SOX2.p2	
mm9_v1_chr10_-_52058305_52058381	0.358553	SOX2.p2	AK008806|Gopc|94221|golgi associated PDZ and coiled-coil motif containing
mm9_v1_chr12_-_30212990_30213055	0.358008	SOX2.p2	
mm9_v1_chr6_-_92656148_92656177	0.357274	SOX2.p2	BC099897|Prickle2|243548|prickle homolog 2 (Drosophila)	NM_001081146|Prickle2|243548|prickle homolog 2 (Drosophila)
mm9_v1_chr7_+_107641853_107641862	0.354424	SOX2.p2	NM_011671|Ucp2|22228|uncoupling protein 2 (mitochondrial, proton carrier)
mm9_v1_chr9_+_109834266_109834307	0.354273	SOX2.p2	NM_008633|Mtap4|17758|microtubule-associated protein 4	AK046825|Mtap4|17758|microtubule-associated protein 4
mm9_v1_chr1_+_162836541_162836569	0.354249	SOX2.p2	NM_001024952|Rc3h1|381305|RING CCCH (C3H) domains 1	AK139648|Rc3h1|381305|RING CCCH (C3H) domains 1
mm9_v1_chr11_+_43534658_43534687	0.353775	SOX2.p2	AK086604|Pwwp2a|70802|PWWP domain containing 2A	AK039984|Pwwp2a|70802|PWWP domain containing 2A
mm9_v1_chrX_-_45525047_45525061	0.353041	SOX2.p2	
mm9_v1_chr11_-_120489993_120490076	0.352599	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_chr8_+_35217677_35217684	0.352008	SOX2.p2	BC024888|Tmem66|67887|transmembrane protein 66	AK163218|Tmem66|67887|transmembrane protein 66
mm9_v1_chr2_+_4480799_4480871	0.351131	SOX2.p2	AK077327|Frmd4a|209630|FERM domain containing 4A	NM_001177844|Frmd4a|209630|FERM domain containing 4A	AK148414|Frmd4a|209630|FERM domain containing 4A	AK029073|Frmd4a|209630|FERM domain containing 4A	AK171532|Frmd4a|209630|FERM domain containing 4A
mm9_v1_chr13_-_104623606_104623708	0.350606	SOX2.p2	BC005691|Erbb2ip|59079|Erbb2 interacting protein
mm9_v1_chr1_-_36200401_36200606	0.35033	SOX2.p2	AK044321|Uggt1|320011|UDP-glucose glycoprotein glucosyltransferase 1
mm9_v1_chr5_+_123093892_123094082	0.348838	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_chr6_+_30758582_30758676	0.34812	SOX2.p2	AK014219|Copg2as2|100044236|coatomer protein complex, subunit gamma 2, antisense 2
mm9_v1_chr8_+_34842513_34842603	0.348015	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_chr3_-_116671720_116671775	0.347922	SOX2.p2	AK136939|Palmd|114301|palmdelphin
mm9_v1_chr6_-_72908018_72908225	0.347334	SOX2.p2	BC089327|Tmsb10|19240|thymosin, beta 10	Z48496|Tmsb10|19240|thymosin, beta 10	NM_001039392|Tmsb10|19240|thymosin, beta 10
mm9_v1_chr10_+_127896244_127896376	0.346772	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_chr17_+_72119030_72119041	0.346759	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_chr18_-_35114005_35114028	0.346701	SOX2.p2	AK133501|Hspa9|15526|heat shock protein 9	AK159791|Hspa9|15526|heat shock protein 9	AK161587|Hspa9|15526|heat shock protein 9
mm9_v1_chr8_-_87604530_87604644	0.346411	SOX2.p2	BC034842|Wdr83|67836|WD repeat domain containing 83	BC019369|Wdr83|67836|WD repeat domain containing 83	BC094624|Wdr83|67836|WD repeat domain containing 83	AK005790|Wdr83|67836|WD repeat domain containing 83	BC005587|Wdr83|67836|WD repeat domain containing 83	AK020654|Wdr83|67836|WD repeat domain containing 83	AY365434|Wdr83|67836|WD repeat domain containing 83	NM_026399|Wdr83|67836|WD repeat domain containing 83
mm9_v1_chr18_+_34932278_34932429	0.345526	SOX2.p2	AK012724|Fam53c|66306|family with sequence similarity 53, member C	AK205811|Fam53c|66306|family with sequence similarity 53, member C
mm9_v1_chr9_+_99143756_99143900	0.345471	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_chr11_-_60988490_60988572	0.34428	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_chr19_-_39537540_39537568	0.343125	SOX2.p2	AF047725|Cyp2c38|13097|cytochrome P450, family 2, subfamily c, polypeptide 38	AK050051|Cyp2c38|13097|cytochrome P450, family 2, subfamily c, polypeptide 38	BC150721|Cyp2c38|13097|cytochrome P450, family 2, subfamily c, polypeptide 38	NM_010002|Cyp2c38|13097|cytochrome P450, family 2, subfamily c, polypeptide 38
mm9_v1_chr11_-_102308966_102308985	0.342687	SOX2.p2	NM_199200|Fam171a2|217219|family with sequence similarity 171, member A2
mm9_v1_chr9_-_15105965_15105999	0.341113	SOX2.p2	BC016078|4931406C07Rik|70984|RIKEN cDNA 4931406C07 gene	NM_133732|4931406C07Rik|70984|RIKEN cDNA 4931406C07 gene
mm9_v1_chr11_+_20125239_20125296	0.340341	SOX2.p2	AK078671|Rab1|19324|RAB1, member RAS oncogene family
mm9_v1_chr10_+_42481531_42481611	0.338941	SOX2.p2	AY238936|Sec63|140740|SEC63-like (S. cerevisiae)	BC019366|Sec63|140740|SEC63-like (S. cerevisiae)	BC031846|Sec63|140740|SEC63-like (S. cerevisiae)	AK036629|Sec63|140740|SEC63-like (S. cerevisiae)	AK049737|Sec63|140740|SEC63-like (S. cerevisiae)
mm9_v1_chr15_-_76352331_76352558	0.338905	SOX2.p2	BC057562|Scrt1|170729|scratch homolog 1, zinc finger protein (Drosophila)	BC089316|Scrt1|170729|scratch homolog 1, zinc finger protein (Drosophila)	NM_130893|Scrt1|170729|scratch homolog 1, zinc finger protein (Drosophila)
mm9_v1_chr5_-_122822329_122822391	0.337959	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_chr15_-_66117612_66117785	0.337413	SOX2.p2	AY118171|Kcnq3|110862|potassium voltage-gated channel, subfamily Q, member 3	BC116306|Kcnq3|110862|potassium voltage-gated channel, subfamily Q, member 3	NM_152923|Kcnq3|110862|potassium voltage-gated channel, subfamily Q, member 3
mm9_v1_chr13_-_93258004_93258035	0.336507	SOX2.p2	AK134948|Zfyve16|218441|zinc finger, FYVE domain containing 16
mm9_v1_chr12_-_70458116_70458130	0.335845	SOX2.p2	BC037106|Nemf|66244|nuclear export mediator factor	AK039497|Nemf|66244|nuclear export mediator factor
mm9_v1_chr7_-_13595141_13595224	0.335757	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_chr1_-_170085342_170085390	0.334886	SOX2.p2	AK083616|Pbx1|18514|pre B-cell leukemia transcription factor 1
mm9_v1_chr14_+_51544629_51544699	0.334436	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_chr1_-_75250520_75250549	0.334015	SOX2.p2	BC064020|Ptprn|19275|protein tyrosine phosphatase, receptor type, N
mm9_v1_chr7_-_19751441_19751475	0.333781	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_chr2_-_60591836_60591898	0.333689	SOX2.p2	AK159851|Rbms1|56878|RNA binding motif, single stranded interacting protein 1
mm9_v1_chrX_+_150158113_150158178	0.332676	SOX2.p2	AK008724|2210013O21Rik|70123|RIKEN cDNA 2210013O21 gene
mm9_v1_chr2_-_75819804_75820023	0.33266	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_chr9_-_75458865_75458907	0.332253	SOX2.p2	AF237629|Tmod2|50876|tropomodulin 2
mm9_v1_chr9_+_44134859_44135076	0.330511	SOX2.p2	BC010474|Dpagt1|13478|dolichyl-phosphate (UDP-N-acetylglucosamine) acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	NM_007875|Dpagt1|13478|dolichyl-phosphate (UDP-N-acetylglucosamine) acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	AK008246|Dpagt1|13478|dolichyl-phosphate (UDP-N-acetylglucosamine) acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	AK008317|Dpagt1|13478|dolichyl-phosphate (UDP-N-acetylglucosamine) acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	AK164129|Dpagt1|13478|dolichyl-phosphate (UDP-N-acetylglucosamine) acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	X65603|Dpagt1|13478|dolichyl-phosphate (UDP-N-acetylglucosamine) acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)
mm9_v1_chr15_-_57723993_57724037	0.330429	SOX2.p2	AK011499|Derl1|67819|Der1-like domain family, member 1	AK161702|Derl1|67819|Der1-like domain family, member 1	BC003454|Derl1|67819|Der1-like domain family, member 1	BC085490|Derl1|67819|Der1-like domain family, member 1
mm9_v1_chr5_+_123794626_123794632	0.329851	SOX2.p2	BC046777|Bcl7a|77045|B-cell CLL/lymphoma 7A
mm9_v1_chr18_+_78546492_78546501	0.329831	SOX2.p2	BC158101|Gm6133|620155|60S ribosomal protein L17 pseudogene
mm9_v1_chr13_+_15555483_15555555	0.329819	SOX2.p2	AK158261|Gli3|14634|GLI-Kruppel family member GLI3	NM_008130|Gli3|14634|GLI-Kruppel family member GLI3
mm9_v1_chr11_-_51670563_51670645	0.328713	SOX2.p2	AK035317|Phf15|76901|PHD finger protein 15
mm9_v1_chr11_+_116295406_116295422	0.32843	SOX2.p2	AK144901|Fam100b|319370|family with sequence similarity 100, member B	NM_176902|Fam100b|319370|family with sequence similarity 100, member B
mm9_v1_chr11_+_6289339_6289394	0.328123	SOX2.p2	NM_028601|Zmiz2|52915|zinc finger, MIZ-type containing 2
mm9_v1_chr7_+_63305516_63305584	0.328034	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_chr19_+_55816320_55816547	0.327507	SOX2.p2	AK132465|Tcf7l2|21416|transcription factor 7-like 2, T-cell specific, HMG-box	AK035059|Tcf7l2|21416|transcription factor 7-like 2, T-cell specific, HMG-box	AF107298|Tcf7l2|21416|transcription factor 7-like 2, T-cell specific, HMG-box
mm9_v1_chr6_-_115626497_115626580	0.327083	SOX2.p2	BC092040|Raf1|110157|v-raf-leukemia viral oncogene 1	BC015273|Raf1|110157|v-raf-leukemia viral oncogene 1	AK036317|Raf1|110157|v-raf-leukemia viral oncogene 1	BC056439|Raf1|110157|v-raf-leukemia viral oncogene 1
mm9_v1_chr15_+_101974616_101974616	0.325999	SOX2.p2	NM_008344|Igfbp6|16012|insulin-like growth factor binding protein 6
mm9_v1_chr7_-_52308243_52308250	0.325749	SOX2.p2	BC075628|Prr12|233210|proline rich 12	NM_175022|Prr12|233210|proline rich 12
mm9_v1_chr12_+_33832550_33832590	0.325686	SOX2.p2	NM_028139|Atxn7l1|380753|ataxin 7-like 1
mm9_v1_chr11_+_98667577_98667599	0.324764	SOX2.p2	AK031902|Msl1|74026|male-specific lethal 1 homolog (Drosophila)
mm9_v1_chr16_+_91729540_91729753	0.324489	SOX2.p2	AK160949|Itsn1|16443|intersectin 1 (SH3 domain protein 1A)	BC062938|Itsn1|16443|intersectin 1 (SH3 domain protein 1A)	NM_001110275|Itsn1|16443|intersectin 1 (SH3 domain protein 1A)	NM_001110276|Itsn1|16443|intersectin 1 (SH3 domain protein 1A)	NM_010587|Itsn1|16443|intersectin 1 (SH3 domain protein 1A)	AK155397|Itsn1|16443|intersectin 1 (SH3 domain protein 1A)	BC066105|Itsn1|16443|intersectin 1 (SH3 domain protein 1A)
mm9_v1_chr18_+_37663917_37664076	0.324362	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_chr5_+_35384200_35384209	0.324353	SOX2.p2	AB009294|Hgfac|54426|hepatocyte growth factor activator	NM_019447|Hgfac|54426|hepatocyte growth factor activator	AK007987|Hgfac|54426|hepatocyte growth factor activator	AK169989|Hgfac|54426|hepatocyte growth factor activator
mm9_v1_chr2_+_142904128_142904227	0.323463	SOX2.p2	BC139152|Otor|57329|otoraplin	BC139153|Otor|57329|otoraplin	AK047965|Otor|57329|otoraplin	AJ243939|Otor|57329|otoraplin	AF243504|Otor|57329|otoraplin	NM_020595|Otor|57329|otoraplin
mm9_v1_chr2_-_156005873_156005985	0.321695	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_chr19_+_8839421_8839423	0.32142	SOX2.p2	AK184410|Nxf1|53319|nuclear RNA export factor 1 homolog (S. cerevisiae)	AK191466|Nxf1|53319|nuclear RNA export factor 1 homolog (S. cerevisiae)	AK194022|Nxf1|53319|nuclear RNA export factor 1 homolog (S. cerevisiae)
mm9_v1_chr17_+_34168703_34168796	0.321056	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_chr1_-_163748523_163748605	0.320996	SOX2.p2	AK033720|AI848100|226551|expressed sequence AI848100
mm9_v1_chr11_+_117658973_117659056	0.319873	SOX2.p2	NM_029964|6030468B19Rik|77727|RIKEN cDNA 6030468B19 gene	AK020081|6030468B19Rik|77727|RIKEN cDNA 6030468B19 gene
mm9_v1_chr1_-_170361789_170361795	0.31827	SOX2.p2	AK084143|Pbx1|18514|pre B-cell leukemia transcription factor 1
mm9_v1_chr14_+_32149804_32149909	0.317865	SOX2.p2	AK154277|Capn7|12339|calpain 7	AK169334|Capn7|12339|calpain 7	BC095980|Capn7|12339|calpain 7	AB028640|Capn7|12339|calpain 7	NM_009796|Capn7|12339|calpain 7
mm9_v1_chr1_-_30930715_30930760	0.316533	SOX2.p2	AK133490|Phf3|213109|PHD finger protein 3
mm9_v1_chr7_+_97357406_97357492	0.316276	SOX2.p2	AK163129|Picalm|233489|phosphatidylinositol binding clathrin assembly protein
mm9_v1_chr17_+_47730384_47730630	0.315568	SOX2.p2	AK165191|Ccnd3|12445|cyclin D3	NM_007632|Ccnd3|12445|cyclin D3	AK159503|Ccnd3|12445|cyclin D3	AK168290|Ccnd3|12445|cyclin D3	M86183|Ccnd3|12445|cyclin D3	BC004076|Ccnd3|12445|cyclin D3	BC005605|Ccnd3|12445|cyclin D3
mm9_v1_chr4_+_134024234_134024333	0.315271	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_chr9_+_106073265_106073336	0.315231	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_chr5_-_92497375_92497432	0.314536	SOX2.p2	AK200302|G3bp2|23881|GTPase activating protein (SH3 domain) binding protein 2
mm9_v1_chr6_+_54631644_54631765	0.312827	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_chr8_+_86520110_86520238	0.312262	SOX2.p2	AK131888|Prkaca|18747|protein kinase, cAMP dependent, catalytic, alpha
mm9_v1_chr8_-_85690068_85690070	0.310207	SOX2.p2	AK143076|Gm10645|100313944|predicted gene 10645
mm9_v1_chr2_-_125684720_125684819	0.310079	SOX2.p2	AF071312|Cops2|12848|COP9 (constitutive photomorphogenic) homolog, subunit 2 (Arabidopsis thaliana)	BC023096|Cops2|12848|COP9 (constitutive photomorphogenic) homolog, subunit 2 (Arabidopsis thaliana)	AF087688|Cops2|12848|COP9 (constitutive photomorphogenic) homolog, subunit 2 (Arabidopsis thaliana)	AK145225|Cops2|12848|COP9 (constitutive photomorphogenic) homolog, subunit 2 (Arabidopsis thaliana)	AK146153|Cops2|12848|COP9 (constitutive photomorphogenic) homolog, subunit 2 (Arabidopsis thaliana)	AK132207|Cops2|12848|COP9 (constitutive photomorphogenic) homolog, subunit 2 (Arabidopsis thaliana)	AK084421|Cops2|12848|COP9 (constitutive photomorphogenic) homolog, subunit 2 (Arabidopsis thaliana)	AK010383|Cops2|12848|COP9 (constitutive photomorphogenic) homolog, subunit 2 (Arabidopsis thaliana)	AK037757|Cops2|12848|COP9 (constitutive photomorphogenic) homolog, subunit 2 (Arabidopsis thaliana)	AK132776|Cops2|12848|COP9 (constitutive photomorphogenic) homolog, subunit 2 (Arabidopsis thaliana)	NM_009939|Cops2|12848|COP9 (constitutive photomorphogenic) homolog, subunit 2 (Arabidopsis thaliana)
mm9_v1_chr15_-_73253497_73253530	0.309851	SOX2.p2	DQ478404|Ptk2|14083|PTK2 protein tyrosine kinase 2	DQ478405|Ptk2|14083|PTK2 protein tyrosine kinase 2
mm9_v1_chr5_+_119214502_119214629	0.309111	SOX2.p2	AK018557|Med13l|76199|mediator complex subunit 13-like
mm9_v1_chr15_-_99079369_99079394	0.308824	SOX2.p2	AK158611|Mcrs1|51812|microspherule protein 1
mm9_v1_chr9_+_70390703_70390723	0.308078	SOX2.p2	AK162780|Sltm|66660|SAFB-like, transcription modulator	AK017839|Sltm|66660|SAFB-like, transcription modulator
mm9_v1_chr1_-_157264398_157264577	0.307597	SOX2.p2	AK147403|Xpr1|19775|xenotropic and polytropic retrovirus receptor 1	BC153872|Xpr1|19775|xenotropic and polytropic retrovirus receptor 1	AF114753|Xpr1|19775|xenotropic and polytropic retrovirus receptor 1	BC075721|Xpr1|19775|xenotropic and polytropic retrovirus receptor 1	AK141660|Xpr1|19775|xenotropic and polytropic retrovirus receptor 1	NM_011273|Xpr1|19775|xenotropic and polytropic retrovirus receptor 1
mm9_v1_chr11_+_74644479_74644499	0.30757	SOX2.p2	Y07609|Mnt|17428|max binding protein	BC054534|Mnt|17428|max binding protein
mm9_v1_chr18_+_45428413_45428658	0.30704	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_chr1_-_95646769_95646865	0.306249	SOX2.p2	AK213476|Thap4|67026|THAP domain containing 4	BC013538|Thap4|67026|THAP domain containing 4	AK216112|Thap4|67026|THAP domain containing 4
mm9_v1_chr7_+_129363009_129363009	0.305279	SOX2.p2	BC119202|2010110P09Rik|70261|RIKEN cDNA 2010110P09 gene	BC119204|2010110P09Rik|70261|RIKEN cDNA 2010110P09 gene	NM_027363|2010110P09Rik|70261|RIKEN cDNA 2010110P09 gene
mm9_v1_chr2_-_53050207_53050293	0.30513	SOX2.p2	AF135439|Prpf40a|56194|PRP40 pre-mRNA processing factor 40 homolog A (yeast)	NM_018785|Prpf40a|56194|PRP40 pre-mRNA processing factor 40 homolog A (yeast)	AK045207|Prpf40a|56194|PRP40 pre-mRNA processing factor 40 homolog A (yeast)	BC003318|Prpf40a|56194|PRP40 pre-mRNA processing factor 40 homolog A (yeast)	AK087963|Prpf40a|56194|PRP40 pre-mRNA processing factor 40 homolog A (yeast)
mm9_v1_chr17_-_28623006_28623098	0.304736	SOX2.p2	U36220|Fkbp5|14229|FK506 binding protein 5	BC015260|Fkbp5|14229|FK506 binding protein 5	AK169795|Fkbp5|14229|FK506 binding protein 5	NM_010220|Fkbp5|14229|FK506 binding protein 5	U16959|Fkbp5|14229|FK506 binding protein 5
mm9_v1_chr16_+_31948631_31948724	0.303985	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_chr8_-_114516147_114516201	0.303808	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_chr9_+_69837253_69837421	0.303782	SOX2.p2	AK169609|Bnip2|12175|BCL2/adenovirus E1B interacting protein 2	AK054288|Bnip2|12175|BCL2/adenovirus E1B interacting protein 2	NM_016787|Bnip2|12175|BCL2/adenovirus E1B interacting protein 2	AK159745|Bnip2|12175|BCL2/adenovirus E1B interacting protein 2	AK014659|Bnip2|12175|BCL2/adenovirus E1B interacting protein 2	AK161116|Bnip2|12175|BCL2/adenovirus E1B interacting protein 2	BC012670|Bnip2|12175|BCL2/adenovirus E1B interacting protein 2	AF035207|Bnip2|12175|BCL2/adenovirus E1B interacting protein 2
mm9_v1_chr11_+_4886860_4887033	0.303327	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_chr7_-_49948087_49948135	0.303165	SOX2.p2	BC068175|Gm5595|434179|predicted gene 5595	NM_001008427|Gm5595|434179|predicted gene 5595
mm9_v1_chr4_-_104782337_104782438	0.302293	SOX2.p2	AK044030|Prkaa2|108079|protein kinase, AMP-activated, alpha 2 catalytic subunit	AK134573|Prkaa2|108079|protein kinase, AMP-activated, alpha 2 catalytic subunit
mm9_v1_chr4_+_94406002_94406012	0.302091	SOX2.p2	AK053336|Tek|21687|endothelial-specific receptor tyrosine kinase
mm9_v1_chr13_-_76081142_76081219	0.301479	SOX2.p2	AK139158|Rhobtb3|73296|Rho-related BTB domain containing 3	AK020938|Rhobtb3|73296|Rho-related BTB domain containing 3
mm9_v1_chr10_+_74523633_74523640	0.299715	SOX2.p2	NM_001081412|Bcr|110279|breakpoint cluster region
mm9_v1_chr12_+_39510297_39510297	0.298804	SOX2.p2	AK032224|Etv1|14009|ets variant gene 1	NM_001163154|Etv1|14009|ets variant gene 1
mm9_v1_chr14_-_73725611_73725643	0.298562	SOX2.p2	AK141028|Rb1|19645|retinoblastoma 1
mm9_v1_chr15_-_94408654_94408675	0.296467	SOX2.p2	
mm9_v1_chr19_+_45122065_45122176	0.29631	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_chr2_-_131178551_131178627	0.295857	SOX2.p2	BC096529|Rnf24|51902|ring finger protein 24	AK154093|Rnf24|51902|ring finger protein 24	AK048813|Rnf24|51902|ring finger protein 24	AK015699|Rnf24|51902|ring finger protein 24	AK089207|Rnf24|51902|ring finger protein 24	AK083665|Rnf24|51902|ring finger protein 24	NM_178607|Rnf24|51902|ring finger protein 24
mm9_v1_chr18_-_24179208_24179311	0.29565	SOX2.p2	AK146726|Zfp191|59057|zinc finger protein 191	BC054832|Zfp191|59057|zinc finger protein 191	NM_021559|Zfp191|59057|zinc finger protein 191	AY832930|Zfp191|59057|zinc finger protein 191
mm9_v1_chr2_-_131855504_131855666	0.295229	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_chr3_-_151873242_151873265	0.293778	SOX2.p2	NM_027287|Dnajb4|67035|DnaJ (Hsp40) homolog, subfamily B, member 4	AK077587|Dnajb4|67035|DnaJ (Hsp40) homolog, subfamily B, member 4
mm9_v1_chr12_+_70397667_70397700	0.293726	SOX2.p2	AK078408|Klhdc2|69554|kelch domain containing 2	NM_027117|Klhdc2|69554|kelch domain containing 2
mm9_v1_chr11_-_106021399_106021524	0.292818	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_chr1_-_38954933_38955026	0.291627	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_+_67779990_67779991	0.290718	SOX2.p2	AK018716|Stx8|55943|syntaxin 8
mm9_v1_chr4_+_115410677_115410677	0.290096	SOX2.p2	BC059213|4732418C07Rik|230648|RIKEN cDNA 4732418C07 gene	NM_172698|4732418C07Rik|230648|RIKEN cDNA 4732418C07 gene
mm9_v1_chr6_-_71561919_71561988	0.289967	SOX2.p2	AK049243|Kdm3a|104263|lysine (K)-specific demethylase 3A
mm9_v1_chr3_+_153636391_153636423	0.28996	SOX2.p2	BC086641|Slc44a5|242259|solute carrier family 44, member 5	NM_001081263|Slc44a5|242259|solute carrier family 44, member 5
mm9_v1_chr2_+_87642546_87642547	0.289611	SOX2.p2	BC140120|Olfr1143|258290|olfactory receptor 1143	BC140161|Olfr1143|258290|olfactory receptor 1143	BC140202|Olfr1143|258290|olfactory receptor 1143	NM_146293|Olfr1143|258290|olfactory receptor 1143
mm9_v1_chr2_+_34965011_34965138	0.288986	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_chr2_-_120676125_120676339	0.288752	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_chr17_-_13153182_13153211	0.28811	SOX2.p2	AK013275|Acat2|110460|acetyl-Coenzyme A acetyltransferase 2
mm9_v1_chr2_+_34627607_34627658	0.288005	SOX2.p2	NM_001163434|Hspa5|14828|heat shock protein 5	NM_022310|Hspa5|14828|heat shock protein 5	AK077463|Hspa5|14828|heat shock protein 5	AK146647|Hspa5|14828|heat shock protein 5	AK148539|Hspa5|14828|heat shock protein 5	AK149447|Hspa5|14828|heat shock protein 5	AK151647|Hspa5|14828|heat shock protein 5	AK151806|Hspa5|14828|heat shock protein 5	AK152958|Hspa5|14828|heat shock protein 5	AK160821|Hspa5|14828|heat shock protein 5	AK168012|Hspa5|14828|heat shock protein 5	AK169034|Hspa5|14828|heat shock protein 5	AK004578|Hspa5|14828|heat shock protein 5	AK076079|Hspa5|14828|heat shock protein 5	AK144650|Hspa5|14828|heat shock protein 5	AK144742|Hspa5|14828|heat shock protein 5	AK152020|Hspa5|14828|heat shock protein 5	AK159719|Hspa5|14828|heat shock protein 5	AK166207|Hspa5|14828|heat shock protein 5	AK166739|Hspa5|14828|heat shock protein 5	AK167011|Hspa5|14828|heat shock protein 5	AK152521|Hspa5|14828|heat shock protein 5	AK168230|Hspa5|14828|heat shock protein 5	BC050927|Hspa5|14828|heat shock protein 5
mm9_v1_chr13_-_111070392_111070417	0.286399	SOX2.p2	AK014050|Rab3c|67295|RAB3C, member RAS oncogene family	NM_023852|Rab3c|67295|RAB3C, member RAS oncogene family
mm9_v1_chrX_-_92391841_92391855	0.285884	SOX2.p2	AK163874|Arhgef9|236915|CDC42 guanine nucleotide exchange factor (GEF) 9
mm9_v1_chr8_+_85689250_85689250	0.285414	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_chrX_-_91787351_91787352	0.28426	SOX2.p2	BC031461|Maged1|94275|melanoma antigen, family D, 1
mm9_v1_chr2_-_120434984_120435243	0.283941	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_chr11_+_20991321_20991416	0.283746	SOX2.p2	AK151660|Peli1|67245|pellino 1	AK152900|Peli1|67245|pellino 1	AK152997|Peli1|67245|pellino 1	AK153372|Peli1|67245|pellino 1	NM_023324|Peli1|67245|pellino 1	AK167525|Peli1|67245|pellino 1	BC026695|Peli1|67245|pellino 1
mm9_v1_chr3_+_16083164_16083288	0.283204	SOX2.p2	NM_001145919|Ythdf3|229096|YTH domain family 3	NM_172677|Ythdf3|229096|YTH domain family 3	BC067040|Ythdf3|229096|YTH domain family 3	AK039176|Ythdf3|229096|YTH domain family 3	AK137245|Ythdf3|229096|YTH domain family 3	BC067042|Ythdf3|229096|YTH domain family 3	AK053736|Ythdf3|229096|YTH domain family 3	BC057158|Ythdf3|229096|YTH domain family 3
mm9_v1_chr1_-_4350323_4350394	0.282671	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_chr5_-_115750998_115751012	0.282533	SOX2.p2	NM_019682|Dynll1|56455|dynein light chain LC8-type 1
mm9_v1_chr17_+_17539635_17539669	0.281908	SOX2.p2	BC049574|Lix1|66643|limb expression 1 homolog (chicken)	NM_025681|Lix1|66643|limb expression 1 homolog (chicken)
mm9_v1_chr11_-_72990492_72990557	0.281537	SOX2.p2	NM_001168470|Tmem93|66048|transmembrane protein 93	BC022104|Tmem93|66048|transmembrane protein 93	AK002385|Tmem93|66048|transmembrane protein 93	AK012769|Tmem93|66048|transmembrane protein 93	AK003198|Tmem93|66048|transmembrane protein 93	AK004149|Tmem93|66048|transmembrane protein 93	NM_025318|Tmem93|66048|transmembrane protein 93
mm9_v1_chr6_-_116623789_116623853	0.280048	SOX2.p2	AK139284|Rassf4|213391|Ras association (RalGDS/AF-6) domain family member 4	AK170955|Rassf4|213391|Ras association (RalGDS/AF-6) domain family member 4	BC023245|Rassf4|213391|Ras association (RalGDS/AF-6) domain family member 4	AK089460|Rassf4|213391|Ras association (RalGDS/AF-6) domain family member 4	BC060709|Rassf4|213391|Ras association (RalGDS/AF-6) domain family member 4	AK036528|Rassf4|213391|Ras association (RalGDS/AF-6) domain family member 4	AK053578|Rassf4|213391|Ras association (RalGDS/AF-6) domain family member 4	AK151561|Rassf4|213391|Ras association (RalGDS/AF-6) domain family member 4	AK152639|Rassf4|213391|Ras association (RalGDS/AF-6) domain family member 4	AK164357|Rassf4|213391|Ras association (RalGDS/AF-6) domain family member 4	AK160584|Rassf4|213391|Ras association (RalGDS/AF-6) domain family member 4	AK171198|Rassf4|213391|Ras association (RalGDS/AF-6) domain family member 4	NM_178045|Rassf4|213391|Ras association (RalGDS/AF-6) domain family member 4
mm9_v1_chr4_-_63064369_63064478	0.280022	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_chr19_+_5740903_5740936	0.279678	SOX2.p2	AK080869|Ltbp3|16998|latent transforming growth factor beta binding protein 3	NM_008520|Ltbp3|16998|latent transforming growth factor beta binding protein 3
mm9_v1_chr2_+_180716817_180716845	0.278951	SOX2.p2	
mm9_v1_chr7_+_25292375_25292405	0.278759	SOX2.p2	AK139174|Zfp428|232969|zinc finger protein 428
mm9_v1_chr11_+_20991293_20991320	0.278532	SOX2.p2	AK020915|Peli1|67245|pellino 1
mm9_v1_chr6_+_29997972_29998071	0.278531	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_chr2_+_76244578_76244594	0.277929	SOX2.p2	AK044411|Osbpl6|99031|oxysterol binding protein-like 6	NM_145525|Osbpl6|99031|oxysterol binding protein-like 6
mm9_v1_chr10_-_120748007_120748075	0.27745	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_chr11_-_11832366_11832461	0.276698	SOX2.p2	BC033917|Grb10|14783|growth factor receptor bound protein 10	BC036389|Grb10|14783|growth factor receptor bound protein 10
mm9_v1_chr5_+_106305563_106305620	0.276686	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_chr2_-_163450863_163450871	0.27648	SOX2.p2	AK003471|Serinc3|26943|serine incorporator 3
mm9_v1_chr6_+_29325052_29325077	0.276473	SOX2.p2	AF177023|Calu|12321|calumenin
mm9_v1_chr2_-_32136262_32136304	0.276417	SOX2.p2	
mm9_v1_chr11_-_86517662_86517713	0.274885	SOX2.p2	AK167527|Cltc|67300|clathrin, heavy polypeptide (Hc)
mm9_v1_chr14_+_15535538_15535592	0.273677	SOX2.p2	AK152233|Slc4a7|218756|solute carrier family 4, sodium bicarbonate cotransporter, member 7	AK153567|Slc4a7|218756|solute carrier family 4, sodium bicarbonate cotransporter, member 7	NM_001033270|Slc4a7|218756|solute carrier family 4, sodium bicarbonate cotransporter, member 7	AK088400|Slc4a7|218756|solute carrier family 4, sodium bicarbonate cotransporter, member 7	GU386352|Slc4a7|218756|solute carrier family 4, sodium bicarbonate cotransporter, member 7	GU386353|Slc4a7|218756|solute carrier family 4, sodium bicarbonate cotransporter, member 7
mm9_v1_chr7_-_54389053_54389053	0.273361	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_chr10_+_127525425_127525449	0.27236	SOX2.p2	AK003460|Atp5b|11947|ATP synthase, H+ transporting mitochondrial F1 complex, beta subunit
mm9_v1_chr4_+_109650629_109650657	0.271216	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_chr7_+_146434402_146434460	0.271047	SOX2.p2	AK160932|Pwwp2b|101631|PWWP domain containing 2B
mm9_v1_chr2_-_113839354_113839354	0.269999	SOX2.p2	BC058595|Gjd2|14617|gap junction protein, delta 2	NM_010290|Gjd2|14617|gap junction protein, delta 2
mm9_v1_chr5_-_87569342_87569376	0.268648	SOX2.p2	X06358|Ugt2b5|22238|UDP glucuronosyltransferase 2 family, polypeptide B5	BC028262|Ugt2b5|22238|UDP glucuronosyltransferase 2 family, polypeptide B5	AK136480|Ugt2b5|22238|UDP glucuronosyltransferase 2 family, polypeptide B5	NM_009467|Ugt2b5|22238|UDP glucuronosyltransferase 2 family, polypeptide B5
mm9_v1_chr9_-_119932620_119932715	0.268147	SOX2.p2	BC117959|Xirp1|22437|xin actin-binding repeat containing 1	BC117960|Xirp1|22437|xin actin-binding repeat containing 1	AF051945|Xirp1|22437|xin actin-binding repeat containing 1	NM_011724|Xirp1|22437|xin actin-binding repeat containing 1
mm9_v1_chr2_+_33097791_33097802	0.267936	SOX2.p2	AK187902|Angptl2|26360|angiopoietin-like 2	AK205240|Angptl2|26360|angiopoietin-like 2	AK214337|Angptl2|26360|angiopoietin-like 2
mm9_v1_chr17_+_44090139_44090183	0.26775	SOX2.p2	BC049096|Rcan2|53901|regulator of calcineurin 2	NM_030598|Rcan2|53901|regulator of calcineurin 2
mm9_v1_chr19_-_5729623_5729695	0.266826	SOX2.p2	BC030163|Fam89b|17826|family with sequence similarity 89, member B	AK013256|Fam89b|17826|family with sequence similarity 89, member B	AF212921|Fam89b|17826|family with sequence similarity 89, member B	BC013894|Fam89b|17826|family with sequence similarity 89, member B	AF212920|Fam89b|17826|family with sequence similarity 89, member B	AB012726|Fam89b|17826|family with sequence similarity 89, member B	BC056166|Fam89b|17826|family with sequence similarity 89, member B	AK003883|Fam89b|17826|family with sequence similarity 89, member B	NM_023166|Fam89b|17826|family with sequence similarity 89, member B	NM_181452|Fam89b|17826|family with sequence similarity 89, member B
