mm10_v2_chr12_+_72441852_72441866	0.639674	Msx3	ENSMUST00000162159.1|Lrrc9|ENSMUSG00000021090.9|leucine rich repeat containing 9
mm10_v2_chr12_+_72441933_72441970	0.613252	Msx3	ENSMUST00000161284.1|Lrrc9|ENSMUSG00000021090.9|leucine rich repeat containing 9
mm10_v2_chr17_+_21383725_21383766	0.555141	Msx3	ENSMUST00000056107.4|Zfp677|ENSMUSG00000062743.3|zinc finger protein 677 	ENSMUST00000162659.1|Zfp677|ENSMUSG00000062743.3|zinc finger protein 677
mm10_v2_chr2_-_45117349_45117395	0.494488	Msx3	ENSMUST00000176438.2|Zeb2|ENSMUSG00000026872.10|zinc finger E-box binding homeobox 2
mm10_v2_chr13_-_29984219_29984353	0.469318	Msx3	ENSMUST00000146092.1|E2f3|ENSMUSG00000016477.11|E2F transcription factor 3
mm10_v2_chr4_-_14621494_14621506	0.393355	Msx3	ENSMUST00000149633.1|Slc26a7|ENSMUSG00000040569.7|solute carrier family 26, member 7
mm10_v2_chr4_-_14621669_14621786	0.380476	Msx3	ENSMUST00000143105.1|Slc26a7|ENSMUSG00000040569.7|solute carrier family 26, member 7
mm10_v2_chr1_-_52190901_52190915	0.365543	Msx3	ENSMUST00000156887.1|Gls|ENSMUSG00000026103.8|glutaminase 	ENSMUST00000129107.1|Gls|ENSMUSG00000026103.8|glutaminase
mm10_v2_chr3_-_41742471_41742548	0.363191	Msx3	ENSMUST00000026866.8|Sclt1|ENSMUSG00000059834.6|sodium channel and clathrin linker 1
mm10_v2_chr3_+_41742615_41742725	0.351836	Msx3	ENSMUST00000146165.1|D3Ertd751e|ENSMUSG00000025766.8|DNA segment, Chr 3, ERATO Doi 751, expressed 	ENSMUST00000119572.1|D3Ertd751e|ENSMUSG00000025766.8|DNA segment, Chr 3, ERATO Doi 751, expressed 	ENSMUST00000108065.2|D3Ertd751e|ENSMUSG00000025766.8|DNA segment, Chr 3, ERATO Doi 751, expressed 	ENSMUST00000120167.1|D3Ertd751e|ENSMUSG00000025766.8|DNA segment, Chr 3, ERATO Doi 751, expressed 	ENSMUST00000026867.7|D3Ertd751e|ENSMUSG00000025766.8|DNA segment, Chr 3, ERATO Doi 751, expressed 	ENSMUST00000026868.7|D3Ertd751e|ENSMUSG00000025766.8|DNA segment, Chr 3, ERATO Doi 751, expressed
mm10_v2_chr7_+_27486910_27486960	0.326557	Msx3	ENSMUST00000008528.7|Sertad1|ENSMUSG00000008384.8|SERTA domain containing 1
mm10_v2_chrX_-_143933089_143933142	0.314893	Msx3	ENSMUST00000087313.3|Dcx|ENSMUSG00000031285.8|doublecortin
mm10_v2_chr8_+_69659263_69659263	0.282446	Msx3	ENSMUST00000169125.1|Zfp964|ENSMUSG00000091764.1|zinc finger protein 964
mm10_v2_chr4_+_102254739_102254761	0.273833	Msx3	ENSMUST00000106907.2|Pde4b|ENSMUSG00000028525.10|phosphodiesterase 4B, cAMP specific
mm10_v2_chr15_+_44787746_44787782	0.266745	Msx3	ENSMUST00000181839.1|2310069G16Rik|ENSMUSG00000097102.1|RIKEN cDNA 2310069G16 gene
mm10_v2_chrX_-_143933204_143933311	0.26061	Msx3	ENSMUST00000112851.1|Dcx|ENSMUSG00000031285.8|doublecortin 	ENSMUST00000112856.2|Dcx|ENSMUSG00000031285.8|doublecortin 	ENSMUST00000033642.3|Dcx|ENSMUSG00000031285.8|doublecortin
mm10_v2_chrM_+_9870_9885	0.245546	Msx3	ENSMUST00000084013.1|mt-Nd4l|ENSMUSG00000065947.3|mitochondrially encoded NADH dehydrogenase 4L
mm10_v2_chr5_+_14514918_14514951	0.240635	Msx3	ENSMUST00000030691.10|Pclo|ENSMUSG00000061601.9|piccolo (presynaptic cytomatrix protein) 	ENSMUST00000182407.1|Pclo|ENSMUSG00000061601.9|piccolo (presynaptic cytomatrix protein)
mm10_v2_chrM_+_9452_9468	0.231695	Msx3	ENSMUST00000082411.1|mt-Nd3|ENSMUSG00000064360.1|mitochondrially encoded NADH dehydrogenase 3
mm10_v2_chr16_+_49699198_49699304	0.220856	Msx3	ENSMUST00000046777.4|Ift57|ENSMUSG00000032965.4|intraflagellar transport 57 	ENSMUST00000142682.1|Ift57|ENSMUSG00000032965.4|intraflagellar transport 57
mm10_v2_chrX_-_75578188_75578247	0.210055	Msx3	ENSMUST00000033545.5|Rab39b|ENSMUSG00000031202.5|RAB39B, member RAS oncogene family
mm10_v