mm9_v1_chr9_+_82723591_82723695	0.266628	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_+_97177668_97177676	0.26573	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_chr11_+_75300330_75300364	0.265116	SOX2.p2	BC093481|Prpf8|192159|pre-mRNA processing factor 8	AK144232|Prpf8|192159|pre-mRNA processing factor 8
mm9_v1_chr5_+_150242274_150242293	0.264424	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_chr4_-_60594959_60595030	0.262943	SOX2.p2	EU882231|Mup10|100039008|major urinary protein 10	BC055353|LOC100048884|100048884|novel member of the major urinary protein (Mup) gene family	M28649|Mup1|17840|major urinary protein 1	NM_001122647|Mup10|100039008|major urinary protein 10
mm9_v1_chr17_+_4995073_4995073	0.26267	SOX2.p2	NM_001085355|Arid1b|239985|AT rich interactive domain 1B (SWI-like)
mm9_v1_chr9_+_54765084_54765153	0.26237	SOX2.p2	AK085527|Agphd1|235386|aminoglycoside phosphotransferase domain containing 1	AK162425|Agphd1|235386|aminoglycoside phosphotransferase domain containing 1	NM_177351|Agphd1|235386|aminoglycoside phosphotransferase domain containing 1	AK138851|Agphd1|235386|aminoglycoside phosphotransferase domain containing 1	AK083218|Agphd1|235386|aminoglycoside phosphotransferase domain containing 1	AK142509|Agphd1|235386|aminoglycoside phosphotransferase domain containing 1	AK163926|Agphd1|235386|aminoglycoside phosphotransferase domain containing 1	AK048771|Agphd1|235386|aminoglycoside phosphotransferase domain containing 1	BC038618|Agphd1|235386|aminoglycoside phosphotransferase domain containing 1	AK087279|Agphd1|235386|aminoglycoside phosphotransferase domain containing 1
mm9_v1_chr10_+_21602148_21602174	0.262217	SOX2.p2	AK043284|Sgk1|20393|serum/glucocorticoid regulated kinase 1
mm9_v1_chr5_-_114830457_114830513	0.262202	SOX2.p2	AK147714|Kctd10|330171|potassium channel tetramerisation domain containing 10	AK163351|Kctd10|330171|potassium channel tetramerisation domain containing 10	AK161199|Kctd10|330171|potassium channel tetramerisation domain containing 10	AK028657|Kctd10|330171|potassium channel tetramerisation domain containing 10	AK041516|Kctd10|330171|potassium channel tetramerisation domain containing 10	AK145295|Kctd10|330171|potassium channel tetramerisation domain containing 10	AK166505|Kctd10|330171|potassium channel tetramerisation domain containing 10	BC006935|Kctd10|330171|potassium channel tetramerisation domain containing 10	NM_001159941|Kctd10|330171|potassium channel tetramerisation domain containing 10	NM_026145|Kctd10|330171|potassium channel tetramerisation domain containing 10
mm9_v1_chr1_+_169528838_169528848	0.261782	SOX2.p2	M84819|Rxrg|20183|retinoid X receptor gamma
mm9_v1_chr16_+_17045284_17045304	0.261519	SOX2.p2	AK018549|Mapk1|26413|mitogen-activated protein kinase 1
mm9_v1_chr1_-_59820157_59820193	0.261209	SOX2.p2	AK049886|B430105G09Rik|320907|RIKEN cDNA B430105G09 gene
mm9_v1_chr4_-_34562138_34562200	0.260472	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_chr5_+_65928483_65928591	0.260384	SOX2.p2	AK139564|Ube2k|53323|ubiquitin-conjugating enzyme E2K (UBC1 homolog, yeast)	NM_016786|Ube2k|53323|ubiquitin-conjugating enzyme E2K (UBC1 homolog, yeast)	AK048194|Ube2k|53323|ubiquitin-conjugating enzyme E2K (UBC1 homolog, yeast)	AK035371|Ube2k|53323|ubiquitin-conjugating enzyme E2K (UBC1 homolog, yeast)	AK018366|Ube2k|53323|ubiquitin-conjugating enzyme E2K (UBC1 homolog, yeast)	AK160728|Ube2k|53323|ubiquitin-conjugating enzyme E2K (UBC1 homolog, yeast)	AK031055|Ube2k|53323|ubiquitin-conjugating enzyme E2K (UBC1 homolog, yeast)	AK036068|Ube2k|53323|ubiquitin-conjugating enzyme E2K (UBC1 homolog, yeast)	AK162142|Ube2k|53323|ubiquitin-conjugating enzyme E2K (UBC1 homolog, yeast)	AB011081|Ube2k|53323|ubiquitin-conjugating enzyme E2K (UBC1 homolog, yeast)	BC085311|Ube2k|53323|ubiquitin-conjugating enzyme E2K (UBC1 homolog, yeast)	AK166647|Ube2k|53323|ubiquitin-conjugating enzyme E2K (UBC1 homolog, yeast)
mm9_v1_chr16_-_45724720_45724763	0.258475	SOX2.p2	AK012333|Tagln3|56370|transgelin 3
mm9_v1_chr12_+_58331452_58331495	0.258202	SOX2.p2	AK044766|Mipol1|73490|mirror-image polydactyly gene 1 homolog (human)	BC110357|Prps1l3|328099|phosphoribosyl pyrophosphate synthetase 1-like 3
mm9_v1_chr5_+_81450617_81450617	0.257822	SOX2.p2	BC088989|Lphn3|319387|latrophilin 3	NM_198702|Lphn3|319387|latrophilin 3
mm9_v1_chr12_+_18521315_18521452	0.257602	SOX2.p2	AK017753|5730507C01Rik|236366|RIKEN cDNA 5730507C01 gene	AK139861|5730507C01Rik|236366|RIKEN cDNA 5730507C01 gene	NM_001033157|5730507C01Rik|236366|RIKEN cDNA 5730507C01 gene	BC150925|5730507C01Rik|236366|RIKEN cDNA 5730507C01 gene
mm9_v1_chr9_-_44187378_44187532	0.257217	SOX2.p2	AK020500|9430081H08Rik|77430|RIKEN cDNA 9430081H08 gene	AK040656|9430081H08Rik|77430|RIKEN cDNA 9430081H08 gene
mm9_v1_chr5_-_101083995_101084232	0.256885	SOX2.p2	AK213124|Coq2|71883|coenzyme Q2 homolog, prenyltransferase (yeast)	AK209340|Coq2|71883|coenzyme Q2 homolog, prenyltransferase (yeast)	AK211081|Coq2|71883|coenzyme Q2 homolog, prenyltransferase (yeast)	AK213346|Coq2|71883|coenzyme Q2 homolog, prenyltransferase (yeast)
mm9_v1_chr2_-_37225800_37225813	0.256394	SOX2.p2	AK046886|Rc3h2|319817|ring finger and CCCH-type zinc finger domains 2
mm9_v1_chr10_-_14425271_14425365	0.255818	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_chr18_-_35064624_35064726	0.255795	SOX2.p2	AK195141|Etf1|225363|eukaryotic translation termination factor 1	AK218551|Etf1|225363|eukaryotic translation termination factor 1
mm9_v1_chr18_+_37637421_37637642	0.255751	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_chrX_+_156278399_156278494	0.255577	SOX2.p2	AK028299|Sh3kbp1|58194|SH3-domain kinase binding protein 1	NM_001135728|Sh3kbp1|58194|SH3-domain kinase binding protein 1
mm9_v1_chr1_+_74421706_74421882	0.255198	SOX2.p2	AK090303|Slc11a1|18173|solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	NM_013612|Slc11a1|18173|solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	AK171393|Slc11a1|18173|solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	AK144237|Slc11a1|18173|solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	AK171343|Slc11a1|18173|solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	L13732|Slc11a1|18173|solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	X75355|Slc11a1|18173|solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	BC109137|Slc11a1|18173|solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	BC109138|Slc11a1|18173|solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1
mm9_v1_chrX_+_68809092_68809096	0.254604	SOX2.p2	AK141399|Hmgb3|15354|high mobility group box 3	AK146795|Hmgb3|15354|high mobility group box 3
mm9_v1_chr5_+_31191728_31191729	0.254237	SOX2.p2	AK034894|Agbl5|231093|ATP/GTP binding protein-like 5
mm9_v1_chr5_+_106128934_106129078	0.253744	SOX2.p2	AK137459|Lrrc8d|231549|leucine rich repeat containing 8D	NM_001122768|Lrrc8d|231549|leucine rich repeat containing 8D	AK046249|Lrrc8d|231549|leucine rich repeat containing 8D	AK080722|Lrrc8d|231549|leucine rich repeat containing 8D
mm9_v1_chr8_+_74676812_74676920	0.252416	SOX2.p2	
mm9_v1_chr8_+_109867910_109868036	0.251945	SOX2.p2	
mm9_v1_chr4_-_86873866_86873867	0.251102	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_chr13_-_85428605_85428737	0.250952	SOX2.p2	BC065082|Rasa1|218397|RAS p21 protein activator 1	AK161497|Rasa1|218397|RAS p21 protein activator 1
mm9_v1_chr6_+_125045998_125046234	0.249491	SOX2.p2	AK147695|Chd4|107932|chromodomain helicase DNA binding protein 4	AK040005|Chd4|107932|chromodomain helicase DNA binding protein 4	AK132004|Chd4|107932|chromodomain helicase DNA binding protein 4	BC058578|Chd4|107932|chromodomain helicase DNA binding protein 4	NM_145979|Chd4|107932|chromodomain helicase DNA binding protein 4	AK145532|Chd4|107932|chromodomain helicase DNA binding protein 4
mm9_v1_chr13_+_89680393_89680435	0.24896	SOX2.p2	BC066853|Hapln1|12950|hyaluronan and proteoglycan link protein 1
mm9_v1_chr17_+_24889931_24889960	0.248815	SOX2.p2	AK146974|Hs3st6|328779|heparan sulfate (glucosamine) 3-O-sulfotransferase 6	AY574375|Hs3st6|328779|heparan sulfate (glucosamine) 3-O-sulfotransferase 6	NM_001012402|Hs3st6|328779|heparan sulfate (glucosamine) 3-O-sulfotransferase 6	BC132520|Hs3st6|328779|heparan sulfate (glucosamine) 3-O-sulfotransferase 6	BC138814|Hs3st6|328779|heparan sulfate (glucosamine) 3-O-sulfotransferase 6	BC145424|Hs3st6|328779|heparan sulfate (glucosamine) 3-O-sulfotransferase 6
mm9_v1_chr3_-_29912113_29912128	0.248371	SOX2.p2	AK085548|Mecom|14013|MDS1 and EVI1 complex locus	NM_007963|Mecom|14013|MDS1 and EVI1 complex locus
mm9_v1_chr18_-_60661144_60661295	0.247373	SOX2.p2	BC012898|2010002N04Rik|106878|RIKEN cDNA 2010002N04 gene	AF313412|2010002N04Rik|106878|RIKEN cDNA 2010002N04 gene	AK171923|2010002N04Rik|106878|RIKEN cDNA 2010002N04 gene	AK170783|2010002N04Rik|106878|RIKEN cDNA 2010002N04 gene	AK155873|2010002N04Rik|106878|RIKEN cDNA 2010002N04 gene	AK171810|2010002N04Rik|106878|RIKEN cDNA 2010002N04 gene
mm9_v1_chrX_+_7367116_7367152	0.247227	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_+_90303576_90303673	0.246653	SOX2.p2	AK002814|Spp2|75396|secreted phosphoprotein 2	NM_029269|Spp2|75396|secreted phosphoprotein 2	AJ315513|Spp2|75396|secreted phosphoprotein 2	BC027494|Spp2|75396|secreted phosphoprotein 2
mm9_v1_chr5_-_134713853_134713859	0.24655	SOX2.p2	
mm9_v1_chr10_-_81090257_81090352	0.244768	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_chr17_+_36131397_36131470	0.244621	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_chr9_+_74800690_74800753	0.243906	SOX2.p2	AK087474|BC031353|235493|cDNA sequence BC031353
mm9_v1_chr2_-_66094647_66094696	0.243433	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_chr5_+_122804377_122804463	0.242068	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_chr8_+_11313002_11313023	0.241971	SOX2.p2	J04695|Col4a2|12827|collagen, type IV, alpha 2
mm9_v1_chr14_+_58693951_58693999	0.241951	SOX2.p2	AK158584|Fgf9|14180|fibroblast growth factor 9
mm9_v1_chr11_+_110260435_110260577	0.241595	SOX2.p2	AK043482|Map2k6|26399|mitogen-activated protein kinase kinase 6	AK086722|Map2k6|26399|mitogen-activated protein kinase kinase 6	AK138757|Map2k6|26399|mitogen-activated protein kinase kinase 6	NM_011943|Map2k6|26399|mitogen-activated protein kinase kinase 6	AK077712|Map2k6|26399|mitogen-activated protein kinase kinase 6	AK140289|Map2k6|26399|mitogen-activated protein kinase kinase 6	AK141708|Map2k6|26399|mitogen-activated protein kinase kinase 6	BC075652|Map2k6|26399|mitogen-activated protein kinase kinase 6	AK162671|Map2k6|26399|mitogen-activated protein kinase kinase 6	X97052|Map2k6|26399|mitogen-activated protein kinase kinase 6
mm9_v1_chr18_-_37803782_37803859	0.241563	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_chr2_+_162758440_162758589	0.24146	SOX2.p2	AK051608|Srsf6|67996|serine/arginine-rich splicing factor 6
mm9_v1_chr3_-_105746659_105746682	0.241363	SOX2.p2	U29530|Atp5f1|11950|ATP synthase, H+ transporting, mitochondrial F0 complex, subunit B1
mm9_v1_chr19_+_5041341_5041422	0.240995	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_chr18_-_43597640_43597708	0.24067	SOX2.p2	AK149024|Dpysl3|22240|dihydropyrimidinase-like 3
mm9_v1_chr1_-_92740348_92740438	0.240023	SOX2.p2	AF064749|Col6a3|12835|collagen, type VI, alpha 3
mm9_v1_chr2_-_30816439_30816626	0.239755	SOX2.p2	
mm9_v1_chr2_+_31951030_31951062	0.23921	SOX2.p2	AK134638|Ppapdc3|227721|phosphatidic acid phosphatase type 2 domain containing 3
mm9_v1_chr1_-_141456740_141456821	0.238601	SOX2.p2	BC111870|Cfhr1|50702|complement factor H-related 1	M29008|Cfhr1|50702|complement factor H-related 1	NM_015780|Cfhr1|50702|complement factor H-related 1
mm9_v1_chr2_+_131036131_131036175	0.238277	SOX2.p2	AK009634|2310035K24Rik|69596|RIKEN cDNA 2310035K24 gene	AK002807|2310035K24Rik|69596|RIKEN cDNA 2310035K24 gene	BC048399|2310035K24Rik|69596|RIKEN cDNA 2310035K24 gene	NM_027129|2310035K24Rik|69596|RIKEN cDNA 2310035K24 gene
mm9_v1_chr13_-_89881946_89882116	0.237967	SOX2.p2	BC021652|Vcan|13003|versican	AK163927|Vcan|13003|versican	AK135324|Vcan|13003|versican	AK032794|Vcan|13003|versican	NM_001081249|Vcan|13003|versican	NM_001134474|Vcan|13003|versican	NM_001134475|Vcan|13003|versican	NM_019389|Vcan|13003|versican	NM_172955|Vcan|13003|versican
mm9_v1_chr3_+_36451511_36451588	0.237072	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_chr18_-_60907984_60908001	0.236235	SOX2.p2	AF520867|Ndst1|15531|N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1
mm9_v1_chr9_-_101101334_101101402	0.23619	SOX2.p2	AK169510|Ppp2r3a|235542|protein phosphatase 2, regulatory subunit B'', alpha	AK132175|Ppp2r3a|235542|protein phosphatase 2, regulatory subunit B'', alpha	NM_172144|Ppp2r3a|235542|protein phosphatase 2, regulatory subunit B'', alpha
mm9_v1_chr12_+_118997623_118997625	0.235553	SOX2.p2	AK134824|Rapgef5|217944|Rap guanine nucleotide exchange factor (GEF) 5
mm9_v1_chr19_-_10944196_10944284	0.23537	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_chr7_+_146434362_146434395	0.235002	SOX2.p2	BC116669|Pwwp2b|101631|PWWP domain containing 2B	NM_001033206|Pwwp2b|101631|PWWP domain containing 2B	NM_001098636|Pwwp2b|101631|PWWP domain containing 2B	AK158245|Pwwp2b|101631|PWWP domain containing 2B	BC116720|Pwwp2b|101631|PWWP domain containing 2B	AK165809|Pwwp2b|101631|PWWP domain containing 2B
mm9_v1_chr4_-_126210701_126210715	0.233797	SOX2.p2	NM_153177|Eif2c4|76850|eukaryotic translation initiation factor 2C, 4	AK030018|Eif2c4|76850|eukaryotic translation initiation factor 2C, 4
mm9_v1_chr11_+_96668506_96668525	0.233217	SOX2.p2	AK080243|Cbx1|12412|chromobox homolog 1 (Drosophila HP1 beta)	AK088236|Cbx1|12412|chromobox homolog 1 (Drosophila HP1 beta)
mm9_v1_chr3_+_87973934_87974022	0.232931	SOX2.p2	AK032042|Mef2d|17261|myocyte enhancer factor 2D
mm9_v1_chr4_+_103292164_103292269	0.232857	SOX2.p2	BC051993|Dab1|13131|disabled homolog 1 (Drosophila)
mm9_v1_chr5_-_24083185_24083284	0.232707	SOX2.p2	AK087990|Abcf2|27407|ATP-binding cassette, sub-family F (GCN20), member 2	AK137233|Abcf2|27407|ATP-binding cassette, sub-family F (GCN20), member 2	AK147937|Abcf2|27407|ATP-binding cassette, sub-family F (GCN20), member 2	AK151545|Abcf2|27407|ATP-binding cassette, sub-family F (GCN20), member 2	NM_001190443|Abcf2|27407|ATP-binding cassette, sub-family F (GCN20), member 2	NM_013853|Abcf2|27407|ATP-binding cassette, sub-family F (GCN20), member 2
mm9_v1_chr5_-_24781987_24782111	0.232624	SOX2.p2	AK077567|Mll3|231051|myeloid/lymphoid or mixed-lineage leukemia 3
mm9_v1_chr11_+_67779992_67780002	0.231611	SOX2.p2	AK166117|Stx8|55943|syntaxin 8	AF036716|Stx8|55943|syntaxin 8
mm9_v1_chr3_-_137794277_137794364	0.231548	SOX2.p2	L47970|Mttp|17777|microsomal triglyceride transfer protein	BC012686|Mttp|17777|microsomal triglyceride transfer protein	AK146553|Mttp|17777|microsomal triglyceride transfer protein	NM_008642|Mttp|17777|microsomal triglyceride transfer protein
mm9_v1_chr9_+_79914685_79914721	0.231154	SOX2.p2	AK053904|Senp6|215351|SUMO/sentrin specific peptidase 6	NM_146003|Senp6|215351|SUMO/sentrin specific peptidase 6
mm9_v1_chr2_+_71227270_71227349	0.230922	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_chr14_+_121310342_121310481	0.230422	SOX2.p2	AK161668|Ipo5|70572|importin 5	NM_023579|Ipo5|70572|importin 5	AK079134|Ipo5|70572|importin 5	AK049422|Ipo5|70572|importin 5	AK169664|Ipo5|70572|importin 5	AK053681|Ipo5|70572|importin 5	AK017701|Ipo5|70572|importin 5	AK167303|Ipo5|70572|importin 5	AF294327|Ipo5|70572|importin 5	BC052392|Ipo5|70572|importin 5
mm9_v1_chr2_-_77541328_77541435	0.230344	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_chr2_-_91773029_91773128	0.23003	SOX2.p2	
mm9_v1_chr2_-_77357674_77357722	0.229168	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_chr18_+_48206298_48206369	0.229103	SOX2.p2	
mm9_v1_chr4_-_131767968_131768170	0.2271	SOX2.p2	AK083882|Ythdf2|213541|YTH domain family 2	BC028994|Ythdf2|213541|YTH domain family 2	BC014797|Ythdf2|213541|YTH domain family 2	AK150350|Ythdf2|213541|YTH domain family 2	AK150669|Ythdf2|213541|YTH domain family 2	AK151392|Ythdf2|213541|YTH domain family 2	AK151862|Ythdf2|213541|YTH domain family 2	AK159548|Ythdf2|213541|YTH domain family 2	AK031616|Ythdf2|213541|YTH domain family 2	AK144209|Ythdf2|213541|YTH domain family 2	AK034655|Ythdf2|213541|YTH domain family 2	NM_145393|Ythdf2|213541|YTH domain family 2
mm9_v1_chr7_-_67285104_67285104	0.226338	SOX2.p2	NM_001082962|Snrpn|20646|small nuclear ribonucleoprotein N
mm9_v1_chr8_-_72441630_72441693	0.226306	SOX2.p2	
mm9_v1_chr2_+_127429570_127429640	0.22602	SOX2.p2	AK047438|Mrps5|77721|mitochondrial ribosomal protein S5
mm9_v1_chr2_+_181572558_181572632	0.225712	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_chr11_+_108781772_108781797	0.225644	SOX2.p2	AF073788|Axin2|12006|axin2
mm9_v1_chr4_+_116924633_116924654	0.224741	SOX2.p2	BC019937|Tmem53|68777|transmembrane protein 53	BC020121|Tmem53|68777|transmembrane protein 53	AK005104|Tmem53|68777|transmembrane protein 53
mm9_v1_chr8_-_89269823_89269841	0.22462	SOX2.p2	Z19579|Siah1a|20437|seven in absentia 1A
mm9_v1_chr11_+_77524899_77525029	0.223949	SOX2.p2	AK003251|Nufip2|68564|nuclear fragile X mental retardation protein interacting protein 2
mm9_v1_chr17_+_25325290_25325342	0.223055	SOX2.p2	AK054549|Unkl|74154|unkempt-like (Drosophila)
mm9_v1_chr2_+_84679564_84679595	0.222806	SOX2.p2	NM_001081349|Slc43a1|72401|solute carrier family 43, member 1	AK011417|Slc43a1|72401|solute carrier family 43, member 1	AK046758|Slc43a1|72401|solute carrier family 43, member 1	AK165374|Slc43a1|72401|solute carrier family 43, member 1	AB103034|Slc43a1|72401|solute carrier family 43, member 1
mm9_v1_chr7_+_53693190_53693196	0.222596	SOX2.p2	AK079373|Kcnc1|16502|potassium voltage gated channel, Shaw-related subfamily, member 1
mm9_v1_chr16_-_88826362_88826389	0.221931	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_chr12_+_70397702_70397722	0.221542	SOX2.p2	AK082528|Klhdc2|69554|kelch domain containing 2	AY513272|Klhdc2|69554|kelch domain containing 2
mm9_v1_chr5_-_117041815_117041859	0.221433	SOX2.p2	BC056392|Srrm4|68955|serine/arginine repetitive matrix 4	AK005085|Srrm4|68955|serine/arginine repetitive matrix 4	NM_026886|Srrm4|68955|serine/arginine repetitive matrix 4
mm9_v1_chr2_-_158187209_158187269	0.220719	SOX2.p2	AK046044|9430008C03Rik|68108|RIKEN cDNA 9430008C03 gene	AK040893|9430008C03Rik|68108|RIKEN cDNA 9430008C03 gene	AK007971|9430008C03Rik|68108|RIKEN cDNA 9430008C03 gene	AK079109|9430008C03Rik|68108|RIKEN cDNA 9430008C03 gene
mm9_v1_chr19_-_5799376_5799434	0.220589	SOX2.p2	AK020483|Malat1|72289|metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)
mm9_v1_chr11_-_106860750_106860783	0.218253	SOX2.p2	BC094011|Kpna2|16647|karyopherin (importin) alpha 2	BC106110|Kpna2|16647|karyopherin (importin) alpha 2	BC082280|Kpna2|16647|karyopherin (importin) alpha 2	BC086789|Kpna2|16647|karyopherin (importin) alpha 2	BC006720|Kpna2|16647|karyopherin (importin) alpha 2	BC003274|Kpna2|16647|karyopherin (importin) alpha 2	U12270|Kpna2|16647|karyopherin (importin) alpha 2	AK139850|Kpna2|16647|karyopherin (importin) alpha 2	AK166982|Kpna2|16647|karyopherin (importin) alpha 2	AK075952|Kpna2|16647|karyopherin (importin) alpha 2	AK088496|Kpna2|16647|karyopherin (importin) alpha 2	AK147135|Kpna2|16647|karyopherin (importin) alpha 2	AK165577|Kpna2|16647|karyopherin (importin) alpha 2	AK166790|Kpna2|16647|karyopherin (importin) alpha 2	AK167551|Kpna2|16647|karyopherin (importin) alpha 2	AK169283|Kpna2|16647|karyopherin (importin) alpha 2	AK166577|Kpna2|16647|karyopherin (importin) alpha 2
mm9_v1_chr9_-_44611055_44611072	0.217781	SOX2.p2	AK149384|Ttc36|192653|tetratricopeptide repeat domain 36
mm9_v1_chr5_-_136849232_136849238	0.217535	SOX2.p2	AF004225|Cux1|13047|cut-like homeobox 1
mm9_v1_chr1_+_45402907_45402949	0.216546	SOX2.p2	AK029451|Col3a1|12825|collagen, type III, alpha 1
mm9_v1_chr5_+_35384213_35384292	0.216478	SOX2.p2	AK165433|Hgfac|54426|hepatocyte growth factor activator	AK144554|Hgfac|54426|hepatocyte growth factor activator	BC019376|Hgfac|54426|hepatocyte growth factor activator	AK149522|Hgfac|54426|hepatocyte growth factor activator	AF099017|Hgfac|54426|hepatocyte growth factor activator	AF224724|Hgfac|54426|hepatocyte growth factor activator	AK075718|Hgfac|54426|hepatocyte growth factor activator
mm9_v1_chr2_+_48669675_48669676	0.215966	SOX2.p2	AK041246|Acvr2a|11480|activin receptor IIA
mm9_v1_chr15_-_96473193_96473343	0.215858	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_chr19_-_37250472_37250552	0.215708	SOX2.p2	AK147243|Cpeb3|208922|cytoplasmic polyadenylation element binding protein 3
mm9_v1_chr4_+_98213324_98213424	0.215645	SOX2.p2	NM_001005787|Inadl|12695|InaD-like (Drosophila)	NM_007704|Inadl|12695|InaD-like (Drosophila)	AF060539|Inadl|12695|InaD-like (Drosophila)
mm9_v1_chr8_+_35224310_35224396	0.215166	SOX2.p2	AK185123|Tmem66|67887|transmembrane protein 66	AK180893|Tmem66|67887|transmembrane protein 66	AK197284|Tmem66|67887|transmembrane protein 66	AK207744|Tmem66|67887|transmembrane protein 66	AK213493|Tmem66|67887|transmembrane protein 66	AK211246|Tmem66|67887|transmembrane protein 66
mm9_v1_chr9_-_73781373_73781373	0.214519	SOX2.p2	NM_001081153|Unc13c|208898|unc-13 homolog C (C. elegans)
mm9_v1_chr9_+_109954534_109954609	0.213052	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_chrX_+_102318792_102318798	0.212341	SOX2.p2	AK209904|Magee1|107528|melanoma antigen, family E, 1
mm9_v1_chr10_-_41738158_41738199	0.211883	SOX2.p2	AK011447|Armc2|213402|armadillo repeat containing 2	NM_001034858|Armc2|213402|armadillo repeat containing 2
mm9_v1_chr17_-_55851857_55851925	0.211024	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_chr14_+_14286471_14286627	0.210971	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_chr4_+_130225132_130225155	0.21079	SOX2.p2	AK154059|Pum1|80912|pumilio 1 (Drosophila)
mm9_v1_chr13_+_3477477_3477548	0.210255	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_chr6_-_23600205_23600304	0.209919	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_chr6_-_29129579_29129583	0.209836	SOX2.p2	BC140954|Prrt4|101359|proline-rich transmembrane protein 4	AK052319|Prrt4|101359|proline-rich transmembrane protein 4	NM_001101443|Prrt4|101359|proline-rich transmembrane protein 4
mm9_v1_chr8_-_59029657_59029687	0.209519	SOX2.p2	
mm9_v1_chr4_-_129419450_129419570	0.208852	SOX2.p2	BC002051|Khdrbs1|20218|KH domain containing, RNA binding, signal transduction associated 1	U17046|Khdrbs1|20218|KH domain containing, RNA binding, signal transduction associated 1	AK146815|Khdrbs1|20218|KH domain containing, RNA binding, signal transduction associated 1	U17961|Khdrbs1|20218|KH domain containing, RNA binding, signal transduction associated 1	AK150687|Khdrbs1|20218|KH domain containing, RNA binding, signal transduction associated 1	AK152084|Khdrbs1|20218|KH domain containing, RNA binding, signal transduction associated 1	NM_011317|Khdrbs1|20218|KH domain containing, RNA binding, signal transduction associated 1	AK044927|Khdrbs1|20218|KH domain containing, RNA binding, signal transduction associated 1	AK050520|Khdrbs1|20218|KH domain containing, RNA binding, signal transduction associated 1	AK137122|Khdrbs1|20218|KH domain containing, RNA binding, signal transduction associated 1
mm9_v1_chr11_+_86940545_86940631	0.208683	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_chr2_+_49307005_49307084	0.208489	SOX2.p2	NM_172663|Epc2|227867|enhancer of polycomb homolog 2 (Drosophila)	AK031025|Epc2|227867|enhancer of polycomb homolog 2 (Drosophila)
mm9_v1_chr13_+_113657736_113657889	0.208361	SOX2.p2	
mm9_v1_chr8_+_131248283_131248313	0.208289	SOX2.p2	AK085828|Itgb1|16412|integrin beta 1 (fibronectin receptor beta)	U37029|Itgb1|16412|integrin beta 1 (fibronectin receptor beta)
mm9_v1_chr10_-_126467848_126467902	0.208187	SOX2.p2	BC034286|Tsfm|66399|Ts translation elongation factor, mitochondrial	AK020437|Tsfm|66399|Ts translation elongation factor, mitochondrial	AK169164|Tsfm|66399|Ts translation elongation factor, mitochondrial	AK018591|Tsfm|66399|Ts translation elongation factor, mitochondrial	AK141183|Tsfm|66399|Ts translation elongation factor, mitochondrial	AK012240|Tsfm|66399|Ts translation elongation factor, mitochondrial	AK171656|Tsfm|66399|Ts translation elongation factor, mitochondrial	AK172112|Tsfm|66399|Ts translation elongation factor, mitochondrial	BC057904|Tsfm|66399|Ts translation elongation factor, mitochondrial	NM_025537|Tsfm|66399|Ts translation elongation factor, mitochondrial
mm9_v1_chr1_-_174149989_174150025	0.207796	SOX2.p2	NM_009813|Casq1|12372|calsequestrin 1
mm9_v1_chr15_-_72929166_72929248	0.20735	SOX2.p2	AK148725|2310051F07Rik|108745|RIKEN cDNA 2310051F07 gene
mm9_v1_chr2_-_180396124_180396180	0.206353	SOX2.p2	AK031764|Dido1|23856|death inducer-obliterator 1
mm9_v1_chr15_-_98781060_98781163	0.206196	SOX2.p2	M28729|Tuba1a|22142|tubulin, alpha 1A	AK201449|Tuba1a|22142|tubulin, alpha 1A
mm9_v1_chr14_-_32594734_32594785	0.20598	SOX2.p2	AK158845|3110068a07rik|73207|RIKEN cDNA 3110068A07 gene
mm9_v1_chr4_-_134828699_134828733	0.205832	SOX2.p2	AK170942|Clic4|29876|chloride intracellular channel 4 (mitochondrial)
mm9_v1_chr11_-_121084021_121084125	0.205708	SOX2.p2	AK215969|BC017643|217370|cDNA sequence BC017643
mm9_v1_chr4_-_148000832_148000895	0.205629	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_chr8_+_94881694_94881780	0.203611	SOX2.p2	BC056994|Irx5|54352|Iroquois related homeobox 5 (Drosophila)	NM_018826|Irx5|54352|Iroquois related homeobox 5 (Drosophila)
mm9_v1_chr5_-_137510950_137511054	0.203581	SOX2.p2	AK192071|Ap1s1|11769|adaptor protein complex AP-1, sigma 1
mm9_v1_chr15_+_85889141_85889301	0.203547	SOX2.p2	BC085148|Gramd4|223752|GRAM domain containing 4	AK142266|Gramd4|223752|GRAM domain containing 4
mm9_v1_chr7_+_52471122_52471152	0.202039	SOX2.p2	D50563|Tead2|21677|TEA domain family member 2	NM_011565|Tead2|21677|TEA domain family member 2
mm9_v1_chr7_+_111054855_111054855	0.201965	SOX2.p2	BC137766|Olfr65|18365|olfactory receptor 65	NM_013616|Olfr65|18365|olfactory receptor 65
mm9_v1_chr8_-_108467275_108467292	0.201865	SOX2.p2	AK004914|Lcat|16816|lecithin cholesterol acyltransferase	J05154|Lcat|16816|lecithin cholesterol acyltransferase	BC028861|Lcat|16816|lecithin cholesterol acyltransferase
mm9_v1_chr11_-_115884712_115884736	0.20113	SOX2.p2	AK213191|H3f3b|15081|H3 histone, family 3B
mm9_v1_chr9_-_123626642_123626742	0.201081	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_chr18_+_35750406_35750586	0.200785	SOX2.p2	AK139050|Matr3|17184|matrin 3	AK084822|Matr3|17184|matrin 3	AK148059|Matr3|17184|matrin 3
mm9_v1_chr13_-_25112189_25112247	0.200588	SOX2.p2	NM_001013389|Mrs2|380836|MRS2 magnesium homeostasis factor homolog (S. cerevisiae)
mm9_v1_chr18_+_3383216_3383321	0.200563	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_chr2_-_71384748_71384810	0.199919	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_chr17_+_24078962_24078969	0.199448	SOX2.p2	BC049605|Sbp|20234|spermine binding protein	NM_011321|Sbp|20234|spermine binding protein	X06246|Sbp|20234|spermine binding protein
mm9_v1_chr6_-_23082901_23082994	0.199355	SOX2.p2	AK149400|Aass|30956|aminoadipate-semialdehyde synthase	AK098141|Aass|30956|aminoadipate-semialdehyde synthase	AK136216|Aass|30956|aminoadipate-semialdehyde synthase	BC005420|Aass|30956|aminoadipate-semialdehyde synthase	AK044323|Aass|30956|aminoadipate-semialdehyde synthase	NM_013930|Aass|30956|aminoadipate-semialdehyde synthase
mm9_v1_chrX_-_98417753_98417901	0.198087	SOX2.p2	AK168604|Snx12|55988|sorting nexin 12	AK011257|Snx12|55988|sorting nexin 12	AK170403|Snx12|55988|sorting nexin 12	AK049561|Snx12|55988|sorting nexin 12	AK146833|Snx12|55988|sorting nexin 12	AF062484|Snx12|55988|sorting nexin 12	BC002009|Snx12|55988|sorting nexin 12	AK148235|Snx12|55988|sorting nexin 12	AK169569|Snx12|55988|sorting nexin 12	AK170992|Snx12|55988|sorting nexin 12	AK131838|Snx12|55988|sorting nexin 12	NM_001110310|Snx12|55988|sorting nexin 12	NM_001110311|Snx12|55988|sorting nexin 12	NM_018875|Snx12|55988|sorting nexin 12
mm9_v1_chr15_+_97942484_97942592	0.197687	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_chr19_+_12284057_12284057	0.197598	SOX2.p2	BC133710|Olfr1431|258409|olfactory receptor 1431	NM_146414|Olfr1431|258409|olfactory receptor 1431
mm9_v1_chr3_-_88306724_88306855	0.197542	SOX2.p2	AK180919|Lmna|16905|lamin A
mm9_v1_chr17_-_65929913_65929945	0.197498	SOX2.p2	
mm9_v1_chr4_+_126803305_126803317	0.197468	SOX2.p2	AK156456|Gm12942|100039968|predicted gene 12942
mm9_v1_chr13_-_74199688_74199784	0.197339	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_chr5_-_133017901_133018025	0.19659	SOX2.p2	AK085946|Auts2|319974|autism susceptibility candidate 2
mm9_v1_chr4_-_118862555_118862615	0.195274	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_-_6918703_6918738	0.195236	SOX2.p2	AK051947|Tox|252838|thymocyte selection-associated high mobility group box
mm9_v1_chr6_-_28084368_28084420	0.195094	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_chr17_-_37400606_37400693	0.194858	SOX2.p2	NM_146510|Olfr98|258503|olfactory receptor 98	BC134363|Olfr97|258505|olfactory receptor 97	BC119060|Olfr98|258503|olfactory receptor 98	BC120744|Olfr98|258503|olfactory receptor 98
mm9_v1_chr2_-_88842442_88842446	0.19435	SOX2.p2	BC127970|Olfr1215|258451|olfactory receptor 1215	NM_146459|Olfr1215|258451|olfactory receptor 1215
mm9_v1_chr7_-_133929571_133929602	0.193548	SOX2.p2	AK211564|Ppp4c|56420|protein phosphatase 4, catalytic subunit
mm9_v1_chr5_+_34338625_34338665	0.192868	SOX2.p2	AK147307|Nat8l|269642|N-acetyltransferase 8-like	NM_001001985|Nat8l|269642|N-acetyltransferase 8-like
mm9_v1_chr8_+_13705888_13705888	0.190908	SOX2.p2	AK038767|4932443I19Rik|403185|RIKEN cDNA 4932443I19 gene	NM_001101519|4932443I19Rik|403185|RIKEN cDNA 4932443I19 gene
mm9_v1_chrX_-_102052460_102052605	0.190042	SOX2.p2	BC132640|Magee2|272790|melanoma antigen, family E, 2	BC138210|Magee2|272790|melanoma antigen, family E, 2	BC094361|Magee2|272790|melanoma antigen, family E, 2	AK134670|Magee2|272790|melanoma antigen, family E, 2	AK036343|Magee2|272790|melanoma antigen, family E, 2	NM_053206|Magee2|272790|melanoma antigen, family E, 2
mm9_v1_chr14_+_30791522_30791616	0.189779	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_chr15_-_72926936_72926959	0.189686	SOX2.p2	AK003962|1110029L17Rik|68722|RIKEN cDNA 1110029L17 gene
mm9_v1_chr12_+_75028976_75029036	0.188996	SOX2.p2	AK076395|Hif1a|15251|hypoxia inducible factor 1, alpha subunit
mm9_v1_chr12_-_21396339_21396369	0.188252	SOX2.p2	
mm9_v1_chr7_-_125629996_125630002	0.187865	SOX2.p2	AK164927|Itpripl2|319622|inositol 1,4,5-triphosphate receptor interacting protein-like 2	AK081844|Itpripl2|319622|inositol 1,4,5-triphosphate receptor interacting protein-like 2
mm9_v1_chr18_+_76219111_76219147	0.187379	SOX2.p2	BC018187|Zbtb7c|207259|zinc finger and BTB domain containing 7C	AK156372|Zbtb7c|207259|zinc finger and BTB domain containing 7C
mm9_v1_chr2_+_145686480_145686484	0.187179	SOX2.p2	AK171064|Rin2|74030|Ras and Rab interactor 2
mm9_v1_chr17_-_37451325_37451381	0.186766	SOX2.p2	BC111097|Olfr100|404307|olfactory receptor 100	BC127233|Olfr100|404307|olfactory receptor 100	BC127234|Olfr100|404307|olfactory receptor 100	NM_207673|Olfr100|404307|olfactory receptor 100	BC139114|Olfr102|258218|olfactory receptor 102	BC139115|Olfr102|258218|olfactory receptor 102	NM_001011721|Olfr102|258218|olfactory receptor 102
mm9_v1_chr9_-_15084310_15084404	0.186457	SOX2.p2	BC020185|Med17|234959|mediator complex subunit 17	NM_144933|Med17|234959|mediator complex subunit 17	AK033151|Med17|234959|mediator complex subunit 17	AK142033|Med17|234959|mediator complex subunit 17	AK038451|Med17|234959|mediator complex subunit 17	AK049112|Med17|234959|mediator complex subunit 17	AK151377|Med17|234959|mediator complex subunit 17
mm9_v1_chr1_+_169287454_169287527	0.185738	SOX2.p2	AK179746|Aldh9a1|56752|aldehyde dehydrogenase 9, subfamily A1	AK180861|Aldh9a1|56752|aldehyde dehydrogenase 9, subfamily A1	AK184027|Aldh9a1|56752|aldehyde dehydrogenase 9, subfamily A1	AK188805|Aldh9a1|56752|aldehyde dehydrogenase 9, subfamily A1	AK199575|Aldh9a1|56752|aldehyde dehydrogenase 9, subfamily A1	AK203750|Aldh9a1|56752|aldehyde dehydrogenase 9, subfamily A1	AK211951|Aldh9a1|56752|aldehyde dehydrogenase 9, subfamily A1
mm9_v1_chr19_-_4801605_4801652	0.185362	SOX2.p2	
mm9_v1_chr10_+_41250456_41250646	0.185098	SOX2.p2	AK217133|Cd164|53599|CD164 antigen	AK135616|Cd164|53599|CD164 antigen
mm9_v1_chr5_+_17468366_17468438	0.184915	SOX2.p2	BC147449|Gnat3|242851|guanine nucleotide binding protein, alpha transducing 3	BC147466|Gnat3|242851|guanine nucleotide binding protein, alpha transducing 3	AK040065|Gnat3|242851|guanine nucleotide binding protein, alpha transducing 3	NM_001081143|Gnat3|242851|guanine nucleotide binding protein, alpha transducing 3	BC147839|Gnat3|242851|guanine nucleotide binding protein, alpha transducing 3	BC147841|Gnat3|242851|guanine nucleotide binding protein, alpha transducing 3
mm9_v1_chr15_+_81626455_81626512	0.184879	SOX2.p2	AJ223207|Zc3h7b|20286|zinc finger CCCH type containing 7B
mm9_v1_chr14_+_8767143_8767187	0.183615	SOX2.p2	AK172258|Flnb|286940|filamin, beta
mm9_v1_chr13_+_89680457_89680462	0.18353	SOX2.p2	AK048107|Hapln1|12950|hyaluronan and proteoglycan link protein 1	AK003582|Hapln1|12950|hyaluronan and proteoglycan link protein 1
mm9_v1_chr14_-_60059565_60059740	0.183453	SOX2.p2	EU155090|Setdb2|239122|SET domain, bifurcated 2	EU155091|Setdb2|239122|SET domain, bifurcated 2	EU155093|Setdb2|239122|SET domain, bifurcated 2	EU155094|Setdb2|239122|SET domain, bifurcated 2	BC157926|Setdb2|239122|SET domain, bifurcated 2	BC172021|Setdb2|239122|SET domain, bifurcated 2	EU155092|Setdb2|239122|SET domain, bifurcated 2	EU155098|Setdb2|239122|SET domain, bifurcated 2	EU155099|Setdb2|239122|SET domain, bifurcated 2	EU155095|Setdb2|239122|SET domain, bifurcated 2	EU155097|Setdb2|239122|SET domain, bifurcated 2	AK089197|Setdb2|239122|SET domain, bifurcated 2	NM_001081024|Setdb2|239122|SET domain, bifurcated 2
mm9_v1_chr6_-_119913623_119913750	0.183426	SOX2.p2	BC146009|Wnk1|232341|WNK lysine deficient protein kinase 1	BC146011|Wnk1|232341|WNK lysine deficient protein kinase 1
mm9_v1_chr13_-_45648492_45648493	0.183173	SOX2.p2	AK019314|2900016G23Rik|78659|RIKEN cDNA 2900016G23 gene
mm9_v1_chr7_-_87543749_87543798	0.182929	SOX2.p2	X54056|Furin|18550|furin (paired basic amino acid cleaving enzyme)	BC048234|Furin|18550|furin (paired basic amino acid cleaving enzyme)
mm9_v1_chr13_-_13325178_13325235	0.182842	SOX2.p2	AK184566|Ywhaq|22630|tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide	AK187011|Ywhaq|22630|tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide
mm9_v1_chr7_+_28964518_28964559	0.182701	SOX2.p2	AK148342|Dyrk1b|13549|dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1b
mm9_v1_chr10_-_128397928_128398043	0.181974	SOX2.p2	BC024898|Mettl7b|71664|methyltransferase like 7B	AK002239|Mettl7b|71664|methyltransferase like 7B	NM_027853|Mettl7b|71664|methyltransferase like 7B
mm9_v1_chr1_+_44040367_44040379	0.18191	SOX2.p2	AK214518|Tpp2|22019|tripeptidyl peptidase II
mm9_v1_chr9_+_108698323_108698461	0.181289	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_chr19_+_46227031_46227037	0.181186	SOX2.p2	AK143358|Gbf1|107338|golgi-specific brefeldin A-resistance factor 1
mm9_v1_chr8_+_86132073_86132203	0.181049	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_chr2_-_72931338_72931457	0.181046	SOX2.p2	
mm9_v1_chr16_-_45844409_45844495	0.180888	SOX2.p2	AK165251|Phldb2|208177|pleckstrin homology-like domain, family B, member 2	AF506821|Phldb2|208177|pleckstrin homology-like domain, family B, member 2	NM_153412|Phldb2|208177|pleckstrin homology-like domain, family B, member 2
mm9_v1_chr2_-_155183133_155183168	0.180192	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_chr18_+_31963757_31963829	0.179965	SOX2.p2	BC030076|Wdr33|74320|WD repeat domain 33	BC011156|Wdr33|74320|WD repeat domain 33	BC064745|Wdr33|74320|WD repeat domain 33
mm9_v1_chr13_+_49678115_49678143	0.179587	SOX2.p2	AB007848|Omd|27047|osteomodulin	NM_012050|Omd|27047|osteomodulin	BC095997|Omd|27047|osteomodulin
mm9_v1_chr2_-_156688501_156688698	0.179328	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_chr13_+_47138896_47138963	0.179222	SOX2.p2	NM_172262|Kdm1b|218214|lysine (K)-specific demethylase 1B	BC023917|Kdm1b|218214|lysine (K)-specific demethylase 1B
mm9_v1_chr10_-_7400836_7400969	0.179048	SOX2.p2	AK030763|BC020402|407824|cDNA sequence BC020402	BC020402|BC020402|407824|cDNA sequence BC020402	AK132475|BC020402|407824|cDNA sequence BC020402
mm9_v1_chr6_-_51419726_51419880	0.178737	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_chr13_-_58316923_58316959	0.178608	SOX2.p2	AK048534|Ubqln1|56085|ubiquilin 1	BC028857|Ubqln1|56085|ubiquilin 1
mm9_v1_chr2_+_88231404_88231405	0.178395	SOX2.p2	BC140109|Olfr1178|258203|olfactory receptor 1178	BC140153|Olfr1178|258203|olfactory receptor 1178	BC143174|Olfr1178|258203|olfactory receptor 1178	NM_001011868|Olfr1178|258203|olfactory receptor 1178
mm9_v1_chr14_+_37881214_37881259	0.178137	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_chr8_-_107813357_107813427	0.177968	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_chr3_+_67406958_67407063	0.177678	SOX2.p2	AK171855|Mfsd1|66868|major facilitator superfamily domain containing 1
mm9_v1_chr19_+_4878667_4878752	0.177553	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_chr4_-_148800731_148800857	0.177089	SOX2.p2	AK016689|Ube4b|63958|ubiquitination factor E4B, UFD2 homolog (S. cerevisiae)	NM_022022|Ube4b|63958|ubiquitination factor E4B, UFD2 homolog (S. cerevisiae)	AF260926|Ube4b|63958|ubiquitination factor E4B, UFD2 homolog (S. cerevisiae)
mm9_v1_chr9_-_108984865_108984900	0.17655	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_-_44613544_44613680	0.176166	SOX2.p2	
mm9_v1_chr7_+_53138934_53138972	0.176076	SOX2.p2	
mm9_v1_chr11_+_67779978_67779989	0.175465	SOX2.p2	AK035105|Stx8|55943|syntaxin 8	BC048167|Stx8|55943|syntaxin 8	NM_018768|Stx8|55943|syntaxin 8	BC038186|Stx8|55943|syntaxin 8	AF093064|Stx8|55943|syntaxin 8	AB040054|Stx8|55943|syntaxin 8
mm9_v1_chr8_+_91115856_91115922	0.175353	SOX2.p2	AK192443|Nkd1|93960|naked cuticle 1 homolog (Drosophila)	AK193874|Nkd1|93960|naked cuticle 1 homolog (Drosophila)
mm9_v1_chr12_+_58331420_58331438	0.174538	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_chr4_-_151235861_151235879	0.174468	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_chr19_-_14671832_14671910	0.174199	SOX2.p2	AF229633|Tle4|21888|transducin-like enhancer of split 4, homolog of Drosophila E(spl)
mm9_v1_chr18_+_65210574_65210693	0.173635	SOX2.p2	BC082281|Nedd4l|83814|neural precursor cell expressed, developmentally down-regulated gene 4-like
mm9_v1_chr3_+_9403021_9403077	0.173263	SOX2.p2	AK039918|C030034L19Rik|320088|RIKEN cDNA C030034L19 gene	AK053975|C030034L19Rik|320088|RIKEN cDNA C030034L19 gene	AK081263|C030034L19Rik|320088|RIKEN cDNA C030034L19 gene	AK030949|C030034L19Rik|320088|RIKEN cDNA C030034L19 gene
mm9_v1_chr3_+_45182311_45182350	0.172797	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_chr19_+_46227029_46227030	0.172793	SOX2.p2	AK039570|Gbf1|107338|golgi-specific brefeldin A-resistance factor 1
mm9_v1_chr17_+_34701239_34701309	0.172684	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_chr12_+_37968225_37968446	0.172455	SOX2.p2	AK040702|Tmem195|319660|transmembrane protein 195	NM_178767|Tmem195|319660|transmembrane protein 195	BC038044|Tmem195|319660|transmembrane protein 195	AK050246|Tmem195|319660|transmembrane protein 195	AK163155|Tmem195|319660|transmembrane protein 195
mm9_v1_chr2_+_173603706_173603746	0.172314	SOX2.p2	BC024562|Vapb|56491|vesicle-associated membrane protein, associated protein B and C	AK205322|Vapb|56491|vesicle-associated membrane protein, associated protein B and C	AK182293|Vapb|56491|vesicle-associated membrane protein, associated protein B and C
mm9_v1_chr11_+_64792527_64792682	0.172069	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_chr11_+_97177029_97177191	0.171871	SOX2.p2	NM_025927|Mrpl45|67036|mitochondrial ribosomal protein L45	AK011163|Mrpl45|67036|mitochondrial ribosomal protein L45	AK011605|Mrpl45|67036|mitochondrial ribosomal protein L45	AK081922|Mrpl45|67036|mitochondrial ribosomal protein L45	AK157771|Mrpl45|67036|mitochondrial ribosomal protein L45	BC020130|Mrpl45|67036|mitochondrial ribosomal protein L45	AK198473|Mrpl45|67036|mitochondrial ribosomal protein L45
mm9_v1_chrX_+_39503858_39503966	0.171852	SOX2.p2	AK146718|Stag2|20843|stromal antigen 2	AK168899|Stag2|20843|stromal antigen 2	NM_021465|Stag2|20843|stromal antigen 2
mm9_v1_chr8_+_94192087_94192089	0.171795	SOX2.p2	
mm9_v1_chr2_+_58607580_58607600	0.171666	SOX2.p2	AY152393|Upp2|76654|uridine phosphorylase 2	NM_029692|Upp2|76654|uridine phosphorylase 2	AK149444|Upp2|76654|uridine phosphorylase 2
mm9_v1_chr18_-_35113995_35113999	0.17161	SOX2.p2	AK030299|Hspa9|15526|heat shock protein 9	AK145965|Hspa9|15526|heat shock protein 9	AK167856|Hspa9|15526|heat shock protein 9
mm9_v1_chrX_-_9694712_9694834	0.170623	SOX2.p2	AB028049|Srpx|51795|sushi-repeat-containing protein	AB028050|Srpx|51795|sushi-repeat-containing protein	BC022572|Srpx|51795|sushi-repeat-containing protein	AK034696|Srpx|51795|sushi-repeat-containing protein	NM_016911|Srpx|51795|sushi-repeat-containing protein	BC027630|Srpx|51795|sushi-repeat-containing protein	AK159662|Srpx|51795|sushi-repeat-containing protein
mm9_v1_chr8_+_26629736_26629790	0.169827	SOX2.p2	S47233|Fgfr1|14182|fibroblast growth factor receptor 1	AK028354|Fgfr1|14182|fibroblast growth factor receptor 1
mm9_v1_chr11_-_100122302_100122344	0.169527	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_chr7_-_107663293_107663468	0.169205	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_chr2_+_156688814_156688934	0.169197	SOX2.p2	NM_026124|1110008F13Rik|67388|RIKEN cDNA 1110008F13 gene	AK003568|1110008F13Rik|67388|RIKEN cDNA 1110008F13 gene	AK078178|1110008F13Rik|67388|RIKEN cDNA 1110008F13 gene	AK031002|1110008F13Rik|67388|RIKEN cDNA 1110008F13 gene	AK002452|1110008F13Rik|67388|RIKEN cDNA 1110008F13 gene	AK155559|1110008F13Rik|67388|RIKEN cDNA 1110008F13 gene	BC019445|1110008F13Rik|67388|RIKEN cDNA 1110008F13 gene
mm9_v1_chr14_+_55713609_55713673	0.16918	SOX2.p2	NM_153083|Thtpa|105663|thiamine triphosphatase
mm9_v1_chr3_+_88500529_88500661	0.169061	SOX2.p2	AK193095|2810403A07Rik|74200|RIKEN cDNA 2810403A07 gene
mm9_v1_chr11_+_98630271_98630309	0.168832	SOX2.p2	AK053029|Nr1d1|217166|nuclear receptor subfamily 1, group D, member 1
mm9_v1_chr8_+_35870347_35870357	0.168441	SOX2.p2	AK165991|Dusp4|319520|dual specificity phosphatase 4
mm9_v1_chr9_+_107949197_107949310	0.167786	SOX2.p2	
mm9_v1_chr13_-_14615371_14615494	0.167039	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_chr16_+_23224889_23224926	0.166788	SOX2.p2	BC096026|St6gal1|20440|beta galactoside alpha 2,6 sialyltransferase 1	AF153680|St6gal1|20440|beta galactoside alpha 2,6 sialyltransferase 1
mm9_v1_chr4_-_135429739_135429747	0.166746	SOX2.p2	AK012073|Pnrc2|52830|proline-rich nuclear receptor coactivator 2	AK013163|Pnrc2|52830|proline-rich nuclear receptor coactivator 2	AK031048|Pnrc2|52830|proline-rich nuclear receptor coactivator 2	AK075816|Pnrc2|52830|proline-rich nuclear receptor coactivator 2
mm9_v1_chrX_-_16896428_16896493	0.166485	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_chr16_-_45724422_45724643	0.166484	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_chr8_+_74675802_74675827	0.166285	SOX2.p2	
mm9_v1_chr1_+_91476810_91476856	0.165429	SOX2.p2	AK147521|Agap1|347722|ArfGAP with GTPase domain, ankyrin repeat and PH domain 1
mm9_v1_chr2_-_22751051_22751075	0.165162	SOX2.p2	AK079472|A130006I12Rik|319264|RIKEN cDNA A130006I12 gene
mm9_v1_chr2_-_155937623_155937702	0.165059	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_chr6_-_85087735_85087775	0.164841	SOX2.p2	BC054423|Spr|20751|sepiapterin reductase	BC010400|Spr|20751|sepiapterin reductase	AK004941|Spr|20751|sepiapterin reductase	NM_011467|Spr|20751|sepiapterin reductase	AK154720|Spr|20751|sepiapterin reductase	S77493|Spr|20751|sepiapterin reductase
mm9_v1_chr1_-_21069242_21069313	0.16484	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_chr17_-_85461840_85461859	0.164031	SOX2.p2	AK019367|Prepl|213760|prolyl endopeptidase-like
mm9_v1_chr3_+_51299153_51299205	0.163991	SOX2.p2	
mm9_v1_chr4_-_118081793_118081882	0.163395	SOX2.p2	GU433214|Szt2|230676|seizure threshold 2	FJ998170|Szt2|230676|seizure threshold 2	NM_198170|Szt2|230676|seizure threshold 2
mm9_v1_chr13_-_34222209_34222227	0.162839	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_chr14_-_64162810_64162839	0.162744	SOX2.p2	AK044957|Mtmr9|210376|myotubularin related protein 9
mm9_v1_chr6_+_113573980_113574047	0.162466	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_chr8_-_48373564_48373676	0.162314	SOX2.p2	BC099949|Stox2|71069|storkhead box 2
mm9_v1_chr17_-_35203114_35203128	0.162118	SOX2.p2	GU269270|AU023871|106722|expressed sequence AU023871	AK137516|AU023871|106722|expressed sequence AU023871	NM_001033221|AU023871|106722|expressed sequence AU023871	NM_001191012|AU023871|106722|expressed sequence AU023871
mm9_v1_chr1_+_44176812_44176851	0.161736	SOX2.p2	AK047404|Bivm|246229|basic, immunoglobulin-like variable motif containing	NM_144558|Bivm|246229|basic, immunoglobulin-like variable motif containing	AK032375|Bivm|246229|basic, immunoglobulin-like variable motif containing	AK034329|Bivm|246229|basic, immunoglobulin-like variable motif containing
mm9_v1_chr5_+_37729746_37729775	0.161644	SOX2.p2	BC037473|Evc2|68525|Ellis van Creveld syndrome 2 homolog (human)
mm9_v1_chr1_+_137695997_137696087	0.161602	SOX2.p2	AJ242874|Tnni1|21952|troponin I, skeletal, slow 1	NM_021467|Tnni1|21952|troponin I, skeletal, slow 1	AK012258|Tnni1|21952|troponin I, skeletal, slow 1	NM_001112702|Tnni1|21952|troponin I, skeletal, slow 1
mm9_v1_chr15_+_6395311_6395349	0.161496	SOX2.p2	BC011137|C9|12279|complement component 9	NM_013485|C9|12279|complement component 9
mm9_v1_chr14_+_30781514_30781692	0.161089	SOX2.p2	NM_019979|Selk|80795|selenoprotein K	AK008419|Selk|80795|selenoprotein K	BC038049|Selk|80795|selenoprotein K	AK003206|Selk|80795|selenoprotein K	BC096677|Selk|80795|selenoprotein K	AK007523|Selk|80795|selenoprotein K	AK006674|Selk|80795|selenoprotein K	BC096044|Selk|80795|selenoprotein K
mm9_v1_chr14_+_61351770_61351875	0.160916	SOX2.p2	AK151394|Spata13|219140|spermatogenesis associated 13
mm9_v1_chr1_-_162142846_162143024	0.160877	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_chr2_-_30823346_30823454	0.159868	SOX2.p2	AK082936|Tor1a|30931|torsin family 1, member A (torsin A)	AK079728|Tor1a|30931|torsin family 1, member A (torsin A)	AJ298841|Tor1a|30931|torsin family 1, member A (torsin A)	AK038891|Tor1a|30931|torsin family 1, member A (torsin A)	AK160361|Tor1a|30931|torsin family 1, member A (torsin A)	BC017683|Tor1a|30931|torsin family 1, member A (torsin A)	NM_144884|Tor1a|30931|torsin family 1, member A (torsin A)
mm9_v1_chr10_-_120416369_120416397	0.159794	SOX2.p2	AF112300|Lemd3|380664|LEM domain containing 3	NM_001081193|Lemd3|380664|LEM domain containing 3
mm9_v1_chr3_+_33707638_33707720	0.159719	SOX2.p2	AK016428|Ttc14|67120|tetratricopeptide repeat domain 14	BC103802|Ttc14|67120|tetratricopeptide repeat domain 14
mm9_v1_chr19_+_46576137_46576194	0.158748	SOX2.p2	NM_053100|Trim8|93679|tripartite motif-containing 8	AK155303|Trim8|93679|tripartite motif-containing 8
mm9_v1_chrX_-_91787372_91787452	0.158482	SOX2.p2	AB029448|Maged1|94275|melanoma antigen, family D, 1	NM_019791|Maged1|94275|melanoma antigen, family D, 1
mm9_v1_chr3_-_79371600_79371778	0.157985	SOX2.p2	NM_001162999|Fnip2|329679|folliculin interacting protein 2
mm9_v1_chr17_+_37139856_37139982	0.157746	SOX2.p2	D21850|Zfp57|22715|zinc finger protein 57
mm9_v1_chr2_-_118305356_118305444	0.157337	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_chr7_+_104100067_104100098	0.156945	SOX2.p2	AK164179|Nars2|244141|asparaginyl-tRNA synthetase 2 (mitochondrial)(putative)	AK047091|Nars2|244141|asparaginyl-tRNA synthetase 2 (mitochondrial)(putative)	AK050718|Nars2|244141|asparaginyl-tRNA synthetase 2 (mitochondrial)(putative)
mm9_v1_chr5_+_90947970_90948068	0.156894	SOX2.p2	AK143987|Afm|280662|afamin	BC100597|Afm|280662|afamin	NM_145146|Afm|280662|afamin	BC026681|Afm|280662|afamin
mm9_v1_chr9_+_106073255_106073259	0.156705	SOX2.p2	AK037620|Wdr82|77305|WD repeat domain containing 82	AK035109|Wdr82|77305|WD repeat domain containing 82	AK149692|Wdr82|77305|WD repeat domain containing 82	AK159240|Wdr82|77305|WD repeat domain containing 82	AK172474|Wdr82|77305|WD repeat domain containing 82	NM_029896|Wdr82|77305|WD repeat domain containing 82
mm9_v1_chr5_-_135164426_135164540	0.156411	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_chr1_+_52901772_52901974	0.156362	SOX2.p2	BC026437|Hibch|227095|3-hydroxyisobutyryl-Coenzyme A hydrolase	NM_146108|Hibch|227095|3-hydroxyisobutyryl-Coenzyme A hydrolase	AK076038|Hibch|227095|3-hydroxyisobutyryl-Coenzyme A hydrolase	AK082965|Hibch|227095|3-hydroxyisobutyryl-Coenzyme A hydrolase	AK216816|Hibch|227095|3-hydroxyisobutyryl-Coenzyme A hydrolase
mm9_v1_chr2_-_152142120_152142187	0.156316	SOX2.p2	
mm9_v1_chr9_-_16182674_16182674	0.15599	SOX2.p2	NM_001080814|Fat3|270120|FAT tumor suppressor homolog 3 (Drosophila)
mm9_v1_chr15_-_37389073_37389150	0.155984	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_chr7_-_134537132_134537134	0.155766	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_chr19_+_4962305_4962355	0.155563	SOX2.p2	NM_025553|Mrpl11|66419|mitochondrial ribosomal protein L11	AK010329|Mrpl11|66419|mitochondrial ribosomal protein L11	AB049639|Mrpl11|66419|mitochondrial ribosomal protein L11	AK167247|Mrpl11|66419|mitochondrial ribosomal protein L11	AK002797|Mrpl11|66419|mitochondrial ribosomal protein L11	BC046750|Mrpl11|66419|mitochondrial ribosomal protein L11
mm9_v1_chr5_+_17080553_17080681	0.15502	SOX2.p2	AK034239|Sema3c|20348|sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	AK078589|Sema3c|20348|sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	BC066852|Sema3c|20348|sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	NM_013657|Sema3c|20348|sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	X85994|Sema3c|20348|sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C
mm9_v1_chr3_-_53267127_53267244	0.154894	SOX2.p2	AK133986|Nhlrc3|212114|NHL repeat containing 3	BC087903|Nhlrc3|212114|NHL repeat containing 3	BC107356|Nhlrc3|212114|NHL repeat containing 3	AK029465|Nhlrc3|212114|NHL repeat containing 3	AK033167|Nhlrc3|212114|NHL repeat containing 3	NM_172501|Nhlrc3|212114|NHL repeat containing 3	AK162824|Nhlrc3|212114|NHL repeat containing 3	AK220477|Nhlrc3|212114|NHL repeat containing 3
mm9_v1_chr5_-_134790544_134790615	0.154891	SOX2.p2	AF017085|Gtf2i|14886|general transcription factor II I	AY030290|Gtf2i|14886|general transcription factor II I	AY030291|Gtf2i|14886|general transcription factor II I	AY030292|Gtf2i|14886|general transcription factor II I	AY030293|Gtf2i|14886|general transcription factor II I	AK147201|Gtf2i|14886|general transcription factor II I	BC053044|Gtf2i|14886|general transcription factor II I	NM_001080746|Gtf2i|14886|general transcription factor II I	NM_001080747|Gtf2i|14886|general transcription factor II I	NM_001080748|Gtf2i|14886|general transcription factor II I	NM_001080749|Gtf2i|14886|general transcription factor II I	NM_010365|Gtf2i|14886|general transcription factor II I
mm9_v1_chr5_+_73305509_73305751	0.154847	SOX2.p2	NM_001113423|Slain2|75991|SLAIN motif family, member 2	NM_153567|Slain2|75991|SLAIN motif family, member 2	AK146432|Slain2|75991|SLAIN motif family, member 2	AK129365|Slain2|75991|SLAIN motif family, member 2	BC010836|Slain2|75991|SLAIN motif family, member 2	AK033137|Slain2|75991|SLAIN motif family, member 2	AK039970|Slain2|75991|SLAIN motif family, member 2	BC076573|Slain2|75991|SLAIN motif family, member 2
mm9_v1_chr2_-_152657392_152657404	0.154785	SOX2.p2	AK150028|Bcl2l1|12048|BCL2-like 1
mm9_v1_chr5_+_33361571_33361768	0.154685	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_chr2_-_168415690_168415866	0.154487	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_+_135142673_135142702	0.154458	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_chr11_+_101115016_101115073	0.15441	SOX2.p2	AK150822|Vps25|28084|vacuolar protein sorting 25 (yeast)	AK082933|Vps25|28084|vacuolar protein sorting 25 (yeast)	AK166008|Vps25|28084|vacuolar protein sorting 25 (yeast)	AK145811|Vps25|28084|vacuolar protein sorting 25 (yeast)	AK162230|Vps25|28084|vacuolar protein sorting 25 (yeast)	AK003715|Vps25|28084|vacuolar protein sorting 25 (yeast)	BC029181|Vps25|28084|vacuolar protein sorting 25 (yeast)	NM_026776|Vps25|28084|vacuolar protein sorting 25 (yeast)	AK002500|Vps25|28084|vacuolar protein sorting 25 (yeast)	AK003877|Vps25|28084|vacuolar protein sorting 25 (yeast)	AK005149|Vps25|28084|vacuolar protein sorting 25 (yeast)
mm9_v1_chr7_+_35905996_35906277	0.15434	SOX2.p2	BC106174|Cebpa|12606|CCAAT/enhancer binding protein (C/EBP), alpha	AK160443|Cebpa|12606|CCAAT/enhancer binding protein (C/EBP), alpha
mm9_v1_chr12_-_58646914_58647013	0.153891	SOX2.p2	X74936|Foxa1|15375|forkhead box A1	U44752|Foxa1|15375|forkhead box A1
mm9_v1_chr9_+_75623899_75624064	0.153841	SOX2.p2	L41145|Bmp5|12160|bone morphogenetic protein 5	BC100751|Bmp5|12160|bone morphogenetic protein 5	BC100752|Bmp5|12160|bone morphogenetic protein 5	BC100753|Bmp5|12160|bone morphogenetic protein 5	BC100754|Bmp5|12160|bone morphogenetic protein 5	AK160412|Bmp5|12160|bone morphogenetic protein 5
mm9_v1_chr11_+_87912709_87912809	0.153688	SOX2.p2	BC025434|Cuedc1|103841|CUE domain containing 1	BC024476|Cuedc1|103841|CUE domain containing 1
mm9_v1_chr18_-_21458623_21458645	0.153619	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_chr8_-_18741455_18741532	0.153396	SOX2.p2	BC138309|Angpt2|11601|angiopoietin 2	BC138313|Angpt2|11601|angiopoietin 2	AF004326|Angpt2|11601|angiopoietin 2	BC027216|Angpt2|11601|angiopoietin 2	AK048622|Angpt2|11601|angiopoietin 2	AK156132|Angpt2|11601|angiopoietin 2
mm9_v1_chr4_+_140703847_140703905	0.153154	SOX2.p2	AK165284|Fbxo42|213499|F-box protein 42	AK151503|Fbxo42|213499|F-box protein 42
mm9_v1_chr6_-_142456402_142456478	0.152407	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_chr2_+_181336020_181336108	0.151896	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_chr11_-_68635236_68635451	0.151874	SOX2.p2	AK194070|Ndel1|83431|nuclear distribution gene E-like homolog 1 (A. nidulans)
mm9_v1_chr13_+_55736365_55736414	0.151564	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_chr15_+_91958558_91958558	0.151551	SOX2.p2	NM_007727|Cntn1|12805|contactin 1
mm9_v1_chr13_-_58227306_58227430	0.151471	SOX2.p2	BC048746|Hnrnpa0|77134|heterogeneous nuclear ribonucleoprotein A0
mm9_v1_chr3_-_75760820_75760839	0.151376	SOX2.p2	AK149286|Golim4|73124|golgi integral membrane protein 4
mm9_v1_chr6_+_54251485_54251608	0.151256	SOX2.p2	
mm9_v1_chr17_+_71202075_71202104	0.15101	SOX2.p2	AK082636|C230073G13Rik|320430|RIKEN cDNA C230073G13 gene
mm9_v1_chr4_+_106986972_106987035	0.150907	SOX2.p2	AK138108|Yipf1|230584|Yip1 domain family, member 1	AK081205|Yipf1|230584|Yip1 domain family, member 1	AK157536|Yipf1|230584|Yip1 domain family, member 1	AK077502|Yipf1|230584|Yip1 domain family, member 1	BC009080|Yipf1|230584|Yip1 domain family, member 1	NM_145550|Yipf1|230584|Yip1 domain family, member 1
mm9_v1_chr12_+_99506844_99506881	0.150285	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_chr11_-_98010872_98010958	0.149761	SOX2.p2	AK220232|Fbxl20|72194|F-box and leucine-rich repeat protein 20	AK161566|Fbxl20|72194|F-box and leucine-rich repeat protein 20	AK144786|Fbxl20|72194|F-box and leucine-rich repeat protein 20	NM_028149|Fbxl20|72194|F-box and leucine-rich repeat protein 20	AK012109|Fbxl20|72194|F-box and leucine-rich repeat protein 20
mm9_v1_chr10_-_90579986_90580013	0.149544	SOX2.p2	AK198800|Slc25a3|18674|solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	AK190863|Slc25a3|18674|solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	AK184040|Slc25a3|18674|solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	AK191542|Slc25a3|18674|solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	AK191799|Slc25a3|18674|solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	AK194450|Slc25a3|18674|solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	AK194768|Slc25a3|18674|solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	AK200191|Slc25a3|18674|solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	AK200546|Slc25a3|18674|solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	AK200877|Slc25a3|18674|solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	AK202780|Slc25a3|18674|solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	AK203032|Slc25a3|18674|solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	AK203930|Slc25a3|18674|solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	AK213202|Slc25a3|18674|solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	AK215444|Slc25a3|18674|solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	AK193469|Slc25a3|18674|solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	AK196032|Slc25a3|18674|solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3
mm9_v1_chr11_+_117222099_117222144	0.148971	SOX2.p2	
mm9_v1_chrX_+_101609180_101609330	0.14866	SOX2.p2	
mm9_v1_chr7_+_90780446_90780552	0.1485	SOX2.p2	AK077328|Stard5|170460|StAR-related lipid transfer (START) domain containing 5	AK142503|Stard5|170460|StAR-related lipid transfer (START) domain containing 5	AK080060|Stard5|170460|StAR-related lipid transfer (START) domain containing 5	AK085852|Stard5|170460|StAR-related lipid transfer (START) domain containing 5	AK009980|Stard5|170460|StAR-related lipid transfer (START) domain containing 5	BC031733|Stard5|170460|StAR-related lipid transfer (START) domain containing 5	AK158178|Stard5|170460|StAR-related lipid transfer (START) domain containing 5	BC058226|Stard5|170460|StAR-related lipid transfer (START) domain containing 5	NM_023377|Stard5|170460|StAR-related lipid transfer (START) domain containing 5	AY007808|Stard5|170460|StAR-related lipid transfer (START) domain containing 5	AF480302|Stard5|170460|StAR-related lipid transfer (START) domain containing 5
mm9_v1_chr11_+_60513191_60513346	0.148257	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_chr4_+_135699733_135699741	0.147124	SOX2.p2	BC145871|Id3|15903|inhibitor of DNA binding 3	BC145873|Id3|15903|inhibitor of DNA binding 3	M60523|Id3|15903|inhibitor of DNA binding 3	NM_008321|Id3|15903|inhibitor of DNA binding 3	AK002820|Id3|15903|inhibitor of DNA binding 3	AK031499|Id3|15903|inhibitor of DNA binding 3
mm9_v1_chr3_+_129235336_129235458	0.147054	SOX2.p2	AK167373|Elovl6|170439|ELOVL family member 6, elongation of long chain fatty acids (yeast)	AB072039|Elovl6|170439|ELOVL family member 6, elongation of long chain fatty acids (yeast)	BC040097|Elovl6|170439|ELOVL family member 6, elongation of long chain fatty acids (yeast)	BC100576|Elovl6|170439|ELOVL family member 6, elongation of long chain fatty acids (yeast)	AF480860|Elovl6|170439|ELOVL family member 6, elongation of long chain fatty acids (yeast)	AK165847|Elovl6|170439|ELOVL family member 6, elongation of long chain fatty acids (yeast)	BC098492|Elovl6|170439|ELOVL family member 6, elongation of long chain fatty acids (yeast)
mm9_v1_chr5_-_30460623_30460706	0.147027	SOX2.p2	AK179416|Hadha|97212|hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit	AK188264|Hadha|97212|hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit	AK217494|Hadha|97212|hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit
mm9_v1_chr18_-_39572137_39572180	0.146841	SOX2.p2	AK171439|Nr3c1|14815|nuclear receptor subfamily 3, group C, member 1	AK163857|Nr3c1|14815|nuclear receptor subfamily 3, group C, member 1
mm9_v1_chr1_-_33871218_33871259	0.146788	SOX2.p2	BC062154|Zfp451|98403|zinc finger protein 451
mm9_v1_chr2_+_179759610_179759731	0.146287	SOX2.p2	BC040823|Lsm14b|241846|LSM14 homolog B (SCD6, S. cerevisiae)	NM_177727|Lsm14b|241846|LSM14 homolog B (SCD6, S. cerevisiae)
mm9_v1_chr6_+_87852230_87852326	0.146254	SOX2.p2	AK193696|Copg|54161|coatomer protein complex, subunit gamma	AK194411|Copg|54161|coatomer protein complex, subunit gamma	AK195632|Copg|54161|coatomer protein complex, subunit gamma	AK197699|Copg|54161|coatomer protein complex, subunit gamma	AK201780|Copg|54161|coatomer protein complex, subunit gamma	AK204845|Copg|54161|coatomer protein complex, subunit gamma
mm9_v1_chr1_-_65003291_65003407	0.146165	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_chr5_-_100588586_100588606	0.146152	SOX2.p2	AK044570|Tmem150c|231503|transmembrane protein 150C	BC062109|Tmem150c|231503|transmembrane protein 150C
mm9_v1_chr7_+_114179649_114179650	0.145741	SOX2.p2	NM_147034|Olfr713|259036|olfactory receptor 713	BC100704|Olfr713|259036|olfactory receptor 713
mm9_v1_chr2_-_26264694_26264752	0.145684	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_chr7_+_140175699_140175731	0.145218	SOX2.p2	AJ250693|Zranb1|360216|zinc finger, RAN-binding domain containing 1
mm9_v1_chr14_-_47407948_47408042	0.145186	SOX2.p2	AK154479|Cnih|12793|cornichon homolog (Drosophila)	AK152432|Cnih|12793|cornichon homolog (Drosophila)	AK168154|Cnih|12793|cornichon homolog (Drosophila)	AK011200|Cnih|12793|cornichon homolog (Drosophila)	BC034868|Cnih|12793|cornichon homolog (Drosophila)	AK002293|Cnih|12793|cornichon homolog (Drosophila)	AF022811|Cnih|12793|cornichon homolog (Drosophila)	NM_009919|Cnih|12793|cornichon homolog (Drosophila)
mm9_v1_chrM_+_7009_7016	0.144931	SOX2.p2	AF378830|COX2|17709|cytochrome c oxidase subunit II	AK131586|COX2|17709|cytochrome c oxidase subunit II
mm9_v1_chr9_-_103125290_103125306	0.144666	SOX2.p2	J03299|Trf|22041|transferrin	M23014|Trf|22041|transferrin
mm9_v1_chr8_-_63433528_63433596	0.144499	SOX2.p2	BC057133|Clcn3|12725|chloride channel 3	NM_173876|Clcn3|12725|chloride channel 3
mm9_v1_chr11_+_83560497_83560515	0.144171	SOX2.p2	AK003352|1100001G20Rik|66107|RIKEN cDNA 1100001G20 gene	AK003164|1100001G20Rik|66107|RIKEN cDNA 1100001G20 gene	BC096415|1100001G20Rik|66107|RIKEN cDNA 1100001G20 gene
mm9_v1_chr17_+_75578120_75578285	0.143798	SOX2.p2	AK036047|Ltbp1|268977|latent transforming growth factor beta binding protein 1	NM_206958|Ltbp1|268977|latent transforming growth factor beta binding protein 1	AF280604|Ltbp1|268977|latent transforming growth factor beta binding protein 1
mm9_v1_chr15_-_77949709_77949709	0.143141	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_chr3_-_38349112_38349206	0.143124	SOX2.p2	BC051515|Ankrd50|99696|ankyrin repeat domain 50
mm9_v1_chr11_+_96164825_96164850	0.142979	SOX2.p2	M26283|Hoxb5|15413|homeobox B5	NM_008268|Hoxb5|15413|homeobox B5
mm9_v1_chr2_+_167802175_167802258	0.142664	SOX2.p2	AK179877|Ptpn1|19246|protein tyrosine phosphatase, non-receptor type 1
mm9_v1_chr18_-_34666454_34666491	0.1423	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_chr11_+_100442831_100442963	0.142097	SOX2.p2	AK217119|Cnp|12799|2',3'-cyclic nucleotide 3' phosphodiesterase
mm9_v1_chr5_+_89194155_89194268	0.142079	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_chr1_-_136700389_136700428	0.141841	SOX2.p2	AK035285|Ppp1r12b|329251|protein phosphatase 1, regulatory (inhibitor) subunit 12B
mm9_v1_chr19_+_12770279_12770282	0.141837	SOX2.p2	NM_029550|Keg1|64697|kidney expressed gene 1	AK002360|Keg1|64697|kidney expressed gene 1	AK165349|Keg1|64697|kidney expressed gene 1	AK165515|Keg1|64697|kidney expressed gene 1
mm9_v1_chr18_+_31963675_31963753	0.141097	SOX2.p2	BC019463|Wdr33|74320|WD repeat domain 33	NM_001170966|Wdr33|74320|WD repeat domain 33	NM_001170967|Wdr33|74320|WD repeat domain 33	NM_001170970|Wdr33|74320|WD repeat domain 33	NM_028866|Wdr33|74320|WD repeat domain 33	AK003256|Wdr33|74320|WD repeat domain 33	AK018408|Wdr33|74320|WD repeat domain 33	AK078286|Wdr33|74320|WD repeat domain 33	AK009297|Wdr33|74320|WD repeat domain 33	AK045125|Wdr33|74320|WD repeat domain 33	AK045923|Wdr33|74320|WD repeat domain 33	AK050653|Wdr33|74320|WD repeat domain 33	AK161982|Wdr33|74320|WD repeat domain 33
mm9_v1_chr4_+_102242664_102242699	0.140856	SOX2.p2	NM_001177980|Pde4b|18578|phosphodiesterase 4B, cAMP specific	BC023751|Pde4b|18578|phosphodiesterase 4B, cAMP specific
mm9_v1_chr4_+_116230293_116230350	0.140287	SOX2.p2	AK037224|Gpbp1l1|77110|GC-rich promoter binding protein 1-like 1	AK133761|Gpbp1l1|77110|GC-rich promoter binding protein 1-like 1	AK019942|Gpbp1l1|77110|GC-rich promoter binding protein 1-like 1	BC066034|Gpbp1l1|77110|GC-rich promoter binding protein 1-like 1	NM_029868|Gpbp1l1|77110|GC-rich promoter binding protein 1-like 1
mm9_v1_chr18_+_78028651_78028681	0.140202	SOX2.p2	AK163337|Pstpip2|19201|proline-serine-threonine phosphatase-interacting protein 2	AK031963|Pstpip2|19201|proline-serine-threonine phosphatase-interacting protein 2
mm9_v1_chr11_+_68939734_68939879	0.140135	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_chr19_+_46227016_46227019	0.140125	SOX2.p2	AK041959|Gbf1|107338|golgi-specific brefeldin A-resistance factor 1
mm9_v1_chr9_+_106105422_106105590	0.140084	SOX2.p2	AK084026|Twf2|23999|twinfilin, actin-binding protein, homolog 2 (Drosophila)	NM_011876|Twf2|23999|twinfilin, actin-binding protein, homolog 2 (Drosophila)	AK155204|Twf2|23999|twinfilin, actin-binding protein, homolog 2 (Drosophila)	AK166900|Twf2|23999|twinfilin, actin-binding protein, homolog 2 (Drosophila)	BC003338|Twf2|23999|twinfilin, actin-binding protein, homolog 2 (Drosophila)	AK170441|Twf2|23999|twinfilin, actin-binding protein, homolog 2 (Drosophila)	AK157886|Twf2|23999|twinfilin, actin-binding protein, homolog 2 (Drosophila)	Y17808|Twf2|23999|twinfilin, actin-binding protein, homolog 2 (Drosophila)	AY267189|Twf2|23999|twinfilin, actin-binding protein, homolog 2 (Drosophila)
mm9_v1_chr8_-_95861063_95861110	0.139895	SOX2.p2	AK162328|Ces1g|12623|carboxylesterase 1G	BC026897|Ces1g|12623|carboxylesterase 1G	Y12887|Ces1g|12623|carboxylesterase 1G	AK136446|Ces1g|12623|carboxylesterase 1G	AK136588|Ces1g|12623|carboxylesterase 1G	AK149446|Ces1g|12623|carboxylesterase 1G	NM_021456|Ces1g|12623|carboxylesterase 1G
mm9_v1_chr5_+_151755181_151755278	0.139803	SOX2.p2	BC138258|Kl|16591|klotho	BC138259|Kl|16591|klotho	NM_013823|Kl|16591|klotho	AB005141|Kl|16591|klotho	AB010088|Kl|16591|klotho
mm9_v1_chr17_+_23949101_23949124	0.139756	SOX2.p2	AK081577|Srrm2|75956|serine/arginine repetitive matrix 2
mm9_v1_chr5_+_31357119_31357185	0.139746	SOX2.p2	BC053097|Cad|69719|carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	NM_023525|Cad|69719|carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	BC060119|Cad|69719|carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase
mm9_v1_chr11_+_51817722_51817929	0.138982	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_chr5_+_150480804_150480876	0.138489	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_chr10_-_126558207_126558220	0.138153	SOX2.p2	NM_001171026|Os9|216440|amplified in osteosarcoma	NM_177614|Os9|216440|amplified in osteosarcoma
mm9_v1_chr9_+_92502076_92502169	0.138122	SOX2.p2	
mm9_v1_chr3_-_89206571_89206714	0.138013	SOX2.p2	NM_020517|Lenep|57275|lens epithelial protein	AK053703|Lenep|57275|lens epithelial protein	BC006806|Lenep|57275|lens epithelial protein
mm9_v1_chr10_-_62784937_62784977	0.137897	SOX2.p2	AK139946|Sirt1|93759|sirtuin 1 (silent mating type information regulation 2, homolog) 1 (S. cerevisiae)
mm9_v1_chr6_+_88052091_88052141	0.13753	SOX2.p2	
mm9_v1_chr4_+_133952274_133952296	0.137269	SOX2.p2	AK144090|Pafah2|100163|platelet-activating factor acetylhydrolase 2	NM_133880|Pafah2|100163|platelet-activating factor acetylhydrolase 2	AK145092|Pafah2|100163|platelet-activating factor acetylhydrolase 2
mm9_v1_chr2_-_35973217_35973333	0.137201	SOX2.p2	
mm9_v1_chr2_+_152561983_152562076	0.137146	SOX2.p2	M31885|Id1|15901|inhibitor of DNA binding 1	AK008264|Id1|15901|inhibitor of DNA binding 1	BC025073|Id1|15901|inhibitor of DNA binding 1	NM_010495|Id1|15901|inhibitor of DNA binding 1	U43884|Id1|15901|inhibitor of DNA binding 1	AB221668|Id1|15901|inhibitor of DNA binding 1	CT010243|Id1|15901|inhibitor of DNA binding 1
mm9_v1_chr9_+_48303540_48303564	0.137123	SOX2.p2	AK007723|Gm5617|434402|predicted gene 5617	BC011344|Gm5617|434402|predicted gene 5617
mm9_v1_chr14_-_48037815_48037862	0.136533	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_chr18_+_52928026_52928056	0.13639	SOX2.p2	AK042895|Gm5078|320291|predicted gene 5078	AK016941|Sncaip|67847|synuclein, alpha interacting protein (synphilin)
mm9_v1_chr17_+_85025830_85025873	0.136075	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_chr3_+_145650833_145650943	0.136032	SOX2.p2	NM_001166064|Syde2|214804|synapse defective 1, Rho GTPase, homolog 2 (C. elegans)
mm9_v1_chr11_+_62364951_62365050	0.13598	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_chr2_-_87475901_87475901	0.135426	SOX2.p2	NM_146836|Olfr1132|258833|olfactory receptor 1132
mm9_v1_chr11_-_4999069_4999098	0.134986	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_chr19_+_56536126_56536129	0.133915	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_chr12_+_109661287_109661388	0.133774	SOX2.p2	AK044662|Eml1|68519|echinoderm microtubule associated protein like 1	BC079582|Eml1|68519|echinoderm microtubule associated protein like 1
mm9_v1_chr18_+_77303959_77304054	0.133619	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_chr6_-_51419881_51419892	0.133456	SOX2.p2	AK049771|Hnrnpa2b1|53379|heterogeneous nuclear ribonucleoprotein A2/B1	AK137214|Hnrnpa2b1|53379|heterogeneous nuclear ribonucleoprotein A2/B1	NM_016806|Hnrnpa2b1|53379|heterogeneous nuclear ribonucleoprotein A2/B1	NM_182650|Hnrnpa2b1|53379|heterogeneous nuclear ribonucleoprotein A2/B1
mm9_v1_chr12_+_121184294_121184434	0.133246	SOX2.p2	AK132117|Tmem196|217951|transmembrane protein 196	NM_001160385|Tmem196|217951|transmembrane protein 196
mm9_v1_chr6_-_4036892_4036992	0.133177	SOX2.p2	AF007552|Bet1|12068|blocked early in transport 1 homolog (S. cerevisiae)	AK078796|Bet1|12068|blocked early in transport 1 homolog (S. cerevisiae)	BC005572|Bet1|12068|blocked early in transport 1 homolog (S. cerevisiae)	NM_009748|Bet1|12068|blocked early in transport 1 homolog (S. cerevisiae)	AK053940|Bet1|12068|blocked early in transport 1 homolog (S. cerevisiae)
mm9_v1_chr15_+_88890519_88890533	0.132649	SOX2.p2	DQ093579|Panx2|406218|pannexin 2
mm9_v1_chr14_-_14953416_14953474	0.13252	SOX2.p2	BC006869|Psmd6|66413|proteasome (prosome, macropain) 26S subunit, non-ATPase, 6	NM_025550|Psmd6|66413|proteasome (prosome, macropain) 26S subunit, non-ATPase, 6	AK002343|Psmd6|66413|proteasome (prosome, macropain) 26S subunit, non-ATPase, 6	AK010287|Psmd6|66413|proteasome (prosome, macropain) 26S subunit, non-ATPase, 6	AJ252147|Psmd6|66413|proteasome (prosome, macropain) 26S subunit, non-ATPase, 6
mm9_v1_chr11_-_106860803_106860838	0.132155	SOX2.p2	NM_010655|Kpna2|16647|karyopherin (importin) alpha 2
mm9_v1_chr19_-_60302398_60302548	0.132011	SOX2.p2	BC061459|D19Ertd737e|76539|DNA segment, Chr 19, ERATO Doi 737, expressed	AK162079|D19Ertd737e|76539|DNA segment, Chr 19, ERATO Doi 737, expressed
mm9_v1_chr14_+_48283430_48283453	0.131861	SOX2.p2	NM_008477|Ktn1|16709|kinectin 1	L43326|Ktn1|16709|kinectin 1
mm9_v1_chr19_+_46227039_46227050	0.131536	SOX2.p2	BC076569|Gbf1|107338|golgi-specific brefeldin A-resistance factor 1	NM_178930|Gbf1|107338|golgi-specific brefeldin A-resistance factor 1
mm9_v1_chr14_+_75132097_75132190	0.131434	SOX2.p2	AK010683|Esd|13885|esterase D/formylglutathione hydrolase	AK007527|Esd|13885|esterase D/formylglutathione hydrolase	AB025408|Esd|13885|esterase D/formylglutathione hydrolase	AK180750|Esd|13885|esterase D/formylglutathione hydrolase	AK079131|Esd|13885|esterase D/formylglutathione hydrolase	NM_016903|Esd|13885|esterase D/formylglutathione hydrolase	AK021209|Esd|13885|esterase D/formylglutathione hydrolase	AK163074|Esd|13885|esterase D/formylglutathione hydrolase	BC046766|Esd|13885|esterase D/formylglutathione hydrolase	BC096644|Esd|13885|esterase D/formylglutathione hydrolase	AK088115|Esd|13885|esterase D/formylglutathione hydrolase
mm9_v1_chr14_+_31948038_31948038	0.131314	SOX2.p2	BC011230|Nt5dc2|70021|5'-nucleotidase domain containing 2	NM_027289|Nt5dc2|70021|5'-nucleotidase domain containing 2
mm9_v1_chr9_-_107516538_107516684	0.130557	SOX2.p2	
mm9_v1_chr14_-_55482884_55482994	0.130323	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_chr11_-_70223528_70223535	0.130265	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_chr1_+_88600370_88600431	0.129952	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_chr10_+_4978808_4978917	0.129825	SOX2.p2	AK148504|Syne1|64009|synaptic nuclear envelope 1
mm9_v1_chr5_-_31490075_31490203	0.129545	SOX2.p2	
mm9_v1_chr6_+_127837606_127837652	0.129526	SOX2.p2	AK087294|Tspan11|68498|tetraspanin 11	NM_026743|Tspan11|68498|tetraspanin 11	AK090022|Tspan11|68498|tetraspanin 11	AK053788|Tspan11|68498|tetraspanin 11
mm9_v1_chr11_+_118884275_118884425	0.12952	SOX2.p2	X62537|Cbx2|12416|chromobox homolog 2 (Drosophila Pc class)	BC035199|Cbx2|12416|chromobox homolog 2 (Drosophila Pc class)	NM_007623|Cbx2|12416|chromobox homolog 2 (Drosophila Pc class)	AK157869|Cbx2|12416|chromobox homolog 2 (Drosophila Pc class)	Y13274|Cbx2|12416|chromobox homolog 2 (Drosophila Pc class)
mm9_v1_chr6_+_145159653_145159723	0.129451	SOX2.p2	NM_001163628|Lyrm5|67636|LYR motif containing 5	AF412300|Lyrm5|67636|LYR motif containing 5	NM_133688|Lyrm5|67636|LYR motif containing 5	AY753325|Lyrm5|67636|LYR motif containing 5	AF412298|Lyrm5|67636|LYR motif containing 5	AK075835|Lyrm5|67636|LYR motif containing 5	AF412299|Lyrm5|67636|LYR motif containing 5	AK015530|Lyrm5|67636|LYR motif containing 5	AK046179|Lyrm5|67636|LYR motif containing 5	BC021522|Lyrm5|67636|LYR motif containing 5
mm9_v1_chr19_-_21547072_21547150	0.129435	SOX2.p2	AF174583|Gda|14544|guanine deaminase	AK044078|Gda|14544|guanine deaminase	AK173138|Gda|14544|guanine deaminase	AK041056|Gda|14544|guanine deaminase	AK079459|Gda|14544|guanine deaminase	AK157014|Gda|14544|guanine deaminase	NM_010266|Gda|14544|guanine deaminase
mm9_v1_chr2_+_153571990_153572007	0.129413	SOX2.p2	BC052405|Mapre1|13589|microtubule-associated protein, RP/EB family, member 1
mm9_v1_chr3_+_59885811_59885831	0.129181	SOX2.p2	BC096665|Sucnr1|84112|succinate receptor 1
mm9_v1_chrX_+_5977130_5977262	0.129041	SOX2.p2	DQ435686|Shroom4|208431|shroom family member 4	DQ435687|Shroom4|208431|shroom family member 4	NM_001040459|Shroom4|208431|shroom family member 4
mm9_v1_chr11_-_120441643_120441696	0.128165	SOX2.p2	AK075656|Arhgdia|192662|Rho GDP dissociation inhibitor (GDI) alpha
mm9_v1_chr4_+_34497840_34497946	0.127826	SOX2.p2	NM_001007589|Akirin2|433693|akirin 2	BC082305|Akirin2|433693|akirin 2
mm9_v1_chr14_-_51544497_51544585	0.127323	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_chr5_-_122267654_122267839	0.127287	SOX2.p2	AK210164|Sh2b3|16923|SH2B adaptor protein 3	AK212257|Sh2b3|16923|SH2B adaptor protein 3
mm9_v1_chr18_+_21119972_21120137	0.127097	SOX2.p2	AK016103|Rnf125|67664|ring finger protein 125	AB259692|Rnf125|67664|ring finger protein 125
mm9_v1_chr18_-_35114000_35114003	0.12693	SOX2.p2	AK165958|Hspa9|15526|heat shock protein 9
mm9_v1_chr19_-_4201541_4201648	0.126068	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_chr14_+_69647294_69647485	0.125776	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_chr2_+_26775279_26775409	0.12558	SOX2.p2	AK215042|Surf2|20931|surfeit gene 2
mm9_v1_chr4_-_131978279_131978374	0.125377	SOX2.p2	BC096033|Phactr4|100169|phosphatase and actin regulator 4	AK049209|Phactr4|100169|phosphatase and actin regulator 4	BC075672|Phactr4|100169|phosphatase and actin regulator 4	AK220496|Phactr4|100169|phosphatase and actin regulator 4	NM_001161797|Phactr4|100169|phosphatase and actin regulator 4	NM_175306|Phactr4|100169|phosphatase and actin regulator 4
mm9_v1_chr11_+_49273182_49273182	0.125315	SOX2.p2	NM_146473|Olfr1387|258465|olfactory receptor 1387
mm9_v1_chr7_+_63049505_63049618	0.125157	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_chr16_+_20548675_20548742	0.125157	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_chr5_-_87355527_87355556	0.125003	SOX2.p2	BC027200|Ugt2b1|71773|UDP glucuronosyltransferase 2 family, polypeptide B1	NM_152811|Ugt2b1|71773|UDP glucuronosyltransferase 2 family, polypeptide B1	AK004971|Ugt2b1|71773|UDP glucuronosyltransferase 2 family, polypeptide B1	AK050435|Ugt2b1|71773|UDP glucuronosyltransferase 2 family, polypeptide B1
mm9_v1_chr5_+_31552275_31552343	0.124823	SOX2.p2	AK215481|Nrbp1|192292|nuclear receptor binding protein 1	AK182568|Nrbp1|192292|nuclear receptor binding protein 1	AK185308|Nrbp1|192292|nuclear receptor binding protein 1	AK196002|Nrbp1|192292|nuclear receptor binding protein 1	AK219460|Nrbp1|192292|nuclear receptor binding protein 1
mm9_v1_chr9_+_99476204_99476272	0.124799	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_chr10_-_26094990_26095024	0.124731	SOX2.p2	AK045667|L3mbtl3|237339|l(3)mbt-like 3 (Drosophila)	NM_172787|L3mbtl3|237339|l(3)mbt-like 3 (Drosophila)	AK049597|L3mbtl3|237339|l(3)mbt-like 3 (Drosophila)
mm9_v1_chr5_-_138362822_138362852	0.124196	SOX2.p2	X63023|Cyp3a13|13113|cytochrome P450, family 3, subfamily a, polypeptide 13	BC046592|Cyp3a13|13113|cytochrome P450, family 3, subfamily a, polypeptide 13	AK136494|Cyp3a13|13113|cytochrome P450, family 3, subfamily a, polypeptide 13	AK136529|Cyp3a13|13113|cytochrome P450, family 3, subfamily a, polypeptide 13	AK149572|Cyp3a13|13113|cytochrome P450, family 3, subfamily a, polypeptide 13	NM_007819|Cyp3a13|13113|cytochrome P450, family 3, subfamily a, polypeptide 13
mm9_v1_chr6_+_81873662_81873720	0.12339	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_chr12_+_3365102_3365131	0.123343	SOX2.p2	AK220283|Kif3c|16570|kinesin family member 3C	NM_008445|Kif3c|16570|kinesin family member 3C
mm9_v1_chr11_+_98011055_98011069	0.123332	SOX2.p2	
mm9_v1_chr17_+_71368860_71368930	0.122519	SOX2.p2	AJ012072|Myom1|17929|myomesin 1	NM_001083934|Myom1|17929|myomesin 1	NM_010867|Myom1|17929|myomesin 1	Z22866|Myom1|17929|myomesin 1	AK052539|Myom1|17929|myomesin 1
mm9_v1_chr3_-_103545641_103545788	0.12244	SOX2.p2	AK159746|Hipk1|15257|homeodomain interacting protein kinase 1	AK076611|Hipk1|15257|homeodomain interacting protein kinase 1
mm9_v1_chr11_+_103053625_103053722	0.122373	SOX2.p2	AK158820|Fmnl1|57778|formin-like 1
mm9_v1_chr2_+_22751081_22751226	0.122246	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_chr11_+_64248779_64248833	0.122231	SOX2.p2	BC094320|Hs3st3a1|15478|heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1	AK051284|Hs3st3a1|15478|heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1	NM_178870|Hs3st3a1|15478|heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1
mm9_v1_chr11_-_97627829_97627926	0.121644	SOX2.p2	BC021478|Cwc25|67480|CWC25 spliceosome-associated protein homolog (S. cerevisiae)	BC079553|Cwc25|67480|CWC25 spliceosome-associated protein homolog (S. cerevisiae)	AK030628|Cwc25|67480|CWC25 spliceosome-associated protein homolog (S. cerevisiae)	AK035158|Cwc25|67480|CWC25 spliceosome-associated protein homolog (S. cerevisiae)	AK004983|Cwc25|67480|CWC25 spliceosome-associated protein homolog (S. cerevisiae)	AK017849|Cwc25|67480|CWC25 spliceosome-associated protein homolog (S. cerevisiae)	NM_026186|Cwc25|67480|CWC25 spliceosome-associated protein homolog (S. cerevisiae)
mm9_v1_chrX_-_93152223_93152253	0.121632	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_chr1_+_95395940_95395952	0.121276	SOX2.p2	AK196297|Sept2|18000|septin 2	AK216929|Sept2|18000|septin 2
mm9_v1_chr2_+_69877182_69877182	0.12118	SOX2.p2	NM_177376|Myo3b|329421|myosin IIIB
mm9_v1_chr15_-_36724292_36724292	0.120912	SOX2.p2	NM_011740|Ywhaz|22631|tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide
mm9_v1_chr18_-_35114004_35114004	0.120047	SOX2.p2	BC052727|Hspa9|15526|heat shock protein 9	BC057343|Hspa9|15526|heat shock protein 9	NM_010481|Hspa9|15526|heat shock protein 9
mm9_v1_chr12_-_80292830_80292851	0.119827	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_chr17_-_31266539_31266557	0.119775	SOX2.p2	BC011042|Tff3|21786|trefoil factor 3, intestinal	AK008538|Tff3|21786|trefoil factor 3, intestinal	D38410|Tff3|21786|trefoil factor 3, intestinal	NM_011575|Tff3|21786|trefoil factor 3, intestinal
mm9_v1_chr3_+_87600872_87601015	0.119713	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_chr9_+_39421128_39421153	0.119569	SOX2.p2	BC125353|Olfr148|258498|olfactory receptor 148	BC132239|Olfr148|258498|olfactory receptor 148	NM_146505|Olfr148|258498|olfactory receptor 148
mm9_v1_chr13_+_21275678_21275791	0.119184	SOX2.p2	
mm9_v1_chr3_+_63099408_63099509	0.119149	SOX2.p2	AK076908|Mme|17380|membrane metallo endopeptidase
mm9_v1_chr10_-_57252184_57252250	0.118986	SOX2.p2	BC017148|Serinc1|56442|serine incorporator 1	AK159280|Serinc1|56442|serine incorporator 1
mm9_v1_chr9_-_21043503_21043590	0.118611	SOX2.p2	BC023945|Keap1|50868|kelch-like ECH-associated protein 1	AK154430|Keap1|50868|kelch-like ECH-associated protein 1	AK155507|Keap1|50868|kelch-like ECH-associated protein 1
mm9_v1_chrX_+_151696991_151697138	0.118094	SOX2.p2	AK168713|Acot9|56360|acyl-CoA thioesterase 9	NM_019736|Acot9|56360|acyl-CoA thioesterase 9	AK076513|Acot9|56360|acyl-CoA thioesterase 9	BC021763|Acot9|56360|acyl-CoA thioesterase 9	AK002892|Acot9|56360|acyl-CoA thioesterase 9	AK009717|Acot9|56360|acyl-CoA thioesterase 9	AK088082|Acot9|56360|acyl-CoA thioesterase 9	AK170876|Acot9|56360|acyl-CoA thioesterase 9	AJ238893|Acot9|56360|acyl-CoA thioesterase 9	AB028898|Acot9|56360|acyl-CoA thioesterase 9
mm9_v1_chrX_+_34666757_34666828	0.11741	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_chr18_+_37911236_37911432	0.117132	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_chr14_+_55713789_55713939	0.116987	SOX2.p2	AF432864|Thtpa|105663|thiamine triphosphatase	AK085173|Thtpa|105663|thiamine triphosphatase	AK132479|Thtpa|105663|thiamine triphosphatase
mm9_v1_chr6_-_88834347_88834425	0.116832	SOX2.p2	AK198580|Mcm2|17216|minichromosome maintenance deficient 2 mitotin (S. cerevisiae)
mm9_v1_chr10_+_62562532_62562550	0.116618	SOX2.p2	BC092234|Atoh7|53404|atonal homolog 7 (Drosophila)
mm9_v1_chr4_+_144483110_144483188	0.116391	SOX2.p2	AK087137|Dhrs3|20148|dehydrogenase/reductase (SDR family) member 3
mm9_v1_chr4_+_66488753_66488865	0.116376	SOX2.p2	AK154297|Tlr4|21898|toll-like receptor 4	AK170566|Tlr4|21898|toll-like receptor 4	AF110133|Tlr4|21898|toll-like receptor 4	NM_021297|Tlr4|21898|toll-like receptor 4	AF185285|Tlr4|21898|toll-like receptor 4
mm9_v1_chr15_+_59480237_59480243	0.115972	SOX2.p2	AK080228|Trib1|211770|tribbles homolog 1 (Drosophila)
mm9_v1_chr4_-_43058685_43058696	0.115696	SOX2.p2	BC044832|B230312A22Rik|230088|RIKEN cDNA B230312A22 gene
mm9_v1_chr13_+_64533703_64533885	0.115197	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_chr8_-_73174451_73174575	0.114609	SOX2.p2	
mm9_v1_chr7_-_148358709_148358768	0.114341	SOX2.p2	AK145173|Rnh1|107702|ribonuclease/angiogenin inhibitor 1	NM_001172100|Rnh1|107702|ribonuclease/angiogenin inhibitor 1
mm9_v1_chr3_-_105735506_105735581	0.114286	SOX2.p2	BC147821|I830077J02Rik|433638|RIKEN cDNA I830077J02 gene	BC147828|I830077J02Rik|433638|RIKEN cDNA I830077J02 gene	AK152510|I830077J02Rik|433638|RIKEN cDNA I830077J02 gene	NM_001033780|I830077J02Rik|433638|RIKEN cDNA I830077J02 gene
mm9_v1_chr2_-_63022140_63022343	0.11402	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_chr11_+_22902273_22902372	0.113946	SOX2.p2	
mm9_v1_chr18_-_70212948_70213022	0.113895	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_chr2_-_155999858_155999931	0.113589	SOX2.p2	BC082607|Rbm39|170791|RNA binding motif protein 39
mm9_v1_chr16_-_18629938_18630073	0.113405	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_chr18_+_52927574_52927797	0.112821	SOX2.p2	BC130225|Sncaip|67847|synuclein, alpha interacting protein (synphilin)	BC152544|Sncaip|67847|synuclein, alpha interacting protein (synphilin)	AK160111|Sncaip|67847|synuclein, alpha interacting protein (synphilin)	AF348447|Sncaip|67847|synuclein, alpha interacting protein (synphilin)	AK046597|Gm5078|320291|predicted gene 5078	BC098489|Sncaip|67847|synuclein, alpha interacting protein (synphilin)	AK044974|Sncaip|67847|synuclein, alpha interacting protein (synphilin)	AK081942|Sncaip|67847|synuclein, alpha interacting protein (synphilin)
mm9_v1_chr18_+_36919868_36919931	0.112634	SOX2.p2	AK146093|Wdr55|67936|WD repeat domain 55	AK075958|Wdr55|67936|WD repeat domain 55	NM_026464|Wdr55|67936|WD repeat domain 55	BC131932|Wdr55|67936|WD repeat domain 55	BC131934|Wdr55|67936|WD repeat domain 55	AK018469|Wdr55|67936|WD repeat domain 55	AK017695|Wdr55|67936|WD repeat domain 55	BC064750|Wdr55|67936|WD repeat domain 55
mm9_v1_chr9_+_98886784_98886846	0.112417	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_chr19_+_42164922_42164992	0.112253	SOX2.p2	NM_145501|Pi4k2a|84095|phosphatidylinositol 4-kinase type 2 alpha	AK030725|Pi4k2a|84095|phosphatidylinositol 4-kinase type 2 alpha	BC110363|Pi4k2a|84095|phosphatidylinositol 4-kinase type 2 alpha	BC089309|Pi4k2a|84095|phosphatidylinositol 4-kinase type 2 alpha
mm9_v1_chr11_-_76031013_76031165	0.112191	SOX2.p2	BC031425|Gemin4|276919|gem (nuclear organelle) associated protein 4	AK028076|Gemin4|276919|gem (nuclear organelle) associated protein 4	AK165864|Gemin4|276919|gem (nuclear organelle) associated protein 4	BC062157|Gemin4|276919|gem (nuclear organelle) associated protein 4	AK141078|Gemin4|276919|gem (nuclear organelle) associated protein 4	AK154061|Gemin4|276919|gem (nuclear organelle) associated protein 4	NM_177367|Gemin4|276919|gem (nuclear organelle) associated protein 4	AK133821|Gemin4|276919|gem (nuclear organelle) associated protein 4
mm9_v1_chr19_+_46730385_46730488	0.111891	SOX2.p2	
mm9_v1_chr9_-_110018085_110018088	0.11179	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_chr19_-_5843325_5843365	0.111685	SOX2.p2	AK206554|Neat1|66961|nuclear paraspeckle assembly transcript 1 (non-protein coding)
mm9_v1_chr17_+_26852581_26852657	0.111624	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_chr14_-_73725413_73725527	0.111492	SOX2.p2	DQ400415|Rb1|19645|retinoblastoma 1
mm9_v1_chr5_+_13399301_13399308	0.111241	SOX2.p2	D85028|Sema3a|20346|sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	NM_009152|Sema3a|20346|sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A
mm9_v1_chr14_-_52525156_52525167	0.11115	SOX2.p2	AK004051|Ndrg2|29811|N-myc downstream regulated gene 2
mm9_v1_chrX_+_72627673_72627773	0.110992	SOX2.p2	NM_026126|Fundc2|67391|FUN14 domain containing 2	AK013460|Fundc2|67391|FUN14 domain containing 2	AK014705|Fundc2|67391|FUN14 domain containing 2	AK031214|Fundc2|67391|FUN14 domain containing 2	BC049566|Fundc2|67391|FUN14 domain containing 2	BC061464|Fundc2|67391|FUN14 domain containing 2	AY234858|Fundc2|67391|FUN14 domain containing 2
mm9_v1_chr11_+_96133224_96133235	0.110874	SOX2.p2	M34857|Hoxb9|15417|homeobox B9
mm9_v1_chr3_+_64913289_64913311	0.110791	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_chr5_-_145017034_145017054	0.110345	SOX2.p2	AK013828|2900089D17Rik|67277|RIKEN cDNA 2900089D17 gene	AK019366|2900089D17Rik|67277|RIKEN cDNA 2900089D17 gene
mm9_v1_chr7_+_19425314_19425337	0.110263	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_-_32079317_32079415	0.110201	SOX2.p2	BC086650|Pak2|224105|p21 protein (Cdc42/Rac)-activated kinase 2	NM_177326|Pak2|224105|p21 protein (Cdc42/Rac)-activated kinase 2
mm9_v1_chr16_+_91658149_91658193	0.108864	SOX2.p2	BC003245|Son|20658|Son DNA binding protein
mm9_v1_chr2_-_17978221_17978239	0.10885	SOX2.p2	AK007903|1810059C17Rik|69818|RIKEN cDNA 1810059C17 gene
mm9_v1_chr17_-_24210402_24210430	0.108815	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_chr9_+_74918821_74918973	0.10873	SOX2.p2	AK134367|Myo5a|17918|myosin VA
mm9_v1_chr5_-_147395979_147395979	0.108695	SOX2.p2	BC055746|Gpr12|14738|G-protein coupled receptor 12	NM_008151|Gpr12|14738|G-protein coupled receptor 12
mm9_v1_chr9_-_14588941_14589004	0.108243	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_chr2_-_174289526_174289563	0.108083	SOX2.p2	BC046612|Atp5e|67126|ATP synthase, H+ transporting, mitochondrial F1 complex, epsilon subunit
mm9_v1_chr11_-_48927255_48927258	0.107855	SOX2.p2	BC110470|Olfr1396|258334|olfactory receptor 1396	BC110471|Olfr1396|258334|olfactory receptor 1396	NM_146337|Olfr1396|258334|olfactory receptor 1396
mm9_v1_chr13_-_55528131_55528182	0.107549	SOX2.p2	BC037085|F12|58992|coagulation factor XII (Hageman factor)	X99571|F12|58992|coagulation factor XII (Hageman factor)	BC049867|F12|58992|coagulation factor XII (Hageman factor)	BC057921|F12|58992|coagulation factor XII (Hageman factor)	NM_021489|F12|58992|coagulation factor XII (Hageman factor)
mm9_v1_chr10_+_74646587_74646710	0.107164	SOX2.p2	
mm9_v1_chrX_-_165110450_165110461	0.107131	SOX2.p2	AK089368|Msl3|17692|male-specific lethal 3 homolog (Drosophila)
mm9_v1_chr9_-_39380841_39380898	0.107086	SOX2.p2	NM_146508|Olfr959|258501|olfactory receptor 959	BC120617|Olfr959|258501|olfactory receptor 959	BC120619|Olfr959|258501|olfactory receptor 959
mm9_v1_chr3_+_88125464_88125582	0.107017	SOX2.p2	
mm9_v1_chr8_-_114434098_114434098	0.106687	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_chr8_+_11556062_11556065	0.106374	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_chr16_+_13265171_13265171	0.10628	SOX2.p2	BC028459|Mkl2|239719|MKL/myocardin-like 2	NM_181860|Mkl2|239719|MKL/myocardin-like 2
mm9_v1_chr17_+_24546733_24546845	0.105766	SOX2.p2	BC038271|Abca3|27410|ATP-binding cassette, sub-family A (ABC1), member 3
mm9_v1_chr9_-_79607490_79607521	0.105688	SOX2.p2	X58486|Cox7a2|12866|cytochrome c oxidase, subunit VIIa 2	BC010979|Cox7a2|12866|cytochrome c oxidase, subunit VIIa 2	AK019210|Cox7a2|12866|cytochrome c oxidase, subunit VIIa 2	AK011269|Cox7a2|12866|cytochrome c oxidase, subunit VIIa 2
mm9_v1_chr5_-_114292851_114293254	0.10564	SOX2.p2	AK201602|Coro1c|23790|coronin, actin binding protein 1C
mm9_v1_chr18_+_32416881_32416904	0.10562	SOX2.p2	BC024446|Ercc3|13872|excision repair cross-complementing rodent repair deficiency, complementation group 3
mm9_v1_chr6_-_116532961_116533048	0.105512	SOX2.p2	NM_146446|Olfr215|258438|olfactory receptor 215	BC125561|Olfr215|258438|olfactory receptor 215	BC125563|Olfr215|258438|olfactory receptor 215
mm9_v1_chr2_-_131855722_131855755	0.105307	SOX2.p2	NM_175445|Rassf2|215653|Ras association (RalGDS/AF-6) domain family member 2
mm9_v1_chr8_+_108939222_108939238	0.10527	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_chr16_-_18248701_18248813	0.10486	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_chr6_+_54987993_54988082	0.104826	SOX2.p2	NM_180678|Gars|353172|glycyl-tRNA synthetase	AK012758|Gars|353172|glycyl-tRNA synthetase	BC021747|Gars|353172|glycyl-tRNA synthetase	AK146238|Gars|353172|glycyl-tRNA synthetase	AK165857|Gars|353172|glycyl-tRNA synthetase
mm9_v1_chr11_+_11586215_11586246	0.10481	SOX2.p2	NM_001025597|Ikzf1|22778|IKAROS family zinc finger 1	NM_009578|Ikzf1|22778|IKAROS family zinc finger 1	AK036833|Ikzf1|22778|IKAROS family zinc finger 1	AK040268|Ikzf1|22778|IKAROS family zinc finger 1
mm9_v1_chr12_-_70298068_70298133	0.104748	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_chr3_+_90097269_90097314	0.104598	SOX2.p2	AK041594|Gatad2b|229542|GATA zinc finger domain containing 2B
mm9_v1_chr5_-_105411580_105411736	0.104448	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_+_3795221_3795283	0.104282	SOX2.p2	NM_173745|Dusp18|75219|dual specificity phosphatase 18	AK079664|Dusp18|75219|dual specificity phosphatase 18	BC020036|Dusp18|75219|dual specificity phosphatase 18	AK015917|Dusp18|75219|dual specificity phosphatase 18	AK081916|Dusp18|75219|dual specificity phosphatase 18
mm9_v1_chr4_-_129952771_129952844	0.104064	SOX2.p2	AK075863|Serinc2|230779|serine incorporator 2	BC031720|Serinc2|230779|serine incorporator 2	NM_172702|Serinc2|230779|serine incorporator 2
mm9_v1_chr9_-_20700331_20700394	0.103968	SOX2.p2	
mm9_v1_chr10_-_88289526_88289560	0.103939	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_chr1_-_53813191_53813277	0.103685	SOX2.p2	
mm9_v1_chr12_-_86682028_86682042	0.103601	SOX2.p2	
mm9_v1_chr1_-_153275461_153275510	0.103486	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_-_41905549_41905563	0.103391	SOX2.p2	AK041595|Foxo3|56484|forkhead box O3	AK159465|Foxo3|56484|forkhead box O3
mm9_v1_chr10_+_128787620_128787620	0.103372	SOX2.p2	NM_001011797|Olfr782|257985|olfactory receptor 782
mm9_v1_chr10_-_33816255_33816324	0.103296	SOX2.p2	AK161070|Fam26e|103511|family with sequence similarity 26, member E	AK052861|Fam26e|103511|family with sequence similarity 26, member E	AK078850|Fam26e|103511|family with sequence similarity 26, member E	BC025893|Fam26e|103511|family with sequence similarity 26, member E	AK085925|Fam26e|103511|family with sequence similarity 26, member E	NM_178908|Fam26e|103511|family with sequence similarity 26, member E
mm9_v1_chr8_+_81552335_81552485	0.103019	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_chr4_+_13711928_13711928	0.102897	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_chr17_-_34880784_34880841	0.102783	SOX2.p2	BC158005|C4b|12268|complement component 4B (Childo blood group)	BC150743|C4b|12268|complement component 4B (Childo blood group)	BC039141|C4b|12268|complement component 4B (Childo blood group)	BC067394|C4b|12268|complement component 4B (Childo blood group)	BC067409|C4b|12268|complement component 4B (Childo blood group)	BC055297|C4b|12268|complement component 4B (Childo blood group)	AK172637|C4b|12268|complement component 4B (Childo blood group)	AK157954|C4b|12268|complement component 4B (Childo blood group)	AK158256|C4b|12268|complement component 4B (Childo blood group)	AK158475|C4b|12268|complement component 4B (Childo blood group)	AK171644|C4b|12268|complement component 4B (Childo blood group)	M11729|C4b|12268|complement component 4B (Childo blood group)	NM_009780|C4b|12268|complement component 4B (Childo blood group)
mm9_v1_chr4_-_149072713_149072721	0.102782	SOX2.p2	AK149935|Pik3cd|18707|phosphatidylinositol 3-kinase catalytic delta polypeptide	AK150649|Pik3cd|18707|phosphatidylinositol 3-kinase catalytic delta polypeptide	AK151482|Pik3cd|18707|phosphatidylinositol 3-kinase catalytic delta polypeptide	AK152661|Pik3cd|18707|phosphatidylinositol 3-kinase catalytic delta polypeptide
mm9_v1_chr1_+_65357830_65357830	0.102006	SOX2.p2	AK045576|Pth2r|213527|parathyroid hormone 2 receptor	NM_139270|Pth2r|213527|parathyroid hormone 2 receptor
mm9_v1_chr14_+_14845004_14845173	0.101957	SOX2.p2	AK046679|Atxn7|246103|ataxin 7	NM_139227|Atxn7|246103|ataxin 7	BC137846|Atxn7|246103|ataxin 7
mm9_v1_chr10_-_94877824_94877916	0.101715	SOX2.p2	U88327|Socs2|216233|suppressor of cytokine signaling 2	NM_001168657|Socs2|216233|suppressor of cytokine signaling 2
mm9_v1_chr13_+_23831738_23831861	0.101642	SOX2.p2	AK207079|Hist1h1c|50708|histone cluster 1, H1c	AK215388|Hist1h1c|50708|histone cluster 1, H1c	AK216099|Hist1h1c|50708|histone cluster 1, H1c	AK216922|Hist1h1c|50708|histone cluster 1, H1c
mm9_v1_chr13_-_113385269_113385392	0.101035	SOX2.p2	
mm9_v1_chr12_-_81744771_81744855	0.100687	SOX2.p2	BC107315|Erh|13877|enhancer of rudimentary homolog (Drosophila)	BC107316|Erh|13877|enhancer of rudimentary homolog (Drosophila)	BC132421|Erh|13877|enhancer of rudimentary homolog (Drosophila)	BC132423|Erh|13877|enhancer of rudimentary homolog (Drosophila)	U66870|Erh|13877|enhancer of rudimentary homolog (Drosophila)	BC099476|Erh|13877|enhancer of rudimentary homolog (Drosophila)	U01140|Erh|13877|enhancer of rudimentary homolog (Drosophila)	BC083141|Erh|13877|enhancer of rudimentary homolog (Drosophila)	AK171834|Erh|13877|enhancer of rudimentary homolog (Drosophila)	AK010451|Erh|13877|enhancer of rudimentary homolog (Drosophila)	D73368|Erh|13877|enhancer of rudimentary homolog (Drosophila)	AK168188|Erh|13877|enhancer of rudimentary homolog (Drosophila)	AK080617|Erh|13877|enhancer of rudimentary homolog (Drosophila)	NM_007951|Erh|13877|enhancer of rudimentary homolog (Drosophila)
mm9_v1_chr4_+_134481298_134481299	0.100644	SOX2.p2	
mm9_v1_chr5_-_136646451_136646559	0.100539	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_chr8_+_73224288_73224388	0.100492	SOX2.p2	AK131827|Jund|16478|Jun proto-oncogene related gene d
mm9_v1_chr5_+_145016734_145016797	0.100488	SOX2.p2	X61454|Bri3|55950|brain protein I3
mm9_v1_chr11_-_120441272_120441356	0.100372	SOX2.p2	AK204953|Arhgdia|192662|Rho GDP dissociation inhibitor (GDI) alpha
mm9_v1_chr19_+_12770289_12770302	0.0998498	SOX2.p2	BC010803|Keg1|64697|kidney expressed gene 1	AK165462|Keg1|64697|kidney expressed gene 1	AB028071|Keg1|64697|kidney expressed gene 1
mm9_v1_chr15_-_38448923_38449033	0.0998496	SOX2.p2	BC046814|Azin1|54375|antizyme inhibitor 1	BC021152|Azin1|54375|antizyme inhibitor 1	BC019412|Azin1|54375|antizyme inhibitor 1	AK088112|Azin1|54375|antizyme inhibitor 1	AK088671|Azin1|54375|antizyme inhibitor 1	AK133914|Azin1|54375|antizyme inhibitor 1	AK049680|Azin1|54375|antizyme inhibitor 1	NM_001102458|Azin1|54375|antizyme inhibitor 1	NM_018745|Azin1|54375|antizyme inhibitor 1
mm9_v1_chr19_+_47654508_47654642	0.099811	SOX2.p2	AF039574|Slk|20874|STE20-like kinase (yeast)	NM_001164639|Slk|20874|STE20-like kinase (yeast)	NM_009289|Slk|20874|STE20-like kinase (yeast)	BC131674|Slk|20874|STE20-like kinase (yeast)	BC131675|Slk|20874|STE20-like kinase (yeast)	AF112855|Slk|20874|STE20-like kinase (yeast)	AK029491|Slk|20874|STE20-like kinase (yeast)
mm9_v1_chr14_-_51766415_51766443	0.0996345	SOX2.p2	M27814|Rnase1|19752|ribonuclease, RNase A family, 1 (pancreatic)	BC030036|Rnase1|19752|ribonuclease, RNase A family, 1 (pancreatic)	AK075775|Rnase1|19752|ribonuclease, RNase A family, 1 (pancreatic)	NM_011271|Rnase1|19752|ribonuclease, RNase A family, 1 (pancreatic)
mm9_v1_chr6_-_38075416_38075515	0.0993344	SOX2.p2	AK141785|D630045J12Rik|330286|RIKEN cDNA D630045J12 gene
mm9_v1_chr11_+_96891270_96891328	0.0991473	SOX2.p2	AK075869|Scrn2|217140|secernin 2	BC021346|Scrn2|217140|secernin 2	BC010784|Scrn2|217140|secernin 2
mm9_v1_chr11_-_6174828_6174898	0.0987582	SOX2.p2	BC023041|Tmed4|103694|transmembrane emp24 protein transport domain containing 4	NM_134020|Tmed4|103694|transmembrane emp24 protein transport domain containing 4	AK078425|Tmed4|103694|transmembrane emp24 protein transport domain containing 4	AF368921|Tmed4|103694|transmembrane emp24 protein transport domain containing 4	AK158876|Tmed4|103694|transmembrane emp24 protein transport domain containing 4
mm9_v1_chr8_+_90642636_90642724	0.0985779	SOX2.p2	NM_029074|Tmem188|382030|transmembrane protein 188	AK146578|Tmem188|382030|transmembrane protein 188	BC018498|Tmem188|382030|transmembrane protein 188	AK017198|Tmem188|382030|transmembrane protein 188	BC094385|Tmem188|382030|transmembrane protein 188	BC118981|Tmem188|382030|transmembrane protein 188	BC148291|Tmem188|382030|transmembrane protein 188
mm9_v1_chr16_+_52031661_52031695	0.0976819	SOX2.p2	NM_001033238|Cblb|208650|Casitas B-lineage lymphoma b	AK147367|Cblb|208650|Casitas B-lineage lymphoma b
mm9_v1_chr6_+_142712854_142712889	0.09742	SOX2.p2	
mm9_v1_chr7_-_133929984_133930019	0.0974096	SOX2.p2	AK199030|Ppp4c|56420|protein phosphatase 4, catalytic subunit
mm9_v1_chr17_-_46168654_46168719	0.0972672	SOX2.p2	AY707864|Vegfa|22339|vascular endothelial growth factor A	AY750956|Vegfa|22339|vascular endothelial growth factor A	AY750957|Vegfa|22339|vascular endothelial growth factor A	EF028705|Vegfa|22339|vascular endothelial growth factor A	BC061468|Vegfa|22339|vascular endothelial growth factor A
mm9_v1_chr13_+_89680240_89680277	0.0971933	SOX2.p2	AK032750|Hapln1|12950|hyaluronan and proteoglycan link protein 1	NM_013500|Hapln1|12950|hyaluronan and proteoglycan link protein 1
mm9_v1_chr4_-_34754469_34754554	0.0968139	SOX2.p2	AB221605|Zfp292|30046|zinc finger protein 292
mm9_v1_chr5_+_93238413_93238466	0.0966882	SOX2.p2	NM_001077595|Shroom3|27428|shroom family member 3	AK164918|Shroom3|27428|shroom family member 3	AF199422|Shroom3|27428|shroom family member 3
mm9_v1_chr11_-_102157904_102158007	0.0961439	SOX2.p2	NM_001098836|Atxn7l3|217218|ataxin 7-like 3	NM_001098837|Atxn7l3|217218|ataxin 7-like 3	AK090368|Atxn7l3|217218|ataxin 7-like 3
mm9_v1_chr7_+_140829388_140829408	0.0959724	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_chrX_+_34142137_34142199	0.0957526	SOX2.p2	
mm9_v1_chr2_+_181599056_181599106	0.0955709	SOX2.p2	NM_025901|Polr3k|67005|polymerase (RNA) III (DNA directed) polypeptide K
mm9_v1_chr14_-_73725546_73725555	0.0954323	SOX2.p2	M26391|Rb1|19645|retinoblastoma 1
mm9_v1_chr1_-_45559700_45559773	0.0950185	SOX2.p2	AK139130|Col5a2|12832|collagen, type V, alpha 2	AK160008|Col5a2|12832|collagen, type V, alpha 2	L02918|Col5a2|12832|collagen, type V, alpha 2	AK084803|Col5a2|12832|collagen, type V, alpha 2
mm9_v1_chr15_+_76174727_76174807	0.0948242	SOX2.p2	AK182781|Cyc1|66445|cytochrome c-1	AK188690|Cyc1|66445|cytochrome c-1	AK184866|Cyc1|66445|cytochrome c-1	AK195664|Cyc1|66445|cytochrome c-1	AK215816|Cyc1|66445|cytochrome c-1
mm9_v1_chr1_-_183141500_183141531	0.0947499	SOX2.p2	AK075743|Wdr26|226757|WD repeat domain 26
mm9_v1_chr17_+_72022598_72022608	0.0947176	SOX2.p2	NM_177087|Fam179a|320159|family with sequence similarity 179, member A
mm9_v1_chr19_-_24758826_24758856	0.0944703	SOX2.p2	AK020587|Pgm5|226041|phosphoglucomutase 5
mm9_v1_chr7_-_106987766_106987861	0.0941817	SOX2.p2	AK180141|Spcs2|66624|signal peptidase complex subunit 2 homolog (S. cerevisiae)
mm9_v1_chr4_-_40883509_40883654	0.0941147	SOX2.p2	AK184952|Bag1|12017|BCL2-associated athanogene 1	AK213721|Bag1|12017|BCL2-associated athanogene 1	AK216811|Bag1|12017|BCL2-associated athanogene 1
mm9_v1_chr6_+_29685629_29685693	0.0935297	SOX2.p2	BC048091|Smo|319757|smoothened homolog (Drosophila)
mm9_v1_chr2_-_105229165_105229175	0.0930954	SOX2.p2	AK179954|Rcn1|19672|reticulocalbin 1
mm9_v1_chr1_+_183081066_183081111	0.093076	SOX2.p2	AK144157|Cnih4|98417|cornichon homolog 4 (Drosophila)	AK021301|Cnih4|98417|cornichon homolog 4 (Drosophila)
mm9_v1_chr11_-_101755622_101755677	0.0923544	SOX2.p2	Z15103|Meox1|17285|mesenchyme homeobox 1	BC011082|Meox1|17285|mesenchyme homeobox 1	NM_010791|Meox1|17285|mesenchyme homeobox 1	AK052370|Meox1|17285|mesenchyme homeobox 1
mm9_v1_chr3_-_80606704_80606756	0.092187	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_chr8_+_34807688_34807718	0.0920256	SOX2.p2	AK027984|Gsr|14782|glutathione reductase
mm9_v1_chr11_+_96164905_96165020	0.0918252	SOX2.p2	BC103595|Hoxb5|15413|homeobox B5	BC103596|Hoxb5|15413|homeobox B5	BC103604|Hoxb5|15413|homeobox B5	BC103607|Hoxb5|15413|homeobox B5	AK133512|Hoxb5|15413|homeobox B5	AK012146|Hoxb5|15413|homeobox B5
mm9_v1_chr1_-_154472199_154472354	0.0915952	SOX2.p2	BC017678|Rgl1|19731|ral guanine nucleotide dissociation stimulator,-like 1	NM_016846|Rgl1|19731|ral guanine nucleotide dissociation stimulator,-like 1	U14103|Rgl1|19731|ral guanine nucleotide dissociation stimulator,-like 1	AK169109|Rgl1|19731|ral guanine nucleotide dissociation stimulator,-like 1	AK169180|Rgl1|19731|ral guanine nucleotide dissociation stimulator,-like 1	AK144218|Rgl1|19731|ral guanine nucleotide dissociation stimulator,-like 1
mm9_v1_chr13_+_43711165_43711165	0.0910294	SOX2.p2	NM_183204|Rnf182|328234|ring finger protein 182
mm9_v1_chr5_-_17341512_17341522	0.0908072	SOX2.p2	AK052825|Cd36|12491|CD36 antigen
mm9_v1_chr9_+_77961044_77961183	0.0907751	SOX2.p2	NM_019987|Ick|56542|intestinal cell kinase	AK045950|Ick|56542|intestinal cell kinase	AK164613|Ick|56542|intestinal cell kinase	AK008991|Ick|56542|intestinal cell kinase	AK133537|Ick|56542|intestinal cell kinase	AK087484|Ick|56542|intestinal cell kinase
mm9_v1_chr4_-_134773161_134773181	0.09072	SOX2.p2	AK195597|Clic4|29876|chloride intracellular channel 4 (mitochondrial)	AK203584|Clic4|29876|chloride intracellular channel 4 (mitochondrial)
mm9_v1_chr11_-_120442851_120442887	0.0904307	SOX2.p2	BC086755|Arhgdia|192662|Rho GDP dissociation inhibitor (GDI) alpha	BC004732|Arhgdia|192662|Rho GDP dissociation inhibitor (GDI) alpha	AK156819|Arhgdia|192662|Rho GDP dissociation inhibitor (GDI) alpha	AK172140|Arhgdia|192662|Rho GDP dissociation inhibitor (GDI) alpha
mm9_v1_chr3_+_37538897_37539001	0.0900424	SOX2.p2	AF176903|Spry1|24063|sprouty homolog 1 (Drosophila)	BC051977|Spry1|24063|sprouty homolog 1 (Drosophila)
mm9_v1_chr5_-_124804538_124804560	0.0899562	SOX2.p2	BC103772|Cdk2ap1|13445|CDK2 (cyclin-dependent kinase 2)-associated protein 1
mm9_v1_chr19_-_5295389_5295474	0.0891016	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_chr10_-_62254978_62254996	0.089084	SOX2.p2	BC079652|Ccar1|67500|cell division cycle and apoptosis regulator 1	BC010199|Ccar1|67500|cell division cycle and apoptosis regulator 1
mm9_v1_chr15_+_6395353_6395370	0.0890831	SOX2.p2	X05475|C9|12279|complement component 9
mm9_v1_chr11_+_29030725_29030774	0.0890597	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_chr13_-_58494637_58494692	0.088407	SOX2.p2	AK207611|Hnrnpk|15387|heterogeneous nuclear ribonucleoprotein K
mm9_v1_chr9_-_48644030_48644051	0.0883407	SOX2.p2	AK040211|Zbtb16|235320|zinc finger and BTB domain containing 16	AK142947|Zbtb16|235320|zinc finger and BTB domain containing 16	NM_001033324|Zbtb16|235320|zinc finger and BTB domain containing 16
mm9_v1_chr9_-_108480927_108481054	0.0882046	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_chr2_-_76820599_76820607	0.0879307	SOX2.p2	AK084718|Ttn|22138|titin	AK052859|Ttn|22138|titin	AK084709|Ttn|22138|titin	AK085811|Ttn|22138|titin	AK085832|Ttn|22138|titin	NM_011652|Ttn|22138|titin	NM_028004|Ttn|22138|titin
mm9_v1_chr10_-_12587945_12588041	0.0878072	SOX2.p2	BC062163|Utrn|22288|utrophin	BC011062|Utrn|22288|utrophin
mm9_v1_chr6_-_49164952_49164952	0.0874557	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_chr4_-_83132289_83132381	0.0864594	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_chr10_+_82448326_82448493	0.0863862	SOX2.p2	BC137629|Chst11|58250|carbohydrate sulfotransferase 11	BC144793|Chst11|58250|carbohydrate sulfotransferase 11
mm9_v1_chr18_-_12394830_12394911	0.0860298	SOX2.p2	AK044878|Npc1|18145|Niemann Pick type C1	AK170880|Npc1|18145|Niemann Pick type C1	AK171371|Npc1|18145|Niemann Pick type C1	AK087174|Npc1|18145|Niemann Pick type C1	AF003348|Npc1|18145|Niemann Pick type C1	AK040367|Npc1|18145|Niemann Pick type C1	BC052437|Npc1|18145|Niemann Pick type C1	BC054539|Npc1|18145|Niemann Pick type C1	NM_008720|Npc1|18145|Niemann Pick type C1
mm9_v1_chr9_+_47338255_47338425	0.0859434	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_chr9_+_77765170_77765271	0.0859345	SOX2.p2	AK031743|Elovl5|68801|ELOVL family member 5, elongation of long chain fatty acids (yeast)	AK162451|Elovl5|68801|ELOVL family member 5, elongation of long chain fatty acids (yeast)	NM_134255|Elovl5|68801|ELOVL family member 5, elongation of long chain fatty acids (yeast)	AK051580|Elovl5|68801|ELOVL family member 5, elongation of long chain fatty acids (yeast)	AK045274|Elovl5|68801|ELOVL family member 5, elongation of long chain fatty acids (yeast)	AK085663|Elovl5|68801|ELOVL family member 5, elongation of long chain fatty acids (yeast)	AK085696|Elovl5|68801|ELOVL family member 5, elongation of long chain fatty acids (yeast)	AK028761|Elovl5|68801|ELOVL family member 5, elongation of long chain fatty acids (yeast)	AK167755|Elovl5|68801|ELOVL family member 5, elongation of long chain fatty acids (yeast)	AK168360|Elovl5|68801|ELOVL family member 5, elongation of long chain fatty acids (yeast)	AK088153|Elovl5|68801|ELOVL family member 5, elongation of long chain fatty acids (yeast)	AK168987|Elovl5|68801|ELOVL family member 5, elongation of long chain fatty acids (yeast)	BC022911|Elovl5|68801|ELOVL family member 5, elongation of long chain fatty acids (yeast)
mm9_v1_chr4_-_150421459_150421590	0.0855809	SOX2.p2	
mm9_v1_chr19_+_53674862_53674958	0.0855755	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_chr11_-_115476794_115476844	0.0855326	SOX2.p2	
mm9_v1_chr15_-_99305127_99305160	0.0854719	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_chr17_+_86020173_86020181	0.0852133	SOX2.p2	NM_011381|Six3|20473|sine oculis-related homeobox 3 homolog (Drosophila)
mm9_v1_chr5_-_134718500_134718616	0.0851105	SOX2.p2	AK183312|Gtf2i|14886|general transcription factor II I	AK211276|Gtf2i|14886|general transcription factor II I
mm9_v1_chr6_+_86321479_86321568	0.0849974	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_chr10_+_61912236_61912284	0.0846652	SOX2.p2	AK135283|4930507D05Rik|74706|RIKEN cDNA 4930507D05 gene	AK042417|4930507D05Rik|74706|RIKEN cDNA 4930507D05 gene	AK054359|4930507D05Rik|74706|RIKEN cDNA 4930507D05 gene	BC019469|4930507D05Rik|74706|RIKEN cDNA 4930507D05 gene
mm9_v1_chr9_+_108393149_108393235	0.0846162	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_chr4_+_126698578_126698591	0.0846098	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_+_76174029_76174095	0.0845735	SOX2.p2	AK192516|Cyc1|66445|cytochrome c-1
mm9_v1_chr11_-_3795097_3795128	0.0845339	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_chr7_+_50817739_50817739	0.0843775	SOX2.p2	AK155078|Zfp658|210104|zinc finger protein 658	NM_001008549|Zfp658|210104|zinc finger protein 658
mm9_v1_chr1_-_135557925_135557932	0.0843184	SOX2.p2	BC066163|Zc3h11a|70579|zinc finger CCCH type containing 11A
mm9_v1_chr7_+_52071622_52071810	0.0841899	SOX2.p2	AK166621|Nup62|18226|nucleoporin 62	BC089317|Nup62|18226|nucleoporin 62	AK149637|Nup62|18226|nucleoporin 62	NM_001171024|Nup62-il4i1|100328588|Nup62-Il4i1 protein	AK169178|Nup62|18226|nucleoporin 62	AK168486|Nup62|18226|nucleoporin 62	AK147894|Nup62|18226|nucleoporin 62	AK133082|Nup62-il4i1|100328588|Nup62-Il4i1 protein	AK155059|Nup62|18226|nucleoporin 62	AK168166|Nup62|18226|nucleoporin 62	AK150087|Nup62|18226|nucleoporin 62	BC005784|Nup62|18226|nucleoporin 62	NM_053074|Nup62|18226|nucleoporin 62	S59342|Nup62|18226|nucleoporin 62
mm9_v1_chr1_-_55084321_55084327	0.0838347	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_chr2_-_26766145_26766181	0.0837402	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_chr9_+_21875410_21875475	0.0833072	SOX2.p2	AK154427|LOC100503652|100503652|hypothetical LOC100503652
mm9_v1_chr11_-_95574067_95574079	0.083071	SOX2.p2	AK027957|1110035M17Rik|432396|RIKEN cDNA 1110035M17 gene
mm9_v1_chr17_-_24781872_24781901	0.0830636	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_chr4_+_32504409_32504501	0.0828752	SOX2.p2	NM_001109661|Bach2|12014|BTB and CNC homology 2	BC131642|Bach2|12014|BTB and CNC homology 2
mm9_v1_chr2_-_26495749_26495770	0.0828182	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_chr5_-_100467887_100467935	0.0822904	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_+_7374435_7374635	0.0820441	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_chr3_+_130320365_130320530	0.0819314	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_chr16_+_4594742_4594894	0.0818826	SOX2.p2	BC021517|Glis2|83396|GLIS family zinc finger 2
mm9_v1_chr6_-_113678282_113678406	0.0814512	SOX2.p2	
mm9_v1_chr4_+_86520317_86520392	0.0808749	SOX2.p2	BC059819|Acer2|230379|alkaline ceramidase 2	NM_139306|Acer2|230379|alkaline ceramidase 2	AK085306|Acer2|230379|alkaline ceramidase 2	AF282864|Acer2|230379|alkaline ceramidase 2	AY312515|Acer2|230379|alkaline ceramidase 2
mm9_v1_chr15_+_35860580_35860704	0.0807585	SOX2.p2	AK007749|Vps13b|666173|vacuolar protein sorting 13B (yeast)
mm9_v1_chr19_-_47993687_47993788	0.0806712	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_chrX_-_70905384_70905478	0.0806327	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_chr16_+_64851768_64851933	0.0805238	SOX2.p2	AK086053|Cggbp1|106143|CGG triplet repeat binding protein 1	AK049631|Cggbp1|106143|CGG triplet repeat binding protein 1	AK052195|Cggbp1|106143|CGG triplet repeat binding protein 1	BC057053|Cggbp1|106143|CGG triplet repeat binding protein 1	AK083450|Cggbp1|106143|CGG triplet repeat binding protein 1	BC043097|Cggbp1|106143|CGG triplet repeat binding protein 1	NM_178647|Cggbp1|106143|CGG triplet repeat binding protein 1
mm9_v1_chr5_+_119214935_119215085	0.0804907	SOX2.p2	AK083611|Med13l|76199|mediator complex subunit 13-like
mm9_v1_chr14_+_31832340_31832345	0.0802762	SOX2.p2	AK166588|Pbrm1|66923|polybromo 1
mm9_v1_chr13_+_49474730_49474801	0.0799653	SOX2.p2	AK189233|Bicd2|76895|bicaudal D homolog 2 (Drosophila)
mm9_v1_chr5_-_115750913_115750938	0.079829	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_chr17_-_56098803_56098845	0.0786918	SOX2.p2	
mm9_v1_chr12_+_59312790_59312790	0.0785453	SOX2.p2	AK046464|Sstr1|20605|somatostatin receptor 1	NM_009216|Sstr1|20605|somatostatin receptor 1
mm9_v1_chr18_-_9450104_9450192	0.0785287	SOX2.p2	BC023321|Ccny|67974|cyclin Y	AK028696|Ccny|67974|cyclin Y	NM_026484|Ccny|67974|cyclin Y	AK014201|Ccny|67974|cyclin Y
mm9_v1_chr10_+_82329370_82329405	0.0782283	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_chr17_+_45704145_45704512	0.0777904	SOX2.p2	AK211181|Slc35b2|73836|solute carrier family 35, member B2	AK212100|Slc35b2|73836|solute carrier family 35, member B2	AK207266|Slc35b2|73836|solute carrier family 35, member B2	AK212091|Slc35b2|73836|solute carrier family 35, member B2	AK214463|Slc35b2|73836|solute carrier family 35, member B2
mm9_v1_chr3_-_84284304_84284362	0.077683	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_chr12_-_56922146_56922187	0.077468	SOX2.p2	AK046680|Ralgapa1|56784|Ral GTPase activating protein, alpha subunit 1	AY596972|Ralgapa1|56784|Ral GTPase activating protein, alpha subunit 1	AY596973|Ralgapa1|56784|Ral GTPase activating protein, alpha subunit 1	AY596974|Ralgapa1|56784|Ral GTPase activating protein, alpha subunit 1	NM_001003719|Ralgapa1|56784|Ral GTPase activating protein, alpha subunit 1	NM_001112714|Ralgapa1|56784|Ral GTPase activating protein, alpha subunit 1	NM_019994|Ralgapa1|56784|Ral GTPase activating protein, alpha subunit 1
mm9_v1_chr16_-_38800293_38800318	0.0767887	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_chrX_-_53851108_53851245	0.0767249	SOX2.p2	AK043524|Mmgt1|236792|membrane magnesium transporter 1	BC032271|Mmgt1|236792|membrane magnesium transporter 1	AK163269|Mmgt1|236792|membrane magnesium transporter 1
mm9_v1_chr5_-_122907002_122907003	0.076523	SOX2.p2	AK134659|Atp2a2|11938|ATPase, Ca++ transporting, cardiac muscle, slow twitch 2
mm9_v1_chr13_-_46060325_46060353	0.0764951	SOX2.p2	BC058178|Atxn1|20238|ataxin 1	AK048268|Atxn1|20238|ataxin 1	NM_009124|Atxn1|20238|ataxin 1	AK169931|Atxn1|20238|ataxin 1
mm9_v1_chr9_-_7835107_7835268	0.076476	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_chr19_-_41151561_41151602	0.0764553	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_chr18_+_83080270_83080270	0.0761173	SOX2.p2	NM_183033|Zfp516|329003|zinc finger protein 516
mm9_v1_chr2_+_49307207_49307338	0.0756136	SOX2.p2	AK047947|Epc2|227867|enhancer of polycomb homolog 2 (Drosophila)
mm9_v1_chr6_+_115189004_115189072	0.0755571	SOX2.p2	AK029181|Syn2|20965|synapsin II
mm9_v1_chr2_+_80171439_80171527	0.0755537	SOX2.p2	AK190686|Dnajc10|66861|DnaJ (Hsp40) homolog, subfamily C, member 10	AK204346|Dnajc10|66861|DnaJ (Hsp40) homolog, subfamily C, member 10	AK206826|Dnajc10|66861|DnaJ (Hsp40) homolog, subfamily C, member 10	BC002207|Dnajc10|66861|DnaJ (Hsp40) homolog, subfamily C, member 10
mm9_v1_chr1_+_109407998_109408121	0.0755211	SOX2.p2	AK081487|Serpinb2|18788|serine (or cysteine) peptidase inhibitor, clade B, member 2	NM_001174170|Serpinb2|18788|serine (or cysteine) peptidase inhibitor, clade B, member 2	NM_011111|Serpinb2|18788|serine (or cysteine) peptidase inhibitor, clade B, member 2	AK090049|Serpinb2|18788|serine (or cysteine) peptidase inhibitor, clade B, member 2
mm9_v1_chr8_-_13890244_13890296	0.0754142	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_chr1_-_45560001_45560126	0.075211	SOX2.p2	AK147328|Col5a2|12832|collagen, type V, alpha 2	NM_007737|Col5a2|12832|collagen, type V, alpha 2
mm9_v1_chr18_+_37649118_37649272	0.0751623	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_chr2_+_157250049_157250129	0.0751473	SOX2.p2	
mm9_v1_chrX_-_101396512_101396524	0.0749266	SOX2.p2	AK054513|C77370|245555|expressed sequence C77370
mm9_v1_chr17_+_47505827_47505888	0.0745619	SOX2.p2	NM_001146211|Mrps10|64657|mitochondrial ribosomal protein S10	NM_001146212|Mrps10|64657|mitochondrial ribosomal protein S10	AK142675|Mrps10|64657|mitochondrial ribosomal protein S10	AK004151|Mrps10|64657|mitochondrial ribosomal protein S10	BC038917|Mrps10|64657|mitochondrial ribosomal protein S10	BC096043|Mrps10|64657|mitochondrial ribosomal protein S10
mm9_v1_chr12_-_113749361_113749362	0.0745601	SOX2.p2	BC055014|Tmem179|104885|transmembrane protein 179
mm9_v1_chr19_+_45101318_45101473	0.0744268	SOX2.p2	AK202462|Lzts2|226154|leucine zipper, putative tumor suppressor 2	AK203408|Lzts2|226154|leucine zipper, putative tumor suppressor 2	AK205448|Lzts2|226154|leucine zipper, putative tumor suppressor 2	AK210216|Lzts2|226154|leucine zipper, putative tumor suppressor 2	AK215584|Lzts2|226154|leucine zipper, putative tumor suppressor 2	AK215776|Lzts2|226154|leucine zipper, putative tumor suppressor 2	AK217660|Lzts2|226154|leucine zipper, putative tumor suppressor 2
mm9_v1_chr10_-_62801726_62801784	0.0744002	SOX2.p2	AK140330|Sirt1|93759|sirtuin 1 (silent mating type information regulation 2, homolog) 1 (S. cerevisiae)	BC152314|Sirt1|93759|sirtuin 1 (silent mating type information regulation 2, homolog) 1 (S. cerevisiae)	NM_001159590|Sirt1|93759|sirtuin 1 (silent mating type information regulation 2, homolog) 1 (S. cerevisiae)	AY377984|Sirt1|93759|sirtuin 1 (silent mating type information regulation 2, homolog) 1 (S. cerevisiae)	AF214646|Sirt1|93759|sirtuin 1 (silent mating type information regulation 2, homolog) 1 (S. cerevisiae)	NM_019812|Sirt1|93759|sirtuin 1 (silent mating type information regulation 2, homolog) 1 (S. cerevisiae)	AK144203|Sirt1|93759|sirtuin 1 (silent mating type information regulation 2, homolog) 1 (S. cerevisiae)	NM_001159589|Sirt1|93759|sirtuin 1 (silent mating type information regulation 2, homolog) 1 (S. cerevisiae)
mm9_v1_chr11_+_49477111_49477127	0.0743697	SOX2.p2	AF313456|Scgb3a1|68662|secretoglobin, family 3A, member 1	AF313457|Scgb3a1|68662|secretoglobin, family 3A, member 1	NM_054037|Scgb3a1|68662|secretoglobin, family 3A, member 1	NM_170727|Scgb3a1|68662|secretoglobin, family 3A, member 1	AK003988|Scgb3a1|68662|secretoglobin, family 3A, member 1	BC086910|Scgb3a1|68662|secretoglobin, family 3A, member 1	AF436840|Scgb3a1|68662|secretoglobin, family 3A, member 1
mm9_v1_chr7_-_31514445_31514522	0.0743616	SOX2.p2	AK008089|Tmem147|69804|transmembrane protein 147	AK007753|Tmem147|69804|transmembrane protein 147	BC147300|Tmem147|69804|transmembrane protein 147	BC147301|Tmem147|69804|transmembrane protein 147
mm9_v1_chr6_+_79969636_79969636	0.0738357	SOX2.p2	NM_178731|Lrrtm4|243499|leucine rich repeat transmembrane neuronal 4
mm9_v1_chr7_-_72516109_72516162	0.0736191	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_chr6_+_65331287_65331386	0.0728814	SOX2.p2	NM_175524|C130060K24Rik|243407|RIKEN cDNA C130060K24 gene	AK051723|C130060K24Rik|243407|RIKEN cDNA C130060K24 gene	AK048439|C130060K24Rik|243407|RIKEN cDNA C130060K24 gene	BC119578|C130060K24Rik|243407|RIKEN cDNA C130060K24 gene	BC119579|C130060K24Rik|243407|RIKEN cDNA C130060K24 gene
mm9_v1_chr11_-_120440835_120441001	0.0728462	SOX2.p2	AK205360|Arhgdia|192662|Rho GDP dissociation inhibitor (GDI) alpha	AK178545|Arhgdia|192662|Rho GDP dissociation inhibitor (GDI) alpha	AK201731|Arhgdia|192662|Rho GDP dissociation inhibitor (GDI) alpha	AK201760|Arhgdia|192662|Rho GDP dissociation inhibitor (GDI) alpha	AK205658|Arhgdia|192662|Rho GDP dissociation inhibitor (GDI) alpha
mm9_v1_chr16_+_21423190_21423247	0.072823	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_chr7_-_28140965_28141037	0.0727299	SOX2.p2	AK160641|Shkbp1|192192|Sh3kbp1 binding protein 1	BC061477|Shkbp1|192192|Sh3kbp1 binding protein 1	AK154779|Shkbp1|192192|Sh3kbp1 binding protein 1	NM_138676|Shkbp1|192192|Sh3kbp1 binding protein 1	AF246218|Shkbp1|192192|Sh3kbp1 binding protein 1
mm9_v1_chr18_+_37885359_37885546	0.0720653	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_chr6_-_52154325_52154433	0.0719337	SOX2.p2	AK144356|Hoxa5|15402|homeobox A5	AB221550|Hoxa5|15402|homeobox A5	BC011063|Hoxa5|15402|homeobox A5
mm9_v1_chr12_+_109609362_109609455	0.0718716	SOX2.p2	BC150975|Eml1|68519|echinoderm microtubule associated protein like 1
mm9_v1_chr4_+_126803283_126803296	0.0718418	SOX2.p2	AK160613|Gm12942|100039968|predicted gene 12942	NM_001099319|Gm12942|100039968|predicted gene 12942
mm9_v1_chr11_-_20612281_20612323	0.0718185	SOX2.p2	AK150458|Aftph|216549|aftiphilin	AK152308|Aftph|216549|aftiphilin	AK152487|Aftph|216549|aftiphilin	AK161532|Aftph|216549|aftiphilin
mm9_v1_chr12_+_52792192_52792204	0.0715465	SOX2.p2	BC053339|Ap4s1|11782|adaptor-related protein complex AP-4, sigma 1	AK005283|Ap4s1|11782|adaptor-related protein complex AP-4, sigma 1
mm9_v1_chr11_-_120442889_120442950	0.0706472	SOX2.p2	AK170553|Arhgdia|192662|Rho GDP dissociation inhibitor (GDI) alpha	AK143516|Arhgdia|192662|Rho GDP dissociation inhibitor (GDI) alpha	AK165241|Arhgdia|192662|Rho GDP dissociation inhibitor (GDI) alpha	AK170718|Arhgdia|192662|Rho GDP dissociation inhibitor (GDI) alpha	NM_133796|Arhgdia|192662|Rho GDP dissociation inhibitor (GDI) alpha
mm9_v1_chr9_+_44307218_44307218	0.0705757	SOX2.p2	AY296058|Bcl9l|80288|B-cell CLL/lymphoma 9-like	NM_030256|Bcl9l|80288|B-cell CLL/lymphoma 9-like
mm9_v1_chr8_+_81033220_81033473	0.0704422	SOX2.p2	NM_029736|Slc10a7|76775|solute carrier family 10 (sodium/bile acid cotransporter family), member 7	AK160402|Slc10a7|76775|solute carrier family 10 (sodium/bile acid cotransporter family), member 7	AK079901|Slc10a7|76775|solute carrier family 10 (sodium/bile acid cotransporter family), member 7	AK152752|Slc10a7|76775|solute carrier family 10 (sodium/bile acid cotransporter family), member 7	AK152849|Slc10a7|76775|solute carrier family 10 (sodium/bile acid cotransporter family), member 7	AK010834|Slc10a7|76775|solute carrier family 10 (sodium/bile acid cotransporter family), member 7	AK165983|Slc10a7|76775|solute carrier family 10 (sodium/bile acid cotransporter family), member 7	AK040517|Slc10a7|76775|solute carrier family 10 (sodium/bile acid cotransporter family), member 7	BC116666|Slc10a7|76775|solute carrier family 10 (sodium/bile acid cotransporter family), member 7	BC116717|Slc10a7|76775|solute carrier family 10 (sodium/bile acid cotransporter family), member 7	AY825926|Slc10a7|76775|solute carrier family 10 (sodium/bile acid cotransporter family), member 7	AY825927|Slc10a7|76775|solute carrier family 10 (sodium/bile acid cotransporter family), member 7	AY825928|Slc10a7|76775|solute carrier family 10 (sodium/bile acid cotransporter family), member 7
mm9_v1_chr1_-_135557934_135557977	0.070174	SOX2.p2	AK148376|Zc3h11a|70579|zinc finger CCCH type containing 11A	AK078105|Zc3h11a|70579|zinc finger CCCH type containing 11A	AK145740|Zc3h11a|70579|zinc finger CCCH type containing 11A	AK167700|Zc3h11a|70579|zinc finger CCCH type containing 11A	AK041148|Zc3h11a|70579|zinc finger CCCH type containing 11A	AK017663|Zc3h11a|70579|zinc finger CCCH type containing 11A	AK035705|Zbed6|667118|zinc finger, BED domain containing 6	NM_144530|Zc3h11a|70579|zinc finger CCCH type containing 11A
mm9_v1_chr14_+_55050530_55050726	0.0699052	SOX2.p2	X83536|Mmp14|17387|matrix metallopeptidase 14 (membrane-inserted)	AK149988|Mmp14|17387|matrix metallopeptidase 14 (membrane-inserted)	DQ249870|Mmp14|17387|matrix metallopeptidase 14 (membrane-inserted)	AK198018|Mmp14|17387|matrix metallopeptidase 14 (membrane-inserted)
mm9_v1_chr16_+_20535519_20535657	0.0698926	SOX2.p2	AK146517|Ap2m1|11773|adaptor protein complex AP-2, mu1	AK168414|Ap2m1|11773|adaptor protein complex AP-2, mu1	NM_009679|Ap2m1|11773|adaptor protein complex AP-2, mu1	U27106|Ap2m1|11773|adaptor protein complex AP-2, mu1	AK159534|Ap2m1|11773|adaptor protein complex AP-2, mu1	BC056352|Ap2m1|11773|adaptor protein complex AP-2, mu1	AK150358|Ap2m1|11773|adaptor protein complex AP-2, mu1	BC089342|Ap2m1|11773|adaptor protein complex AP-2, mu1	BC094510|Ap2m1|11773|adaptor protein complex AP-2, mu1	AK143586|Ap2m1|11773|adaptor protein complex AP-2, mu1	AK141862|Ap2m1|11773|adaptor protein complex AP-2, mu1	AK172889|Ap2m1|11773|adaptor protein complex AP-2, mu1
mm9_v1_chr1_-_130313846_130314003	0.0697675	SOX2.p2	AK169716|Dars|226414|aspartyl-tRNA synthetase	BC008638|Dars|226414|aspartyl-tRNA synthetase	AK152562|Dars|226414|aspartyl-tRNA synthetase	AK153299|Dars|226414|aspartyl-tRNA synthetase	AK151897|Dars|226414|aspartyl-tRNA synthetase	AK152304|Dars|226414|aspartyl-tRNA synthetase	AK153256|Dars|226414|aspartyl-tRNA synthetase	AK166009|Dars|226414|aspartyl-tRNA synthetase	AK169247|Dars|226414|aspartyl-tRNA synthetase	AK077533|Dars|226414|aspartyl-tRNA synthetase	AK146350|Dars|226414|aspartyl-tRNA synthetase	AK151027|Dars|226414|aspartyl-tRNA synthetase	AK144470|Dars|226414|aspartyl-tRNA synthetase	AK077820|Dars|226414|aspartyl-tRNA synthetase	NM_145507|Dars|226414|aspartyl-tRNA synthetase	NM_177445|Dars|226414|aspartyl-tRNA synthetase
mm9_v1_chr17_+_75404893_75404907	0.0694225	SOX2.p2	AF022889|Ltbp1|268977|latent transforming growth factor beta binding protein 1
mm9_v1_chr19_-_34953810_34953944	0.0691326	SOX2.p2	AK017345|Pank1|75735|pantothenate kinase 1	AF347700|Pank1|75735|pantothenate kinase 1	NM_001114339|Pank1|75735|pantothenate kinase 1
mm9_v1_chr9_+_108844100_108844145	0.0690543	SOX2.p2	
mm9_v1_chr10_-_41529396_41529437	0.0688729	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_chr5_+_144309683_144309799	0.0687246	SOX2.p2	BC085297|2810453I06Rik|67238|RIKEN cDNA 2810453I06 gene	AB374429|2810453I06Rik|67238|RIKEN cDNA 2810453I06 gene
mm9_v1_chr12_-_8506790_8506819	0.0686558	SOX2.p2	BC018275|Rhob|11852|ras homolog gene family, member B	NM_007483|Rhob|11852|ras homolog gene family, member B	BC110992|Rhob|11852|ras homolog gene family, member B	AK167917|Rhob|11852|ras homolog gene family, member B	AK086873|Rhob|11852|ras homolog gene family, member B	AK164518|Rhob|11852|ras homolog gene family, member B
mm9_v1_chr2_+_121282841_121282867	0.0684775	SOX2.p2	AK168506|2310003F16Rik|67693|RIKEN cDNA 2310003F16 gene	BC021588|2310003F16Rik|67693|RIKEN cDNA 2310003F16 gene
mm9_v1_chrX_+_7305654_7305720	0.0684199	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_chr13_+_43497279_43497424	0.0681761	SOX2.p2	AK140839|Nol7|70078|nucleolar protein 7
mm9_v1_chr16_-_89488129_89488198	0.068121	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_chr2_+_13501725_13501846	0.0680857	SOX2.p2	AK205443|Vim|22352|vimentin
mm9_v1_chr6_-_124765218_124765272	0.0680391	SOX2.p2	
mm9_v1_chr2_+_127953310_127953338	0.0680316	SOX2.p2	BC058175|Bcl2l11|12125|BCL2-like 11 (apoptosis facilitator)
mm9_v1_chr10_+_45297632_45297737	0.0677444	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_chr1_-_156573049_156573160	0.0676999	SOX2.p2	NM_009782|Cacna1e|12290|calcium channel, voltage-dependent, R type, alpha 1E subunit	BC150750|Cacna1e|12290|calcium channel, voltage-dependent, R type, alpha 1E subunit
mm9_v1_chr6_-_72310580_72310656	0.0676384	SOX2.p2	AK195168|Rnf181|66510|ring finger protein 181	AK202921|Rnf181|66510|ring finger protein 181	AK209718|Rnf181|66510|ring finger protein 181	AK211264|Rnf181|66510|ring finger protein 181	AK211423|Rnf181|66510|ring finger protein 181	AK213249|Rnf181|66510|ring finger protein 181
mm9_v1_chr4_+_43455122_43455148	0.0676141	SOX2.p2	BC099699|Tesk1|21754|testis specific protein kinase 1	NM_011571|Tesk1|21754|testis specific protein kinase 1
mm9_v1_chr4_+_129168433_129168515	0.0673162	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_+_58331537_58331633	0.0667408	SOX2.p2	AK020763|Mipol1|73490|mirror-image polydactyly gene 1 homolog (human)	AK006974|Mipol1|73490|mirror-image polydactyly gene 1 homolog (human)
mm9_v1_chr9_+_38185467_38185476	0.0666373	SOX2.p2	BC106986|Olfr900|258874|olfactory receptor 900	NM_146874|Olfr900|258874|olfactory receptor 900	NM_207553|Olfr251|404313|olfactory receptor 251
mm9_v1_chr16_+_4639921_4640005	0.066407	SOX2.p2	AK132325|Vasn|246154|vasorin	NM_139307|Vasn|246154|vasorin	AK083684|Vasn|246154|vasorin	AK012169|Vasn|246154|vasorin	BC050274|Vasn|246154|vasorin	AJ458938|Vasn|246154|vasorin
mm9_v1_chr9_-_50576208_50576266	0.0661908	SOX2.p2	AJ250230|1110032A03Rik|68721|RIKEN cDNA 1110032A03 gene	AK166202|1110032A03Rik|68721|RIKEN cDNA 1110032A03 gene	BC032012|1110032A03Rik|68721|RIKEN cDNA 1110032A03 gene	AK158460|1110032A03Rik|68721|RIKEN cDNA 1110032A03 gene	AK043513|1110032A03Rik|68721|RIKEN cDNA 1110032A03 gene	NM_023483|1110032A03Rik|68721|RIKEN cDNA 1110032A03 gene
mm9_v1_chr4_-_104782444_104782511	0.0660362	SOX2.p2	NM_178143|Prkaa2|108079|protein kinase, AMP-activated, alpha 2 catalytic subunit	BC138565|Prkaa2|108079|protein kinase, AMP-activated, alpha 2 catalytic subunit	BC138566|Prkaa2|108079|protein kinase, AMP-activated, alpha 2 catalytic subunit
mm9_v1_chr6_-_5143755_5143945	0.0657982	SOX2.p2	BC012706|Pon1|18979|paraoxonase 1	U72636|Pon1|18979|paraoxonase 1	U32684|Pon1|18979|paraoxonase 1	NM_011134|Pon1|18979|paraoxonase 1
mm9_v1_chr4_-_44181148_44181210	0.0654704	SOX2.p2	AK044324|Rnf38|73469|ring finger protein 38	NM_001038993|Rnf38|73469|ring finger protein 38	AK147608|Rnf38|73469|ring finger protein 38
mm9_v1_chr19_-_33466561_33466800	0.0652154	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_chr2_+_74695081_74695176	0.0651332	SOX2.p2	
mm9_v1_chr7_+_99890204_99890223	0.0649206	SOX2.p2	AK142206|Rab30|75985|RAB30, member RAS oncogene family	BC017550|Rab30|75985|RAB30, member RAS oncogene family	NM_029494|Rab30|75985|RAB30, member RAS oncogene family
mm9_v1_chrX_+_149672587_149672587	0.0647752	SOX2.p2	AK044185|Klf8|245671|Kruppel-like factor 8	NM_173780|Klf8|245671|Kruppel-like factor 8
mm9_v1_chr10_+_128242598_128242635	0.0646976	SOX2.p2	AK168935|Dnajc14|74330|DnaJ (Hsp40) homolog, subfamily C, member 14	AK045445|Dnajc14|74330|DnaJ (Hsp40) homolog, subfamily C, member 14	BC011146|Dnajc14|74330|DnaJ (Hsp40) homolog, subfamily C, member 14
mm9_v1_chr5_-_87997908_87998005	0.0646692	SOX2.p2	AF026073|Sult1d1|53315|sulfotransferase family 1D, member 1	AK133530|Sult1d1|53315|sulfotransferase family 1D, member 1	U32371|Sult1d1|53315|sulfotransferase family 1D, member 1	BC066190|Sult1d1|53315|sulfotransferase family 1D, member 1	BC010752|Sult1d1|53315|sulfotransferase family 1D, member 1
mm9_v1_chr7_+_88358623_88358753	0.0645689	SOX2.p2	AF067806|Pde8a|18584|phosphodiesterase 8A	BC125578|Pde8a|18584|phosphodiesterase 8A	BC132145|Pde8a|18584|phosphodiesterase 8A	NM_008803|Pde8a|18584|phosphodiesterase 8A
mm9_v1_chr4_+_150302107_150302108	0.0645364	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_chr9_+_107483603_107483637	0.0644544	SOX2.p2	BC018457|Hyal3|109685|hyaluronoglucosaminidase 3	NM_178020|Hyal3|109685|hyaluronoglucosaminidase 3	AY048681|Hyal3|109685|hyaluronoglucosaminidase 3
mm9_v1_chrX_-_133527570_133527593	0.0643958	SOX2.p2	NM_001114179|Mcart6|67062|mitochondrial carrier triple repeat 6
mm9_v1_chr9_+_43901941_43901990	0.0642386	SOX2.p2	AK047204|Usp2|53376|ubiquitin specific peptidase 2	AK081112|Usp2|53376|ubiquitin specific peptidase 2
mm9_v1_chr1_+_176019168_176019170	0.0640923	SOX2.p2	NM_146722|Olfr429|258717|olfactory receptor 429	BC127973|Olfr429|258717|olfactory receptor 429
mm9_v1_chr7_+_109118356_109118356	0.0637619	SOX2.p2	BC049791|Numa1|101706|nuclear mitotic apparatus protein 1	NM_133947|Numa1|101706|nuclear mitotic apparatus protein 1
mm9_v1_chr5_+_91456489_91456542	0.0636439	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_+_56214442_56214485	0.0636343	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_chr8_-_127275549_127275749	0.0634428	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_chr18_+_37560490_37560542	0.0632871	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_chr17_+_75404865_75404880	0.0632546	SOX2.p2	NM_019919|Ltbp1|268977|latent transforming growth factor beta binding protein 1
mm9_v1_chr11_+_96891242_96891268	0.0631294	SOX2.p2	NM_146027|Scrn2|217140|secernin 2
mm9_v1_chr2_+_76244559_76244570	0.0628093	SOX2.p2	AK004353|Osbpl6|99031|oxysterol binding protein-like 6
mm9_v1_chr13_-_59924405_59924507	0.0623179	SOX2.p2	BC043111|Zcchc6|214290|zinc finger, CCHC domain containing 6	AK031537|Zcchc6|214290|zinc finger, CCHC domain containing 6	NM_153538|Zcchc6|214290|zinc finger, CCHC domain containing 6
mm9_v1_chr4_+_153544821_153544830	0.062044	SOX2.p2	NM_001162977|Megf6|230971|multiple EGF-like-domains 6
mm9_v1_chr14_+_55305007_55305091	0.0620175	SOX2.p2	NM_021437|1700123O20Rik|58248|RIKEN cDNA 1700123O20 gene	AK030845|1700123O20Rik|58248|RIKEN cDNA 1700123O20 gene	AB041657|1700123O20Rik|58248|RIKEN cDNA 1700123O20 gene
mm9_v1_chr17_+_57129686_57129814	0.0619084	SOX2.p2	NM_017393|Clpp|53895|caseinolytic peptidase, ATP-dependent, proteolytic subunit homolog (E. coli)	AK145765|Clpp|53895|caseinolytic peptidase, ATP-dependent, proteolytic subunit homolog (E. coli)	BC001998|Clpp|53895|caseinolytic peptidase, ATP-dependent, proteolytic subunit homolog (E. coli)	AJ005253|Clpp|53895|caseinolytic peptidase, ATP-dependent, proteolytic subunit homolog (E. coli)	AK004024|Clpp|53895|caseinolytic peptidase, ATP-dependent, proteolytic subunit homolog (E. coli)	AK168053|Clpp|53895|caseinolytic peptidase, ATP-dependent, proteolytic subunit homolog (E. coli)	AK002238|Clpp|53895|caseinolytic peptidase, ATP-dependent, proteolytic subunit homolog (E. coli)	AK147719|Clpp|53895|caseinolytic peptidase, ATP-dependent, proteolytic subunit homolog (E. coli)
mm9_v1_chr19_+_46576203_46576224	0.0617636	SOX2.p2	BC029283|Trim8|93679|tripartite motif-containing 8
mm9_v1_chr12_-_105711324_105711536	0.0610619	SOX2.p2	AB221548|Gsc|14836|goosecoid homeobox	Y13150|Gsc|14836|goosecoid homeobox	NM_010351|Gsc|14836|goosecoid homeobox	Y13149|Gsc|14836|goosecoid homeobox	X99239|Gsc|14836|goosecoid homeobox
mm9_v1_chrX_-_93152262_93152300	0.0604939	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_chr12_+_70397795_70397847	0.0603616	SOX2.p2	
mm9_v1_chr17_+_46818005_46818130	0.060183	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_chr12_-_46175433_46175475	0.0590919	SOX2.p2	NM_144552|Stxbp6|217517|syntaxin binding protein 6 (amisyn)
mm9_v1_chr4_-_43013217_43013384	0.059068	SOX2.p2	AK149931|Vcp|269523|valosin containing protein	AK151109|Vcp|269523|valosin containing protein	AK151418|Vcp|269523|valosin containing protein	AK146109|Vcp|269523|valosin containing protein	AK169140|Vcp|269523|valosin containing protein	BC043053|Vcp|269523|valosin containing protein	AK028264|Vcp|269523|valosin containing protein	AK159475|Vcp|269523|valosin containing protein	AK159177|Vcp|269523|valosin containing protein	AK153012|Vcp|269523|valosin containing protein	AK167794|Vcp|269523|valosin containing protein	BC049114|Vcp|269523|valosin containing protein	AK153249|Vcp|269523|valosin containing protein	AK159509|Vcp|269523|valosin containing protein	NM_009503|Vcp|269523|valosin containing protein
mm9_v1_chr4_-_129055233_129055271	0.058591	SOX2.p2	AK010736|Zbtb8a|73680|zinc finger and BTB domain containing 8a	NM_028603|Zbtb8a|73680|zinc finger and BTB domain containing 8a
mm9_v1_chr9_+_111277323_111277357	0.0582707	SOX2.p2	BC086653|Trank1|320429|tetratricopeptide repeat and ankyrin repeat containing 1
mm9_v1_chr19_-_13870096_13870098	0.0582125	SOX2.p2	BC111435|Olfr1497|258736|olfactory receptor 1497	NM_146741|Olfr1497|258736|olfactory receptor 1497
mm9_v1_chr11_-_6328316_6328333	0.0581936	SOX2.p2	
mm9_v1_chr5_+_38430461_38430564	0.0581607	SOX2.p2	AK007700|Stx18|71116|syntaxin 18	AK170165|Stx18|71116|syntaxin 18	NM_026959|Stx18|71116|syntaxin 18	BC021362|Stx18|71116|syntaxin 18	AK169273|Stx18|71116|syntaxin 18	AK016910|Stx18|71116|syntaxin 18
mm9_v1_chr11_-_116712559_116712636	0.0578957	SOX2.p2	AF250133|Srsf2|20382|serine/arginine-rich splicing factor 2
mm9_v1_chr4_+_40669478_40669634	0.0577374	SOX2.p2	NM_008298|Dnaja1|15502|DnaJ (Hsp40) homolog, subfamily A, member 1	AK049963|Dnaja1|15502|DnaJ (Hsp40) homolog, subfamily A, member 1	AK145963|Dnaja1|15502|DnaJ (Hsp40) homolog, subfamily A, member 1	AK083046|Dnaja1|15502|DnaJ (Hsp40) homolog, subfamily A, member 1	AK167139|Dnaja1|15502|DnaJ (Hsp40) homolog, subfamily A, member 1	AK167212|Dnaja1|15502|DnaJ (Hsp40) homolog, subfamily A, member 1	AF055664|Dnaja1|15502|DnaJ (Hsp40) homolog, subfamily A, member 1	BC057876|Dnaja1|15502|DnaJ (Hsp40) homolog, subfamily A, member 1	BC158024|Dnaja1|15502|DnaJ (Hsp40) homolog, subfamily A, member 1
mm9_v1_chr17_-_35183667_35183733	0.0577025	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_chr8_-_26212614_26212665	0.057693	SOX2.p2	AK153117|Plekha2|83436|pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	AK032325|Plekha2|83436|pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2
mm9_v1_chr8_+_109127245_109127278	0.0576077	SOX2.p2	AK076369|Cdh1|12550|cadherin 1	AK166267|Cdh1|12550|cadherin 1	NM_009864|Cdh1|12550|cadherin 1	BC098501|Cdh1|12550|cadherin 1
mm9_v1_chr9_+_108393006_108393101	0.0573088	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_chr11_-_68825972_68825998	0.0569266	SOX2.p2	
mm9_v1_chr11_-_74710462_74710503	0.0566534	SOX2.p2	AK122273|Sgsm2|97761|small G protein signaling modulator 2
mm9_v1_chr7_+_24919177_24919260	0.0563559	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_chr16_+_49868005_49868080	0.0559289	SOX2.p2	BC009094|Cd47|16423|CD47 antigen (Rh-related antigen, integrin-associated signal transducer)
mm9_v1_chr11_-_40568710_40568789	0.0558944	SOX2.p2	AK167486|Ccng1|12450|cyclin G1	AK159429|Ccng1|12450|cyclin G1	AK153392|Ccng1|12450|cyclin G1	AK167052|Ccng1|12450|cyclin G1	AK159831|Ccng1|12450|cyclin G1	L49507|Ccng1|12450|cyclin G1	Z37110|Ccng1|12450|cyclin G1	AK160411|Ccng1|12450|cyclin G1	AK128957|Ccng1|12450|cyclin G1	AK147026|Ccng1|12450|cyclin G1	AK170397|Ccng1|12450|cyclin G1	AK143114|Ccng1|12450|cyclin G1	NM_009831|Ccng1|12450|cyclin G1
mm9_v1_chr15_-_81560283_81560301	0.0557857	SOX2.p2	BC071200|Rangap1|19387|RAN GTPase activating protein 1	AK159009|Rangap1|19387|RAN GTPase activating protein 1
mm9_v1_chr2_-_60800963_60800981	0.0556723	SOX2.p2	AB026569|Rbms1|56878|RNA binding motif, single stranded interacting protein 1
mm9_v1_chr1_+_129999868_129999934	0.0556143	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_chrX_-_91787338_91787350	0.0555343	SOX2.p2	AK220150|Maged1|94275|melanoma antigen, family D, 1	AK132248|Maged1|94275|melanoma antigen, family D, 1
mm9_v1_chr16_+_44370127_44370136	0.0551899	SOX2.p2	BC024956|Spice1|212514|spindle and centriole associated protein 1
mm9_v1_chr2_+_153171562_153171582	0.055069	SOX2.p2	AK081063|Asxl1|228790|additional sex combs like 1 (Drosophila)
mm9_v1_chr12_+_110884340_110884400	0.0549838	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_chr4_+_108673212_108673409	0.0548657	SOX2.p2	AK166470|Nrd1|230598|nardilysin, N-arginine dibasic convertase, NRD convertase 1	BC036128|Nrd1|230598|nardilysin, N-arginine dibasic convertase, NRD convertase 1	BC026832|Nrd1|230598|nardilysin, N-arginine dibasic convertase, NRD convertase 1	AK031548|Nrd1|230598|nardilysin, N-arginine dibasic convertase, NRD convertase 1	NM_146150|Nrd1|230598|nardilysin, N-arginine dibasic convertase, NRD convertase 1
mm9_v1_chr6_-_56851861_56851881	0.0547576	SOX2.p2	BC038029|Nt5c3|107569|5'-nucleotidase, cytosolic III	AK160139|Nt5c3|107569|5'-nucleotidase, cytosolic III
mm9_v1_chr11_+_42234760_42234851	0.0546312	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_chr9_+_108984968_108985054	0.0546127	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_chr9_+_26541302_26541653	0.0545937	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_chr8_+_34763709_34763709	0.0543979	SOX2.p2	BC056357|Gsr|14782|glutathione reductase	BC057325|Gsr|14782|glutathione reductase	NM_010344|Gsr|14782|glutathione reductase
mm9_v1_chr19_+_41904459_41904605	0.0543807	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_chr3_-_103546233_103546253	0.0540861	SOX2.p2	AK031871|Hipk1|15257|homeodomain interacting protein kinase 1
mm9_v1_chr7_+_134655496_134655584	0.0539637	SOX2.p2	AK142089|Srcap|100043597|Snf2-related CREBBP activator protein	AK169954|Srcap|100043597|Snf2-related CREBBP activator protein	AK051146|Srcap|100043597|Snf2-related CREBBP activator protein	BC085144|Srcap|100043597|Snf2-related CREBBP activator protein
mm9_v1_chr14_+_31832347_31832368	0.0538467	SOX2.p2	BC023452|Pbrm1|66923|polybromo 1
mm9_v1_chr4_+_34562190_34562236	0.0537912	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_chr12_+_70269800_70269846	0.0536838	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_chr19_-_43598949_43599094	0.0536151	SOX2.p2	BC002057|Got1|14718|glutamate oxaloacetate transaminase 1, soluble	AK146445|Got1|14718|glutamate oxaloacetate transaminase 1, soluble	AK147934|Got1|14718|glutamate oxaloacetate transaminase 1, soluble	J02623|Got1|14718|glutamate oxaloacetate transaminase 1, soluble	AK147807|Got1|14718|glutamate oxaloacetate transaminase 1, soluble	NM_010324|Got1|14718|glutamate oxaloacetate transaminase 1, soluble
mm9_v1_chr7_-_118125571_118125608	0.0533208	SOX2.p2	AK020536|Mrvi1|17540|MRV integration site 1	AK157169|Mrvi1|17540|MRV integration site 1	NM_194464|Mrvi1|17540|MRV integration site 1
mm9_v1_chr11_-_6174799_6174821	0.053271	SOX2.p2	AK182125|Tmed4|103694|transmembrane emp24 protein transport domain containing 4
mm9_v1_chr9_+_79914751_79914905	0.0530676	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_chr9_+_108199200_108199252	0.0529251	SOX2.p2	BC132277|Amt|434437|aminomethyltransferase	BC132279|Amt|434437|aminomethyltransferase	NM_001013814|Amt|434437|aminomethyltransferase
mm9_v1_chr8_+_74743673_74743687	0.0528368	SOX2.p2	BC006058|Fam32a|67922|family with sequence similarity 32, member A
mm9_v1_chr7_+_18830695_18830771	0.0528056	SOX2.p2	AK029010|Mill1|266815|MHC I like leukocyte 1	NM_153749|Mill1|266815|MHC I like leukocyte 1	BC110547|Mill1|266815|MHC I like leukocyte 1	BC110548|Mill1|266815|MHC I like leukocyte 1	AK030695|Mill1|266815|MHC I like leukocyte 1
mm9_v1_chr14_+_51710846_51710877	0.0525355	SOX2.p2	AB041044|Rnase4|58809|ribonuclease, RNase A family 4	BC061105|Rnase4|58809|ribonuclease, RNase A family 4	BC005569|Rnase4|58809|ribonuclease, RNase A family 4
mm9_v1_chr16_+_33251485_33251551	0.0524439	SOX2.p2	AK007706|Snx4|69150|sorting nexin 4	AK030657|Snx4|69150|sorting nexin 4	AK031368|Snx4|69150|sorting nexin 4	AK135356|Snx4|69150|sorting nexin 4	BC016599|Snx4|69150|sorting nexin 4	NM_080557|Snx4|69150|sorting nexin 4	BC006043|Snx4|69150|sorting nexin 4
mm9_v1_chr11_+_120210028_120210052	0.0523522	SOX2.p2	AK002420|0610009L18Rik|66838|RIKEN cDNA 0610009L18 gene	AK005967|0610009L18Rik|66838|RIKEN cDNA 0610009L18 gene
mm9_v1_chr3_+_90024674_90024714	0.0515178	SOX2.p2	BC027214|Rab13|68328|RAB13, member RAS oncogene family
mm9_v1_chr3_-_30799013_30799120	0.051419	SOX2.p2	AK050678|Phc3|241915|polyhomeotic-like 3 (Drosophila)
mm9_v1_chr2_+_13500063_13500099	0.0511929	SOX2.p2	AK198215|Vim|22352|vimentin	AK208074|Vim|22352|vimentin	AK209588|Vim|22352|vimentin	AK209779|Vim|22352|vimentin	AK210390|Vim|22352|vimentin	AK210884|Vim|22352|vimentin	AK212337|Vim|22352|vimentin	AK212338|Vim|22352|vimentin	AK212907|Vim|22352|vimentin	AK213561|Vim|22352|vimentin	AK216501|Vim|22352|vimentin	AK217097|Vim|22352|vimentin	AK218080|Vim|22352|vimentin	AK218318|Vim|22352|vimentin	AK205873|Vim|22352|vimentin
mm9_v1_chr1_-_157264358_157264387	0.0511839	SOX2.p2	HQ022853|Xpr1|19775|xenotropic and polytropic retrovirus receptor 1	AF131096|Xpr1|19775|xenotropic and polytropic retrovirus receptor 1	AF131098|Xpr1|19775|xenotropic and polytropic retrovirus receptor 1	AF131102|Xpr1|19775|xenotropic and polytropic retrovirus receptor 1	AF198104|Xpr1|19775|xenotropic and polytropic retrovirus receptor 1	HQ022845|Xpr1|19775|xenotropic and polytropic retrovirus receptor 1	HQ323679|Xpr1|19775|xenotropic and polytropic retrovirus receptor 1	HQ323680|Xpr1|19775|xenotropic and polytropic retrovirus receptor 1
mm9_v1_chr12_-_102267159_102267268	0.0511613	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_chr19_+_45005608_45005655	0.0508042	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_chr11_-_29073541_29073557	0.0505642	SOX2.p2	AK042012|A630052C17Rik|320757|RIKEN cDNA A630052C17 gene
mm9_v1_chr3_-_107474108_107474148	0.0490947	SOX2.p2	AK207163|Ahcyl1|229709|S-adenosylhomocysteine hydrolase-like 1
mm9_v1_chr16_+_18249036_18249160	0.0490938	SOX2.p2	AK146391|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)	BC046976|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)	BC027431|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)	AK034102|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)	AK080170|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)	AK133844|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)	AK151422|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)	AK153190|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)	AK169240|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)	AK150482|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)	AK151311|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)	AK151725|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)	AK151778|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)	AK152055|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)	AK152201|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)	AK152363|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)	AK152548|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)	AK152903|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)	AK153043|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)	BC038486|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)
mm9_v1_chr3_-_75760843_75760893	0.0485143	SOX2.p2	AK080456|Golim4|73124|golgi integral membrane protein 4	AK033730|Golim4|73124|golgi integral membrane protein 4	AK048434|Golim4|73124|golgi integral membrane protein 4	AK078928|Golim4|73124|golgi integral membrane protein 4
mm9_v1_chr6_+_125046576_125046586	0.0482874	SOX2.p2	AK020564|Chd4|107932|chromodomain helicase DNA binding protein 4
mm9_v1_chr6_-_29457924_29457972	0.0482613	SOX2.p2	BC119794|Kcp|333088|kielin/chordin-like protein	NM_001029985|Kcp|333088|kielin/chordin-like protein	AY884211|Kcp|333088|kielin/chordin-like protein	AK154369|Kcp|333088|kielin/chordin-like protein
mm9_v1_chr17_+_52742087_52742144	0.048158	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_chr16_+_18248964_18249010	0.0478988	SOX2.p2	AK017819|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)	AK134368|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)	NM_001080999|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)	NM_001081000|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)	NM_001195205|Trmt2a|15547|TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae)
mm9_v1_chr2_+_177876710_177876721	0.0476588	SOX2.p2	BC058621|Phactr3|74189|phosphatase and actin regulator 3
mm9_v1_chr5_+_37729786_37729846	0.0475692	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_chr1_-_14745828_14746072	0.0472289	SOX2.p2	AB221639|Msc|17681|musculin	AF108216|Msc|17681|musculin	BC103594|Msc|17681|musculin	BC103592|Msc|17681|musculin	BC103593|Msc|17681|musculin	BC103623|Msc|17681|musculin	AF087035|Msc|17681|musculin	NM_010827|Msc|17681|musculin	AK138917|Msc|17681|musculin
mm9_v1_chr2_-_103637795_103637829	0.0467095	SOX2.p2	NM_001111291|Caprin1|53872|cell cycle associated protein 1	NM_016739|Caprin1|53872|cell cycle associated protein 1
mm9_v1_chr5_+_125079610_125079769	0.0466438	SOX2.p2	AK170122|Atp6v0a2|21871|ATPase, H+ transporting, lysosomal V0 subunit A2	AF218252|Atp6v0a2|21871|ATPase, H+ transporting, lysosomal V0 subunit A2	NM_011596|Atp6v0a2|21871|ATPase, H+ transporting, lysosomal V0 subunit A2	AK155055|Atp6v0a2|21871|ATPase, H+ transporting, lysosomal V0 subunit A2	AB022323|Atp6v0a2|21871|ATPase, H+ transporting, lysosomal V0 subunit A2	BC112905|Atp6v0a2|21871|ATPase, H+ transporting, lysosomal V0 subunit A2	BC018369|Atp6v0a2|21871|ATPase, H+ transporting, lysosomal V0 subunit A2	BC108991|Atp6v0a2|21871|ATPase, H+ transporting, lysosomal V0 subunit A2	BC108992|Atp6v0a2|21871|ATPase, H+ transporting, lysosomal V0 subunit A2	M31226|Atp6v0a2|21871|ATPase, H+ transporting, lysosomal V0 subunit A2	X55184|Atp6v0a2|21871|ATPase, H+ transporting, lysosomal V0 subunit A2	AK193082|Atp6v0a2|21871|ATPase, H+ transporting, lysosomal V0 subunit A2
mm9_v1_chr11_-_51414445_51414449	0.0465285	SOX2.p2	
mm9_v1_chr14_-_37935305_37935311	0.046447	SOX2.p2	
mm9_v1_chr1_+_173080843_173080843	0.0460413	SOX2.p2	AK089180|Mpz|17528|myelin protein zero	NM_008623|Mpz|17528|myelin protein zero
mm9_v1_chr16_+_32877857_32877985	0.0459769	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_chr5_-_38550248_38550345	0.0457398	SOX2.p2	AF531172|Nsg1|18196|neuron specific gene family member 1
mm9_v1_chr1_+_74283079_74283111	0.0454583	SOX2.p2	AK152356|Arpc2|76709|actin related protein 2/3 complex, subunit 2
mm9_v1_chr7_-_29965500_29965550	0.0450787	SOX2.p2	BC004075|Psmd8|57296|proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	AK159795|Psmd8|57296|proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	AK159926|Psmd8|57296|proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	AK166718|Psmd8|57296|proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	AK002921|Psmd8|57296|proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	AK003436|Psmd8|57296|proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	AK153329|Psmd8|57296|proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	AK150493|Psmd8|57296|proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	AK051257|Psmd8|57296|proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	AK020132|Psmd8|57296|proteasome (prosome, macropain) 26S subunit, non-ATPase, 8
mm9_v1_chr5_+_108698687_108698695	0.0448851	SOX2.p2	AK178588|Dr1|13486|down-regulator of transcription 1	AK211344|Dr1|13486|down-regulator of transcription 1
mm9_v1_chr10_+_76725212_76725223	0.0446278	SOX2.p2	AK190890|Pofut2|80294|protein O-fucosyltransferase 2
mm9_v1_chr19_-_18655597_18655704	0.0441824	SOX2.p2	AK205236|Ostf1|20409|osteoclast stimulating factor 1	AK207431|Ostf1|20409|osteoclast stimulating factor 1	AK209921|Ostf1|20409|osteoclast stimulating factor 1
mm9_v1_chr7_+_115133880_115133880	0.0441194	SOX2.p2	NM_146926|Olfr477|258928|olfactory receptor 477
mm9_v1_chr6_-_72739189_72739247	0.044069	SOX2.p2	AK052721|Tcf7l1|21415|transcription factor 7-like 1 (T-cell specific, HMG box)
mm9_v1_chr14_+_73637961_73638071	0.0440406	SOX2.p2	BC145940|Lpar6|67168|lysophosphatidic acid receptor 6	BC145942|Lpar6|67168|lysophosphatidic acid receptor 6
mm9_v1_chr9_+_106356125_106356294	0.0439835	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_chr3_-_66785062_66785239	0.0439556	SOX2.p2	U67055|Shox2|20429|short stature homeobox 2	AK145063|Shox2|20429|short stature homeobox 2	AK032007|Shox2|20429|short stature homeobox 2
mm9_v1_chr14_-_55305438_55305460	0.0439439	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_chr2_-_52601140_52601264	0.0431714	SOX2.p2	AK214650|Stam2|56324|signal transducing adaptor molecule (SH3 domain and ITAM motif) 2	AK004604|Stam2|56324|signal transducing adaptor molecule (SH3 domain and ITAM motif) 2	NM_019667|Stam2|56324|signal transducing adaptor molecule (SH3 domain and ITAM motif) 2	AB012611|Stam2|56324|signal transducing adaptor molecule (SH3 domain and ITAM motif) 2	AK044230|Stam2|56324|signal transducing adaptor molecule (SH3 domain and ITAM motif) 2	AK159699|Stam2|56324|signal transducing adaptor molecule (SH3 domain and ITAM motif) 2	AK017668|Stam2|56324|signal transducing adaptor molecule (SH3 domain and ITAM motif) 2	AK078244|Stam2|56324|signal transducing adaptor molecule (SH3 domain and ITAM motif) 2	AK168729|Stam2|56324|signal transducing adaptor molecule (SH3 domain and ITAM motif) 2	BC013818|Stam2|56324|signal transducing adaptor molecule (SH3 domain and ITAM motif) 2	DQ141211|Stam2|56324|signal transducing adaptor molecule (SH3 domain and ITAM motif) 2	AK035789|Stam2|56324|signal transducing adaptor molecule (SH3 domain and ITAM motif) 2
mm9_v1_chr2_-_33310186_33310278	0.0431189	SOX2.p2	
mm9_v1_chr5_+_14514906_14514924	0.0431173	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_chr10_-_94878117_94878117	0.0431082	SOX2.p2	NM_001168656|Socs2|216233|suppressor of cytokine signaling 2
mm9_v1_chr2_-_105227142_105227176	0.0428948	SOX2.p2	BC051551|Rcn1|19672|reticulocalbin 1
mm9_v1_chr5_-_123974130_123974185	0.0427547	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_+_35217633_35217673	0.0425474	SOX2.p2	BC022616|Tmem66|67887|transmembrane protein 66	AK093942|Tmem66|67887|transmembrane protein 66
mm9_v1_chr9_+_69860400_69860416	0.0420054	SOX2.p2	BC048705|Gtf2a2|235459|general transcription factor II A, 2
mm9_v1_chr13_-_4522566_4522580	0.041713	SOX2.p2	AB097220|Akr1c20|116852|aldo-keto reductase family 1, member C20	BC021607|Akr1c20|116852|aldo-keto reductase family 1, member C20	AK012162|Akr1c20|116852|aldo-keto reductase family 1, member C20	NM_054080|Akr1c20|116852|aldo-keto reductase family 1, member C20
mm9_v1_chr13_+_94444337_94444432	0.0407474	SOX2.p2	BC089599|Dmgdh|74129|dimethylglycine dehydrogenase precursor	NM_028772|Dmgdh|74129|dimethylglycine dehydrogenase precursor	AK004755|Dmgdh|74129|dimethylglycine dehydrogenase precursor
mm9_v1_chr12_-_86039703_86039802	0.0406597	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_chr11_+_102254949_102254989	0.0406122	SOX2.p2	U73941|Rundc3a|51799|RUN domain containing 3A
mm9_v1_chr15_+_25682945_25682960	0.0405465	SOX2.p2	AK161653|Myo10|17909|myosin X
mm9_v1_chr4_-_14548903_14548926	0.0405142	SOX2.p2	BC026928|Slc26a7|208890|solute carrier family 26, member 7	AK054327|Slc26a7|208890|solute carrier family 26, member 7	NM_145947|Slc26a7|208890|solute carrier family 26, member 7
mm9_v1_chr3_+_102975621_102975695	0.0404896	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_chr10_+_42550365_42550378	0.0404653	SOX2.p2	AK017703|Sec63|140740|SEC63-like (S. cerevisiae)
mm9_v1_chr4_-_129055102_129055140	0.0404446	SOX2.p2	BC017614|Zbtb8a|73680|zinc finger and BTB domain containing 8a
mm9_v1_chr6_-_66987377_66987402	0.0403577	SOX2.p2	BC011141|Gadd45a|13197|growth arrest and DNA-damage-inducible 45 alpha	AK144900|Gadd45a|13197|growth arrest and DNA-damage-inducible 45 alpha	L28177|Gadd45a|13197|growth arrest and DNA-damage-inducible 45 alpha	NM_007836|Gadd45a|13197|growth arrest and DNA-damage-inducible 45 alpha
mm9_v1_chr5_+_34808777_34808878	0.0402174	SOX2.p2	AK134942|Fam193a|231128|family with sequence similarity 193, member A
mm9_v1_chr13_+_51245730_51245816	0.0400083	SOX2.p2	
mm9_v1_chr3_+_88342459_88342597	0.0398922	SOX2.p2	AK012557|Mex3a|72640|mex3 homolog A (C. elegans)
mm9_v1_chr19_-_6532339_6532383	0.0396768	SOX2.p2	AK045662|Gm14964|100008567|predicted gene 14964
mm9_v1_chr12_-_85489188_85489438	0.0396232	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_chr18_-_70301202_70301243	0.0394417	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_chr10_-_80813198_80813232	0.0391783	SOX2.p2	AK153816|Hmg20b|15353|high mobility group 20 B	NM_001163166|Hmg20b|15353|high mobility group 20 B
mm9_v1_chr16_-_17911283_17911450	0.0390666	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_chr4_+_115410325_115410392	0.0389829	SOX2.p2	AK030011|4732418C07Rik|230648|RIKEN cDNA 4732418C07 gene	AK028618|4732418C07Rik|230648|RIKEN cDNA 4732418C07 gene	AK163435|4732418C07Rik|230648|RIKEN cDNA 4732418C07 gene	AK132525|4732418C07Rik|230648|RIKEN cDNA 4732418C07 gene	AK033905|4732418C07Rik|230648|RIKEN cDNA 4732418C07 gene	AK078691|4732418C07Rik|230648|RIKEN cDNA 4732418C07 gene	AK080626|4732418C07Rik|230648|RIKEN cDNA 4732418C07 gene	AK028740|4732418C07Rik|230648|RIKEN cDNA 4732418C07 gene
mm9_v1_chr4_-_154010435_154010475	0.0380628	SOX2.p2	AK042640|5930403L14Rik|320939|RIKEN cDNA 5930403L14 gene	AK141913|5930403L14Rik|320939|RIKEN cDNA 5930403L14 gene
mm9_v1_chr7_+_63305622_63305758	0.0379179	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_chr7_+_108469700_108469743	0.0378867	SOX2.p2	BC058773|Stard10|56018|START domain containing 10	BC046335|Stard10|56018|START domain containing 10
mm9_v1_chr5_-_121614560_121614637	0.0371638	SOX2.p2	AK163809|Ptpn11|19247|protein tyrosine phosphatase, non-receptor type 11
mm9_v1_chr4_-_118954780_118955048	0.0369204	SOX2.p2	AK213887|Ybx1|22608|Y box protein 1	AK208509|Ybx1|22608|Y box protein 1	AK212502|Ybx1|22608|Y box protein 1
mm9_v1_chr11_+_68781623_68781690	0.0365548	SOX2.p2	AK171131|Slc25a35|71998|solute carrier family 25, member 35	AK007453|Slc25a35|71998|solute carrier family 25, member 35	NM_028048|Slc25a35|71998|solute carrier family 25, member 35	AK157873|Slc25a35|71998|solute carrier family 25, member 35	AK035739|Slc25a35|71998|solute carrier family 25, member 35	BC019996|Slc25a35|71998|solute carrier family 25, member 35
mm9_v1_chr14_-_52640348_52640407	0.0362721	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_chr2_+_34627836_34627893	0.0359272	SOX2.p2	AJ002387|Hspa5|14828|heat shock protein 5	AK197258|Hspa5|14828|heat shock protein 5	AK215673|Hspa5|14828|heat shock protein 5
mm9_v1_chr2_+_177876635_177876639	0.0358479	SOX2.p2	AK135144|Phactr3|74189|phosphatase and actin regulator 3	NM_028806|Phactr3|74189|phosphatase and actin regulator 3
mm9_v1_chr1_-_162964371_162964389	0.0358151	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_chr3_-_119486305_119486325	0.0358144	SOX2.p2	AK135738|Ptbp2|56195|polypyrimidine tract binding protein 2	NM_019550|Ptbp2|56195|polypyrimidine tract binding protein 2
mm9_v1_chr19_+_48012171_48012212	0.0356614	SOX2.p2	BC057135|Ccdc147|381229|coiled-coil domain containing 147	NM_001163267|Ccdc147|381229|coiled-coil domain containing 147	BC147530|Ccdc147|381229|coiled-coil domain containing 147	BC147540|Ccdc147|381229|coiled-coil domain containing 147	BC150978|Ccdc147|381229|coiled-coil domain containing 147	BC150979|Ccdc147|381229|coiled-coil domain containing 147
mm9_v1_chr11_+_115015491_115015512	0.0355678	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_chr4_+_155484072_155484109	0.0353858	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_chr10_-_79896330_79896385	0.0353466	SOX2.p2	BC006860|Tcf3|21423|transcription factor 3	AK017617|Tcf3|21423|transcription factor 3	AK156265|Tcf3|21423|transcription factor 3	AK034777|Tcf3|21423|transcription factor 3	AK161009|Tcf3|21423|transcription factor 3	AK038738|Tcf3|21423|transcription factor 3
mm9_v1_chr11_+_98799013_98799173	0.0351154	SOX2.p2	S56656|Rara|19401|retinoic acid receptor, alpha	BC040383|Rara|19401|retinoic acid receptor, alpha	NM_001177302|Rara|19401|retinoic acid receptor, alpha	AK154623|Rara|19401|retinoic acid receptor, alpha
mm9_v1_chr2_-_35972131_35972337	0.0350927	SOX2.p2	AK220096|Rbm18|67889|RNA binding motif protein 18
mm9_v1_chr2_-_147871630_147871640	0.0349705	SOX2.p2	AB231453|Foxa2|15376|forkhead box A2	L10409|Foxa2|15376|forkhead box A2
mm9_v1_chr14_+_31832323_31832337	0.0349078	SOX2.p2	AK165182|Pbrm1|66923|polybromo 1	NM_001081251|Pbrm1|66923|polybromo 1
mm9_v1_chr3_-_92261456_92261538	0.0347879	SOX2.p2	NM_011478|Sprr3|20766|small proline-rich protein 3	BC125629|Sprr3|20766|small proline-rich protein 3
mm9_v1_chr11_-_51813857_51813993	0.0346428	SOX2.p2	AK010432|Ube2b|22210|ubiquitin-conjugating enzyme E2B, RAD6 homology (S. cerevisiae)	AK161008|Ube2b|22210|ubiquitin-conjugating enzyme E2B, RAD6 homology (S. cerevisiae)	X96859|Ube2b|22210|ubiquitin-conjugating enzyme E2B, RAD6 homology (S. cerevisiae)	U57690|Ube2b|22210|ubiquitin-conjugating enzyme E2B, RAD6 homology (S. cerevisiae)	AK011363|Ube2b|22210|ubiquitin-conjugating enzyme E2B, RAD6 homology (S. cerevisiae)	BC132075|Ube2b|22210|ubiquitin-conjugating enzyme E2B, RAD6 homology (S. cerevisiae)	BC132077|Ube2b|22210|ubiquitin-conjugating enzyme E2B, RAD6 homology (S. cerevisiae)	AK152316|Ube2b|22210|ubiquitin-conjugating enzyme E2B, RAD6 homology (S. cerevisiae)	AK152645|Ube2b|22210|ubiquitin-conjugating enzyme E2B, RAD6 homology (S. cerevisiae)	AK153174|Ube2b|22210|ubiquitin-conjugating enzyme E2B, RAD6 homology (S. cerevisiae)	AK169229|Ube2b|22210|ubiquitin-conjugating enzyme E2B, RAD6 homology (S. cerevisiae)	AK147785|Ube2b|22210|ubiquitin-conjugating enzyme E2B, RAD6 homology (S. cerevisiae)	NM_009458|Ube2b|22210|ubiquitin-conjugating enzyme E2B, RAD6 homology (S. cerevisiae)
mm9_v1_chr15_+_10882086_10882145	0.034442	SOX2.p2	AK128898|C1qtnf3|81799|C1q and tumor necrosis factor related protein 3	AF246265|C1qtnf3|81799|C1q and tumor necrosis factor related protein 3	AK029352|C1qtnf3|81799|C1q and tumor necrosis factor related protein 3	AK075867|C1qtnf3|81799|C1q and tumor necrosis factor related protein 3	AK081704|C1qtnf3|81799|C1q and tumor necrosis factor related protein 3	NM_030888|C1qtnf3|81799|C1q and tumor necrosis factor related protein 3	BC055047|C1qtnf3|81799|C1q and tumor necrosis factor related protein 3	BC019636|C1qtnf3|81799|C1q and tumor necrosis factor related protein 3	BC055859|C1qtnf3|81799|C1q and tumor necrosis factor related protein 3
mm9_v1_chr2_-_33226946_33226968	0.03421	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_chr9_-_89633312_89633312	0.034017	SOX2.p2	AK045652|Ankrd34c|330998|ankyrin repeat domain 34C	NM_207260|Ankrd34c|330998|ankyrin repeat domain 34C
mm9_v1_chr15_+_79177959_79178004	0.0338409	SOX2.p2	AK156896|Maff|17133|v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian)
mm9_v1_chr6_-_137519312_137519326	0.0335377	SOX2.p2	AK149683|Eps8|13860|epidermal growth factor receptor pathway substrate 8
mm9_v1_chr1_-_38954763_38954854	0.0334899	SOX2.p2	AF360543|Chst10|98388|carbohydrate sulfotransferase 10	AK046415|Chst10|98388|carbohydrate sulfotransferase 10	AK171758|Chst10|98388|carbohydrate sulfotransferase 10
mm9_v1_chr18_+_37874471_37874595	0.0334615	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_chr9_-_24956188_24956257	0.0331844	SOX2.p2	AK164769|Herpud2|80517|HERPUD family member 2	AK019862|Herpud2|80517|HERPUD family member 2
mm9_v1_chr16_-_20425991_20426058	0.0328883	SOX2.p2	AK050565|Abcc5|27416|ATP-binding cassette, sub-family C (CFTR/MRP), member 5
mm9_v1_chr17_+_66132737_66132780	0.0326223	SOX2.p2	AK166418|Ppp4r1|70351|protein phosphatase 4, regulatory subunit 1	AK167713|Ppp4r1|70351|protein phosphatase 4, regulatory subunit 1	BC029761|Ppp4r1|70351|protein phosphatase 4, regulatory subunit 1	AK133969|Ppp4r1|70351|protein phosphatase 4, regulatory subunit 1
mm9_v1_chr7_+_104728398_104728430	0.0320342	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_chr1_+_94728419_94728433	0.0320029	SOX2.p2	BC062902|Gpc1|14733|glypican 1
mm9_v1_chr6_-_25639812_25639825	0.0319576	SOX2.p2	AK032525|Gpr37|14763|G protein-coupled receptor 37
mm9_v1_chr13_-_21494493_21494508	0.0318765	SOX2.p2	AK220177|Zkscan3|72739|zinc finger with KRAB and SCAN domains 3
mm9_v1_chr9_-_61918412_61918412	0.0317885	SOX2.p2	BC094587|Glce|93683|glucuronyl C5-epimerase	NM_033320|Glce|93683|glucuronyl C5-epimerase
mm9_v1_chr9_-_53012444_53012529	0.0317309	SOX2.p2	AK166787|Ddx10|77591|DEAD (Asp-Glu-Ala-Asp) box polypeptide 10
mm9_v1_chr1_+_51345952_51345993	0.031708	SOX2.p2	AK035324|Sdpr|20324|serum deprivation response	BC027005|Sdpr|20324|serum deprivation response	NM_138741|Sdpr|20324|serum deprivation response	AK132324|Sdpr|20324|serum deprivation response
mm9_v1_chr16_+_10742336_10742473	0.0313067	SOX2.p2	AK028051|Clec16a|74374|C-type lectin domain family 16, member A
mm9_v1_chr12_-_112951127_112951165	0.0312783	SOX2.p2	AK160246|Bag5|70369|BCL2-associated athanogene 5
mm9_v1_chr2_-_126501173_126501305	0.0311749	SOX2.p2	AY282801|Gabpb1|14391|GA repeat binding protein, beta 1	AY282804|Gabpb1|14391|GA repeat binding protein, beta 1	AK146373|Gabpb1|14391|GA repeat binding protein, beta 1	M74517|Gabpb1|14391|GA repeat binding protein, beta 1	NM_010249|Gabpb1|14391|GA repeat binding protein, beta 1	M74516|Gabpb1|14391|GA repeat binding protein, beta 1	NM_207669|Gabpb1|14391|GA repeat binding protein, beta 1	AK140907|Gabpb1|14391|GA repeat binding protein, beta 1	AK140222|Gabpb1|14391|GA repeat binding protein, beta 1	AK052828|Gabpb1|14391|GA repeat binding protein, beta 1
mm9_v1_chr14_-_103498117_103498150	0.0311355	SOX2.p2	AK167409|Fbxl3|50789|F-box and leucine-rich repeat protein 3
mm9_v1_chr9_-_108481069_108481081	0.0310936	SOX2.p2	AB041854|Wdr6|83669|WD repeat domain 6
mm9_v1_chr1_-_25886551_25886551	0.0305881	SOX2.p2	BC099951|Bai3|210933|brain-specific angiogenesis inhibitor 3	NM_175642|Bai3|210933|brain-specific angiogenesis inhibitor 3
mm9_v1_chr12_+_21117704_21117848	0.0304359	SOX2.p2	AK172944|Asap2|211914|ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	BC096022|Asap2|211914|ArfGAP with SH3 domain, ankyrin repeat and PH domain 2
mm9_v1_chr6_-_86476063_86476189	0.030254	SOX2.p2	BC069915|Pcbp1|23983|poly(rC) binding protein 1	NM_011865|Pcbp1|23983|poly(rC) binding protein 1	AF073936|Pcbp1|23983|poly(rC) binding protein 1
mm9_v1_chr15_-_75397243_75397344	0.030122	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_chr18_-_53904193_53904270	0.0300687	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_chr17_+_47506145_47506145	0.0293655	SOX2.p2	BC048912|Mrps10|64657|mitochondrial ribosomal protein S10	NM_183086|Mrps10|64657|mitochondrial ribosomal protein S10
mm9_v1_chr9_-_114549261_114549332	0.0290443	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_chr1_+_169528706_169528770	0.0289665	SOX2.p2	X66225|Rxrg|20183|retinoid X receptor gamma
mm9_v1_chr13_-_94444229_94444287	0.0289464	SOX2.p2	AF257474|Bhmt2|64918|betaine-homocysteine methyltransferase 2	AK090308|Bhmt2|64918|betaine-homocysteine methyltransferase 2	BC013515|Bhmt2|64918|betaine-homocysteine methyltransferase 2	AK145901|Bhmt2|64918|betaine-homocysteine methyltransferase 2	NM_022884|Bhmt2|64918|betaine-homocysteine methyltransferase 2
mm9_v1_chr2_+_84903869_84903875	0.0285765	SOX2.p2	BC024499|Tnks1bp1|228140|tankyrase 1 binding protein 1
mm9_v1_chr5_+_65194627_65194653	0.0285556	SOX2.p2	AK157576|Klf3|16599|Kruppel-like factor 3 (basic)
mm9_v1_chr5_+_34974750_34974884	0.0285499	SOX2.p2	
mm9_v1_chr19_+_22767298_22767313	0.0283018	SOX2.p2	AK052064|Trpm3|226025|transient receptor potential cation channel, subfamily M, member 3	AK084402|Trpm3|226025|transient receptor potential cation channel, subfamily M, member 3	AK044533|Trpm3|226025|transient receptor potential cation channel, subfamily M, member 3	AK051934|Trpm3|226025|transient receptor potential cation channel, subfamily M, member 3
mm9_v1_chr11_-_6171453_6171670	0.0282783	SOX2.p2	AK003613|Tmed4|103694|transmembrane emp24 protein transport domain containing 4
mm9_v1_chr9_-_119213954_119213965	0.0280868	SOX2.p2	AK031790|Oxsr1|108737|oxidative-stress responsive 1	AK075837|Oxsr1|108737|oxidative-stress responsive 1	NM_133985|Oxsr1|108737|oxidative-stress responsive 1
mm9_v1_chr1_+_94728217_94728298	0.0279901	SOX2.p2	AK154899|Gpc1|14733|glypican 1	AF185613|Gpc1|14733|glypican 1	NM_016696|Gpc1|14733|glypican 1
mm9_v1_chr5_+_31357245_31357300	0.0271266	SOX2.p2	BC137856|Cad|69719|carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	BC144972|Cad|69719|carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	BC144973|Cad|69719|carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase
mm9_v1_chr2_-_126501326_126501329	0.0270383	SOX2.p2	AK040722|Gabpb1|14391|GA repeat binding protein, beta 1
mm9_v1_chr5_+_130731488_130731494	0.0268804	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_chr3_-_107563372_107563394	0.0267412	SOX2.p2	AK154261|Csf1|12977|colony stimulating factor 1 (macrophage)	NM_001113529|Csf1|12977|colony stimulating factor 1 (macrophage)	NM_001113530|Csf1|12977|colony stimulating factor 1 (macrophage)	NM_007778|Csf1|12977|colony stimulating factor 1 (macrophage)
mm9_v1_chr6_+_33922645_33922791	0.026689	SOX2.p2	
mm9_v1_chr11_-_70223517_70223527	0.0265992	SOX2.p2	BC090620|Pelp1|75273|proline, glutamic acid and leucine rich protein 1
mm9_v1_chrX_+_71415963_71415984	0.025864	SOX2.p2	
mm9_v1_chr5_+_122822549_122822598	0.0258548	SOX2.p2	AK087968|Gpn3|68080|GPN-loop GTPase 3	AK080720|Gpn3|68080|GPN-loop GTPase 3	AK146783|Gpn3|68080|GPN-loop GTPase 3	AK016996|Gpn3|68080|GPN-loop GTPase 3
mm9_v1_chr7_-_89079335_89079355	0.025816	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_chr7_+_50469408_50469408	0.0256733	SOX2.p2	EU599041|EU599041|100170401|expressed sequence EU599041	EU599042|EU599041|100170401|expressed sequence EU599041	NM_001177525|EU599041|100170401|expressed sequence EU599041
mm9_v1_chr14_-_55305466_55305487	0.0252599	SOX2.p2	AK134147|Acin1|56215|apoptotic chromatin condensation inducer 1
mm9_v1_chr19_+_56948738_56948999	0.0251604	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_chr2_+_120435110_120435179	0.0250856	SOX2.p2	AK012086|Haus2|66296|HAUS augmin-like complex, subunit 2	AK012779|Haus2|66296|HAUS augmin-like complex, subunit 2	AK132300|Haus2|66296|HAUS augmin-like complex, subunit 2	AK010445|Haus2|66296|HAUS augmin-like complex, subunit 2	AK012960|Haus2|66296|HAUS augmin-like complex, subunit 2	NM_025475|Haus2|66296|HAUS augmin-like complex, subunit 2	BC086677|Haus2|66296|HAUS augmin-like complex, subunit 2
mm9_v1_chrX_-_20666354_20666354	0.0249873	SOX2.p2	AK053018|Zfp300|245368|zinc finger protein 300	NM_183185|Zfp300|245368|zinc finger protein 300
mm9_v1_chr5_-_86539474_86539529	0.0248044	SOX2.p2	AK017687|Uba6|231380|ubiquitin-like modifier activating enzyme 6
mm9_v1_chr1_-_134539434_134539434	0.0247382	SOX2.p2	NM_001160316|Nfasc|269116|neurofascin
mm9_v1_chr5_+_116010796_116010949	0.0245301	SOX2.p2	BC030189|Rplp0|11837|ribosomal protein, large, P0	AK193996|Rplp0|11837|ribosomal protein, large, P0	AK205179|Rplp0|11837|ribosomal protein, large, P0
mm9_v1_chr17_-_56615701_56615731	0.0242734	SOX2.p2	AK145036|Gm9258|668592|predicted gene 9258
mm9_v1_chr11_-_70458027_70458216	0.0240919	SOX2.p2	AK206341|Slc25a11|67863|solute carrier family 25 (mitochondrial carrier oxoglutarate carrier), member 11	AK212009|Slc25a11|67863|solute carrier family 25 (mitochondrial carrier oxoglutarate carrier), member 11	AK178451|Slc25a11|67863|solute carrier family 25 (mitochondrial carrier oxoglutarate carrier), member 11	AK210712|Slc25a11|67863|solute carrier family 25 (mitochondrial carrier oxoglutarate carrier), member 11	AK214004|Slc25a11|67863|solute carrier family 25 (mitochondrial carrier oxoglutarate carrier), member 11
mm9_v1_chr14_-_66899764_66899954	0.0239764	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_chr17_+_43153490_43153503	0.0236658	SOX2.p2	AK043823|Tnfrsf21|94185|tumor necrosis factor receptor superfamily, member 21	NM_178589|Tnfrsf21|94185|tumor necrosis factor receptor superfamily, member 21
mm9_v1_chr15_+_3230406_3230616	0.0233704	SOX2.p2	
mm9_v1_chr8_+_91220965_91221031	0.0232557	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_chr18_-_60908058_60908102	0.0229523	SOX2.p2	AK156504|Ndst1|15531|N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1
mm9_v1_chr1_+_157005804_157006022	0.0229281	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_chr18_+_77168765_77168895	0.0226215	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_chr4_+_139200915_139200991	0.0225901	SOX2.p2	AK087796|Aldh4a1|212647|aldehyde dehydrogenase 4 family, member A1
mm9_v1_chr6_-_56319574_56319627	0.0225416	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_chr5_-_101227486_101227632	0.0219911	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_chr7_+_13609719_13609899	0.0218702	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_chr1_+_75542840_75542910	0.0217787	SOX2.p2	NM_009208|Slc4a3|20536|solute carrier family 4 (anion exchanger), member 3	BC080271|Slc4a3|20536|solute carrier family 4 (anion exchanger), member 3	M28383|Slc4a3|20536|solute carrier family 4 (anion exchanger), member 3
mm9_v1_chr16_-_23029154_23029175	0.0217361	SOX2.p2	NM_001102409|Kng2|385643|kininogen 2	NM_001102410|Kng2|385643|kininogen 2	NM_201375|Kng2|385643|kininogen 2
mm9_v1_chr12_-_74147683_74147691	0.0217227	SOX2.p2	BC023304|Six1|20471|sine oculis-related homeobox 1 homolog (Drosophila)
mm9_v1_chr17_+_30141959_30142039	0.0215899	SOX2.p2	AK082915|Zfand3|21769|zinc finger, AN1-type domain 3	AK148316|Zfand3|21769|zinc finger, AN1-type domain 3	BC083124|Zfand3|21769|zinc finger, AN1-type domain 3	NM_148926|Zfand3|21769|zinc finger, AN1-type domain 3
mm9_v1_chr7_-_125676764_125676807	0.0215068	SOX2.p2	AF080580|Coq7|12850|demethyl-Q 7	BC038681|Coq7|12850|demethyl-Q 7
mm9_v1_chr15_-_88991213_88991332	0.0211241	SOX2.p2	BC003293|Plxnb2|140570|plexin B2
mm9_v1_chr5_+_115018259_115018259	0.0209857	SOX2.p2	BC057022|BC057022|433940|cDNA sequence BC057022	NM_001004180|BC057022|433940|cDNA sequence BC057022
mm9_v1_chr5_+_37729712_37729738	0.02078	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_chr16_+_17276384_17276419	0.0205969	SOX2.p2	NM_177473|Tmem191c|224019|transmembrane protein 191C	AK016675|Tmem191c|224019|transmembrane protein 191C
mm9_v1_chr7_-_20262106_20262119	0.0205796	SOX2.p2	AK146468|Apoc2|11813|apolipoprotein C-II	Z15090|Apoc2|11813|apolipoprotein C-II
mm9_v1_chr18_+_30432499_30432592	0.0204008	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_chr12_+_66176588_66176613	0.0200864	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_chr12_+_85291557_85291603	0.0199297	SOX2.p2	BC138094|2410016O06Rik|71952|RIKEN cDNA 2410016O06 gene	NM_023633|2410016O06Rik|71952|RIKEN cDNA 2410016O06 gene
mm9_v1_chr10_-_95010006_95010009	0.0196056	SOX2.p2	AK190818|Nudt4|71207|nudix (nucleoside diphosphate linked moiety X)-type motif 4	AK196789|Nudt4|71207|nudix (nucleoside diphosphate linked moiety X)-type motif 4	AK201590|Nudt4|71207|nudix (nucleoside diphosphate linked moiety X)-type motif 4	AK202794|Nudt4|71207|nudix (nucleoside diphosphate linked moiety X)-type motif 4
mm9_v1_chr6_-_39370351_39370385	0.0195882	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_chr11_-_88725811_88725842	0.0195299	SOX2.p2	BC065135|Akap1|11640|A kinase (PRKA) anchor protein 1
mm9_v1_chr4_+_120550473_120550605	0.0192462	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_chr3_+_20008792_20008792	0.018875	SOX2.p2	BC039796|Hltf|20585|helicase-like transcription factor
mm9_v1_chr13_-_54666552_54666754	0.0183443	SOX2.p2	AK217762|4833439L19Rik|97820|RIKEN cDNA 4833439L19 gene	AK173126|4833439L19Rik|97820|RIKEN cDNA 4833439L19 gene	BC039775|4833439L19Rik|97820|RIKEN cDNA 4833439L19 gene	AK014792|4833439L19Rik|97820|RIKEN cDNA 4833439L19 gene	AK028697|4833439L19Rik|97820|RIKEN cDNA 4833439L19 gene	AK016176|4833439L19Rik|97820|RIKEN cDNA 4833439L19 gene	AK167616|4833439L19Rik|97820|RIKEN cDNA 4833439L19 gene	BC054417|4833439L19Rik|97820|RIKEN cDNA 4833439L19 gene	BC043040|4833439L19Rik|97820|RIKEN cDNA 4833439L19 gene	AK004845|4833439L19Rik|97820|RIKEN cDNA 4833439L19 gene	AK159945|4833439L19Rik|97820|RIKEN cDNA 4833439L19 gene	AK145025|4833439L19Rik|97820|RIKEN cDNA 4833439L19 gene	AK169399|4833439L19Rik|97820|RIKEN cDNA 4833439L19 gene	BC033445|4833439L19Rik|97820|RIKEN cDNA 4833439L19 gene	NM_133797|4833439L19Rik|97820|RIKEN cDNA 4833439L19 gene
mm9_v1_chr13_-_12742377_12742693	0.018336	SOX2.p2	AK190995|Gpr137b|83924|G protein-coupled receptor 137B	AK194643|Gpr137b|83924|G protein-coupled receptor 137B	AK198577|Gpr137b|83924|G protein-coupled receptor 137B	AK201617|Gpr137b|83924|G protein-coupled receptor 137B	AK204136|Gpr137b|83924|G protein-coupled receptor 137B	AK204647|Gpr137b|83924|G protein-coupled receptor 137B	AK195847|Gpr137b|83924|G protein-coupled receptor 137B	AK170650|Gpr137b-ps|664862|G protein-coupled receptor 137B, pseudogene	BC093499|Gpr137b-ps|664862|G protein-coupled receptor 137B, pseudogene	AF154337|Gpr137b-ps|664862|G protein-coupled receptor 137B, pseudogene	AK009736|Gpr137b-ps|664862|G protein-coupled receptor 137B, pseudogene	AK170103|Gpr137b-ps|664862|G protein-coupled receptor 137B, pseudogene	AK087190|Gpr137b-ps|664862|G protein-coupled receptor 137B, pseudogene	AK171335|Gpr137b-ps|664862|G protein-coupled receptor 137B, pseudogene	AK010724|Gpr137b-ps|664862|G protein-coupled receptor 137B, pseudogene
mm9_v1_chr9_-_20447047_20447249	0.0182484	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_chr12_-_84828657_84828685	0.018051	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_chr4_+_59048027_59048124	0.0179281	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_chr4_+_43888373_43888471	0.0176432	SOX2.p2	BC132197|Reck|53614|reversion-inducing-cysteine-rich protein with kazal motifs	BC138065|Reck|53614|reversion-inducing-cysteine-rich protein with kazal motifs	BC145133|Reck|53614|reversion-inducing-cysteine-rich protein with kazal motifs	AK042266|Reck|53614|reversion-inducing-cysteine-rich protein with kazal motifs	NM_016678|Reck|53614|reversion-inducing-cysteine-rich protein with kazal motifs	AK157885|Reck|53614|reversion-inducing-cysteine-rich protein with kazal motifs	AK143657|Reck|53614|reversion-inducing-cysteine-rich protein with kazal motifs	BC053025|Reck|53614|reversion-inducing-cysteine-rich protein with kazal motifs	AB006960|Reck|53614|reversion-inducing-cysteine-rich protein with kazal motifs
mm9_v1_chr11_+_98554734_98554759	0.0175944	SOX2.p2	AK183122|Psmd3|22123|proteasome (prosome, macropain) 26S subunit, non-ATPase, 3	AK205568|Psmd3|22123|proteasome (prosome, macropain) 26S subunit, non-ATPase, 3
mm9_v1_chr12_-_102321911_102321936	0.0172835	SOX2.p2	AK053668|Smek1|68734|SMEK homolog 1, suppressor of mek1 (Dictyostelium)	NM_001160214|Smek1|68734|SMEK homolog 1, suppressor of mek1 (Dictyostelium)	NM_211355|Smek1|68734|SMEK homolog 1, suppressor of mek1 (Dictyostelium)
mm9_v1_chr19_+_23241546_23241602	0.0169709	SOX2.p2	AK009928|Klf9|16601|Kruppel-like factor 9
mm9_v1_chr15_-_81560309_81560370	0.0168209	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_chr17_-_81464406_81464435	0.0168193	SOX2.p2	AK012806|Thumpd2|72167|THUMP domain containing 2	NM_028138|Thumpd2|72167|THUMP domain containing 2
mm9_v1_chr2_-_62411970_62412077	0.0167461	SOX2.p2	BC019190|Fap|14089|fibroblast activation protein	AK051959|Fap|14089|fibroblast activation protein	NM_007986|Fap|14089|fibroblast activation protein	Y10007|Fap|14089|fibroblast activation protein
mm9_v1_chr17_+_28829512_28829512	0.016683	SOX2.p2	AK151348|Mapk14|26416|mitogen-activated protein kinase 14	AK153025|Mapk14|26416|mitogen-activated protein kinase 14	NM_001168513|Mapk14|26416|mitogen-activated protein kinase 14
mm9_v1_chrX_+_148450970_148451017	0.0166361	SOX2.p2	AF047600|Smc1a|24061|structural maintenance of chromosomes 1A	NM_019710|Smc1a|24061|structural maintenance of chromosomes 1A	AK013648|Smc1a|24061|structural maintenance of chromosomes 1A	BC131667|Smc1a|24061|structural maintenance of chromosomes 1A
mm9_v1_chr15_+_12808445_12808493	0.0162087	SOX2.p2	BC040801|Drosha|14000|drosha, ribonuclease type III
mm9_v1_chr19_-_4333914_4333961	0.016194	SOX2.p2	
mm9_v1_chr11_-_116135422_116135530	0.0160271	SOX2.p2	AK076003|Srp68|217337|signal recognition particle 68	AK033010|Srp68|217337|signal recognition particle 68	BC070422|Srp68|217337|signal recognition particle 68	NM_146032|Srp68|217337|signal recognition particle 68
mm9_v1_chr14_-_73725576_73725603	0.015554	SOX2.p2	AK011246|Rb1|19645|retinoblastoma 1	BC096525|Rb1|19645|retinoblastoma 1	NM_009029|Rb1|19645|retinoblastoma 1
mm9_v1_chr14_-_51544484_51544489	0.015483	SOX2.p2	BC091757|Osgep|66246|O-sialoglycoprotein endopeptidase
mm9_v1_chr17_+_47027617_47027637	0.0153682	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_chr11_+_116135575_116135583	0.0152789	SOX2.p2	
mm9_v1_chr8_+_125925000_125925050	0.0152019	SOX2.p2	
mm9_v1_chr8_-_122346577_122346634	0.014501	SOX2.p2	
mm9_v1_chr10_+_14480024_14480094	0.0144874	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_chr10_-_128328773_128328773	0.0144207	SOX2.p2	NM_010272|Gdf11|14561|growth differentiation factor 11
mm9_v1_chr8_-_96496001_96496082	0.0141514	SOX2.p2	AK197102|Amfr|23802|autocrine motility factor receptor
mm9_v1_chr14_+_117324999_117325104	0.0138772	SOX2.p2	AK032866|Gpc6|23888|glypican 6	BC023448|Gpc6|23888|glypican 6
mm9_v1_chr5_-_93612145_93612203	0.0138541	SOX2.p2	AK179364|Ccni|12453|cyclin I
mm9_v1_chr10_-_120748244_120748244	0.0137908	SOX2.p2	NM_029057|Tbc1d30|74694|TBC1 domain family, member 30
mm9_v1_chr1_+_183081112_183081141	0.0137465	SOX2.p2	AK165179|Cnih4|98417|cornichon homolog 4 (Drosophila)	BC065395|Cnih4|98417|cornichon homolog 4 (Drosophila)	AK166153|Cnih4|98417|cornichon homolog 4 (Drosophila)	BC040509|Cnih4|98417|cornichon homolog 4 (Drosophila)
mm9_v1_chr19_+_46227052_46227083	0.0134887	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_chr4_-_129012546_129012617	0.0132718	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_chr11_-_120092784_120092898	0.0130293	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_chr6_+_73221007_73221091	0.0129329	SOX2.p2	AK204482|Suclg1|56451|succinate-CoA ligase, GDP-forming, alpha subunit
mm9_v1_chr6_+_65621583_65621630	0.0127457	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_chr2_+_4073908_4073934	0.0125078	SOX2.p2	NM_172475|Frmd4a|209630|FERM domain containing 4A	AK034706|Frmd4a|209630|FERM domain containing 4A	BC058672|Frmd4a|209630|FERM domain containing 4A	AK163887|Frmd4a|209630|FERM domain containing 4A
mm9_v1_chr18_+_52625323_52625373	0.012265	SOX2.p2	AK012865|Srfbp1|67222|serum response factor binding protein 1	NM_026040|Srfbp1|67222|serum response factor binding protein 1	AK144845|Srfbp1|67222|serum response factor binding protein 1	AK141882|Srfbp1|67222|serum response factor binding protein 1	AK147692|Srfbp1|67222|serum response factor binding protein 1	BC024338|Srfbp1|67222|serum response factor binding protein 1	AY611629|Srfbp1|67222|serum response factor binding protein 1
mm9_v1_chr4_-_116314542_116314556	0.0121349	SOX2.p2	AK178751|Akr1a4|58810|aldo-keto reductase family 1, member A4 (aldehyde reductase)	AK203039|Akr1a4|58810|aldo-keto reductase family 1, member A4 (aldehyde reductase)
mm9_v1_chr1_+_122498985_122498994	0.0120687	SOX2.p2	AK140634|En1|13798|engrailed 1
mm9_v1_chr2_+_121782185_121782265	0.0119978	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_chr2_-_27282344_27282431	0.0118545	SOX2.p2	NM_009500|Vav2|22325|vav 2 oncogene	U37017|Vav2|22325|vav 2 oncogene	BC053060|Vav2|22325|vav 2 oncogene
mm9_v1_chr16_-_34514112_34514198	0.0117607	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_chr7_-_35174519_35174695	0.0117238	SOX2.p2	BC031521|Lsm14a|67070|LSM14 homolog A (SCD6, S. cerevisiae)	NM_025948|Lsm14a|67070|LSM14 homolog A (SCD6, S. cerevisiae)
mm9_v1_chr13_-_38726917_38726993	0.0116561	SOX2.p2	AK075808|Muted|17828|muted	AK170614|Muted|17828|muted	AK039050|Muted|17828|muted	BC024720|Muted|17828|muted	AK147762|Muted|17828|muted	AK171537|Muted|17828|muted	AF426433|Muted|17828|muted	NM_139063|Muted|17828|muted
mm9_v1_chr15_-_76004515_76004599	0.0115371	SOX2.p2	AK137706|Plec|18810|plectin	AY032899|Plec|18810|plectin
mm9_v1_chr9_+_45238375_45238483	0.0111921	SOX2.p2	NM_001081270|Dscaml1|114873|Down syndrome cell adhesion molecule-like 1	AK147531|Dscaml1|114873|Down syndrome cell adhesion molecule-like 1	AF487345|Dscaml1|114873|Down syndrome cell adhesion molecule-like 1	AF487347|Dscaml1|114873|Down syndrome cell adhesion molecule-like 1
mm9_v1_chrX_-_147241307_147241451	0.0111865	SOX2.p2	AK179193|Maged2|80884|melanoma antigen, family D, 2
mm9_v1_chr7_-_110655456_110655457	0.011016	SOX2.p2	BC113199|Olfr610|259085|olfactory receptor 610	NM_147081|Olfr610|259085|olfactory receptor 610
mm9_v1_chr6_-_124688630_124688780	0.0108695	SOX2.p2	AK150509|Ptpn6|15170|protein tyrosine phosphatase, non-receptor type 6	AK132509|Ptpn6|15170|protein tyrosine phosphatase, non-receptor type 6	NM_001077705|Ptpn6|15170|protein tyrosine phosphatase, non-receptor type 6
mm9_v1_chr1_+_60466499_60466554	0.0108298	SOX2.p2	BC079646|Abi2|329165|abl-interactor 2
mm9_v1_chr9_-_116084154_116084277	0.0107275	SOX2.p2	AF406755|Tgfbr2|21813|transforming growth factor, beta receptor II	S69114|Tgfbr2|21813|transforming growth factor, beta receptor II
mm9_v1_chr10_+_82359714_82359858	0.0105719	SOX2.p2	AK007891|Txnrd1|50493|thioredoxin reductase 1	AK202828|Txnrd1|50493|thioredoxin reductase 1	AK204569|Txnrd1|50493|thioredoxin reductase 1	AK217830|Txnrd1|50493|thioredoxin reductase 1	AK194198|Txnrd1|50493|thioredoxin reductase 1	AK203123|Txnrd1|50493|thioredoxin reductase 1
mm9_v1_chr13_-_107727010_107727028	0.0105442	SOX2.p2	AK044487|Ipo11|76582|importin 11	AK087793|Ipo11|76582|importin 11
mm9_v1_chr16_-_78576914_78576958	0.0105131	SOX2.p2	AK044670|D16Ertd472e|67102|DNA segment, Chr 16, ERATO Doi 472, expressed
mm9_v1_chr18_+_37906739_37906841	0.0104692	SOX2.p2	AY013793|Pcdhga10|93722|protocadherin gamma subfamily A, 10	NM_033593|Pcdhga10|93722|protocadherin gamma subfamily A, 10
mm9_v1_chr6_+_4484651_4484672	0.0104545	SOX2.p2	AK159120|Col1a2|12843|collagen, type I, alpha 2
mm9_v1_chr8_+_96738490_96738507	0.010281	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_chr13_-_46060354_46060386	0.0102052	SOX2.p2	AK165114|Atxn1|20238|ataxin 1	AK037692|Atxn1|20238|ataxin 1
mm9_v1_chr1_+_89346303_89346444	0.00983916	SOX2.p2	AK044009|Gigyf2|227331|GRB10 interacting GYF protein 2
mm9_v1_chr3_+_137940628_137940681	0.00966692	SOX2.p2	BC054467|Adh1|11522|alcohol dehydrogenase 1 (class I)
mm9_v1_chr6_-_83781657_83781701	0.00963587	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_chr14_-_31832274_31832280	0.00940991	SOX2.p2	NM_153547|Gnl3|30877|guanine nucleotide binding protein-like 3 (nucleolar)	AK167094|Gnl3|30877|guanine nucleotide binding protein-like 3 (nucleolar)
mm9_v1_chr7_+_18398030_18398100	0.00923339	SOX2.p2	AK005390|Ceacam14|67084|carcinoembryonic antigen-related cell adhesion molecule 14	AK005482|Ceacam14|67084|carcinoembryonic antigen-related cell adhesion molecule 14	AK005509|Ceacam14|67084|carcinoembryonic antigen-related cell adhesion molecule 14	AK005533|Ceacam14|67084|carcinoembryonic antigen-related cell adhesion molecule 14	NM_025957|Ceacam14|67084|carcinoembryonic antigen-related cell adhesion molecule 14	BC099412|Ceacam14|67084|carcinoembryonic antigen-related cell adhesion molecule 14
mm9_v1_chr15_-_81560302_81560307	0.00900064	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_chr2_+_169459145_169459258	0.0088303	SOX2.p2	NM_080455|Tshz2|228911|teashirt zinc finger family member 2	BC079550|Tshz2|228911|teashirt zinc finger family member 2
mm9_v1_chr8_-_26212242_26212282	0.00882829	SOX2.p2	AK042324|Plekha2|83436|pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	AK078212|Plekha2|83436|pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	NM_031257|Plekha2|83436|pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2
mm9_v1_chr4_-_43013064_43013178	0.00882103	SOX2.p2	
mm9_v1_chr19_+_23239333_23239507	0.00879229	SOX2.p2	AK177679|Klf9|16601|Kruppel-like factor 9
mm9_v1_chr12_+_111903331_111903389	0.00867692	SOX2.p2	AK151489|Dync1h1|13424|dynein cytoplasmic 1 heavy chain 1
mm9_v1_chr12_-_32635399_32635399	0.00822301	SOX2.p2	AK133127|Hbp1|73389|high mobility group box transcription factor 1	NM_153198|Hbp1|73389|high mobility group box transcription factor 1	NM_177993|Hbp1|73389|high mobility group box transcription factor 1
mm9_v1_chr19_-_41970627_41970698	0.0080861	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_chr5_+_138526376_138526387	0.00785875	SOX2.p2	AK028932|Zkscan1|74570|zinc finger with KRAB and SCAN domains 1
mm9_v1_chr18_+_52927964_52927973	0.00769555	SOX2.p2	AK082079|Sncaip|67847|synuclein, alpha interacting protein (synphilin)
mm9_v1_chr2_-_65201979_65202090	0.00767434	SOX2.p2	AK041015|Slc38a11|320106|solute carrier family 38, member 11	AK139966|Slc38a11|320106|solute carrier family 38, member 11	NM_177074|Slc38a11|320106|solute carrier family 38, member 11	AK034126|Slc38a11|320106|solute carrier family 38, member 11	AK043610|Slc38a11|320106|solute carrier family 38, member 11
mm9_v1_chr2_-_129525512_129525673	0.00744691	SOX2.p2	BC137571|Pdyn|18610|prodynorphin	BC137572|Pdyn|18610|prodynorphin	AF026537|Pdyn|18610|prodynorphin	AK133597|Pdyn|18610|prodynorphin
mm9_v1_chr17_+_17967938_17968143	0.00725687	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_chr10_-_36858671_36858801	0.00692141	SOX2.p2	BC046601|Marcks|17118|myristoylated alanine rich protein kinase C substrate	M60474|Marcks|17118|myristoylated alanine rich protein kinase C substrate	BC002068|Marcks|17118|myristoylated alanine rich protein kinase C substrate	BC039911|Marcks|17118|myristoylated alanine rich protein kinase C substrate	NM_008538|Marcks|17118|myristoylated alanine rich protein kinase C substrate
mm9_v1_chr5_-_124804583_124804698	0.00685167	SOX2.p2	BC083075|Cdk2ap1|13445|CDK2 (cyclin-dependent kinase 2)-associated protein 1	NM_013812|Cdk2ap1|13445|CDK2 (cyclin-dependent kinase 2)-associated protein 1	AK004852|Cdk2ap1|13445|CDK2 (cyclin-dependent kinase 2)-associated protein 1
mm9_v1_chr11_+_79391766_79391883	0.00680779	SOX2.p2	AK053047|Nf1|18015|neurofibromatosis 1
mm9_v1_chr2_+_145685882_145685886	0.00669323	SOX2.p2	AK163047|Rin2|74030|Ras and Rab interactor 2
mm9_v1_chr5_-_123438517_123438541	0.006461	SOX2.p2	NM_001005866|Kdm2b|30841|lysine (K)-specific demethylase 2B
mm9_v1_chr2_-_30758807_30758816	0.00645571	SOX2.p2	AK150013|Ptges|64292|prostaglandin E synthase	AK080897|Ptges|64292|prostaglandin E synthase	NM_022415|Ptges|64292|prostaglandin E synthase
mm9_v1_chr8_-_125682154_125682179	0.00635811	SOX2.p2	AF026074|Sult5a1|57429|sulfotransferase family 5A, member 1	BC012677|Sult5a1|57429|sulfotransferase family 5A, member 1	AK142243|Sult5a1|57429|sulfotransferase family 5A, member 1	NM_020564|Sult5a1|57429|sulfotransferase family 5A, member 1
mm9_v1_chr5_-_123438493_123438509	0.0063308	SOX2.p2	AK087953|Kdm2b|30841|lysine (K)-specific demethylase 2B
mm9_v1_chr3_-_89832276_89832298	0.00626909	SOX2.p2	AK082804|Ubap2l|74383|ubiquitin associated protein 2-like
mm9_v1_chr8_+_96738448_96738479	0.00602929	SOX2.p2	AK169693|Nup93|71805|nucleoporin 93
mm9_v1_chr9_-_64062342_64062398	0.00561584	SOX2.p2	AK165664|Map2k1|26395|mitogen-activated protein kinase kinase 1
mm9_v1_chr19_-_6067723_6067866	0.00524968	SOX2.p2	AF480070|Tm7sf2|73166|transmembrane 7 superfamily member 2	AK039028|Tm7sf2|73166|transmembrane 7 superfamily member 2	AK155475|Tm7sf2|73166|transmembrane 7 superfamily member 2	AK014166|Tm7sf2|73166|transmembrane 7 superfamily member 2	AK134512|Tm7sf2|73166|transmembrane 7 superfamily member 2	BC014769|Tm7sf2|73166|transmembrane 7 superfamily member 2	AK037325|Tm7sf2|73166|transmembrane 7 superfamily member 2	NM_028454|Tm7sf2|73166|transmembrane 7 superfamily member 2	AK040016|Tm7sf2|73166|transmembrane 7 superfamily member 2	AK043687|Tm7sf2|73166|transmembrane 7 superfamily member 2
mm9_v1_chr10_-_114752600_114752678	0.0052277	SOX2.p2	AK172891|Rab21|216344|RAB21, member RAS oncogene family	BC055042|Rab21|216344|RAB21, member RAS oncogene family	NM_024454|Rab21|216344|RAB21, member RAS oncogene family	BC040104|Rab21|216344|RAB21, member RAS oncogene family
mm9_v1_chr16_-_59027730_59027752	0.00508138	SOX2.p2	NM_146321|Olfr186|258318|olfactory receptor 186	BC150713|Olfr186|258318|olfactory receptor 186
mm9_v1_chr1_+_60466568_60466597	0.00507751	SOX2.p2	BC079545|Abi2|329165|abl-interactor 2
mm9_v1_chr17_-_24210437_24210453	0.00498977	SOX2.p2	AK052960|Kctd5|69259|potassium channel tetramerisation domain containing 5	NM_027008|Kctd5|69259|potassium channel tetramerisation domain containing 5
mm9_v1_chr9_-_65756482_65756602	0.00479636	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_chr17_+_73186891_73186925	0.00446943	SOX2.p2	AK154461|Ypel5|383295|yippee-like 5 (Drosophila)
mm9_v1_chr19_+_45005658_45005755	0.00440324	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_chr1_+_58770105_58770160	0.00426582	SOX2.p2	NM_009805|Cflar|12633|CASP8 and FADD-like apoptosis regulator	NM_207653|Cflar|12633|CASP8 and FADD-like apoptosis regulator	AK143812|Cflar|12633|CASP8 and FADD-like apoptosis regulator	AK161220|Cflar|12633|CASP8 and FADD-like apoptosis regulator	BC029223|Cflar|12633|CASP8 and FADD-like apoptosis regulator
mm9_v1_chr18_+_77303920_77303957	0.00389606	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_chr17_-_33054270_33054330	0.00380738	SOX2.p2	AB037541|Cyp4f14|64385|cytochrome P450, family 4, subfamily f, polypeptide 14	AK005007|Cyp4f14|64385|cytochrome P450, family 4, subfamily f, polypeptide 14	AK018676|Cyp4f14|64385|cytochrome P450, family 4, subfamily f, polypeptide 14
mm9_v1_chr6_-_25639835_25639849	0.00377492	SOX2.p2	BC031918|Gpr37|14763|G protein-coupled receptor 37
mm9_v1_chr10_+_39089853_39089891	0.00352177	SOX2.p2	M27266|Fyn|14360|Fyn proto-oncogene	U70324|Fyn|14360|Fyn proto-oncogene
mm9_v1_chr11_-_110112926_110113089	0.00292571	SOX2.p2	BC132417|Abca6|76184|ATP-binding cassette, sub-family A (ABC1), member 6	BC132419|Abca6|76184|ATP-binding cassette, sub-family A (ABC1), member 6	AK053384|Abca6|76184|ATP-binding cassette, sub-family A (ABC1), member 6	AF498361|Abca6|76184|ATP-binding cassette, sub-family A (ABC1), member 6	AK042934|Abca6|76184|ATP-binding cassette, sub-family A (ABC1), member 6	AK018242|Abca6|76184|ATP-binding cassette, sub-family A (ABC1), member 6	AK040652|Abca6|76184|ATP-binding cassette, sub-family A (ABC1), member 6	NM_001166556|Abca6|76184|ATP-binding cassette, sub-family A (ABC1), member 6	NM_001166557|Abca6|76184|ATP-binding cassette, sub-family A (ABC1), member 6	NM_147218|Abca6|76184|ATP-binding cassette, sub-family A (ABC1), member 6
mm9_v1_chr9_-_21875784_21875847	0.0027443	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_chr17_+_87682206_87682305	0.00242865	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_chr8_-_26212203_26212230	0.00242491	SOX2.p2	BC010215|Plekha2|83436|pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	AF286161|Plekha2|83436|pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2
mm9_v1_chr2_+_34627729_34627749	0.00205172	SOX2.p2	AK151244|Hspa5|14828|heat shock protein 5	D78645|Hspa5|14828|heat shock protein 5
mm9_v1_chr2_+_125499344_125499369	0.00193086	SOX2.p2	AL357452|Eid1|58521|EP300 interacting inhibitor of differentiation 1
mm9_v1_chr7_-_52071027_52071027	0.00191673	SOX2.p2	AF375476|Atf5|107503|activating transcription factor 5	NM_030693|Atf5|107503|activating transcription factor 5
mm9_v1_chr7_+_127883556_127883560	0.0016417	SOX2.p2	AK086942|Vwa3a|233813|von Willebrand factor A domain containing 3A	AK136898|Vwa3a|233813|von Willebrand factor A domain containing 3A
mm9_v1_chr17_+_13414053_13414053	0.00159947	SOX2.p2	AJ245453|Smok2a|27263|sperm motility kinase 2A	NM_013741|Smok2a|27263|sperm motility kinase 2A
mm9_v1_chr14_-_79790474_79790599	0.00154381	SOX2.p2	BC052445|Naa16|66897|N(alpha)-acetyltransferase 16, NatA auxiliary subunit	NM_025832|Naa16|66897|N(alpha)-acetyltransferase 16, NatA auxiliary subunit	AK005056|Naa16|66897|N(alpha)-acetyltransferase 16, NatA auxiliary subunit	AK152498|Naa16|66897|N(alpha)-acetyltransferase 16, NatA auxiliary subunit	AK007755|Naa16|66897|N(alpha)-acetyltransferase 16, NatA auxiliary subunit	AK028432|Naa16|66897|N(alpha)-acetyltransferase 16, NatA auxiliary subunit
mm9_v1_chr7_+_13609462_13609530	0.00154059	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_chr15_-_55738264_55738503	0.00140639	SOX2.p2	BC003748|Sntb1|20649|syntrophin, basic 1	U89997|Sntb1|20649|syntrophin, basic 1	NM_016667|Sntb1|20649|syntrophin, basic 1
mm9_v1_chr18_+_3383009_3383028	0.00116838	SOX2.p2	AK016520|Cul2|71745|cullin 2
mm9_v1_chrX_-_143988623_143988623	0.000855351	SOX2.p2	NM_001081173|Lrch2|210297|leucine-rich repeats and calponin homology (CH) domain containing 2
mm9_v1_chr3_-_66785692_66785692	0.000651725	SOX2.p2	NM_013665|Shox2|20429|short stature homeobox 2	U66918|Shox2|20429|short stature homeobox 2
mm9_v1_chr13_+_67964262_67964324	0.000452734	SOX2.p2	AK133011|BC048507|408058|cDNA sequence BC048507	BC048507|BC048507|408058|cDNA sequence BC048507	NM_001001185|BC048507|408058|cDNA sequence BC048507
mm9_v1_chr9_+_108241754_108241796	0.000428924	SOX2.p2	AK191208|Gpx1|14775|glutathione peroxidase 1	AK191913|Gpx1|14775|glutathione peroxidase 1	AK200043|Gpx1|14775|glutathione peroxidase 1	AK201721|Gpx1|14775|glutathione peroxidase 1	AK202661|Gpx1|14775|glutathione peroxidase 1	AK205185|Gpx1|14775|glutathione peroxidase 1
mm9_v1_chr2_+_52601476_52601507	0.00039899	SOX2.p2	
mm9_v1_chr6_-_8728481_8728486	0.000323822	SOX2.p2	AK005965|Ica1|15893|islet cell autoantigen 1	NM_010492|Ica1|15893|islet cell autoantigen 1	AK016989|Ica1|15893|islet cell autoantigen 1
mm9_v1_chr5_+_65194749_65194773	0.000228633	SOX2.p2	AK143838|Klf3|16599|Kruppel-like factor 3 (basic)	AK007959|Klf3|16599|Kruppel-like factor 3 (basic)	NM_008453|Klf3|16599|Kruppel-like factor 3 (basic)
mm9_v1_chr12_-_56921993_56922083	0.000156669	SOX2.p2	AK153664|Ralgapa1|56784|Ral GTPase activating protein, alpha subunit 1	AK042116|Ralgapa1|56784|Ral GTPase activating protein, alpha subunit 1	BC145119|Ralgapa1|56784|Ral GTPase activating protein, alpha subunit 1	BC150707|Ralgapa1|56784|Ral GTPase activating protein, alpha subunit 1
mm9_v1_chr17_-_33897193_33897231	0.000147994	SOX2.p2	AB232606|Rab11b|19326|RAB11B, member RAS oncogene family	AK146978|Rab11b|19326|RAB11B, member RAS oncogene family	AK148106|Rab11b|19326|RAB11B, member RAS oncogene family
mm9_v1_chr3_-_127202153_127202192	0.000100573	SOX2.p2	AK043034|Ank2|109676|ankyrin 2, brain
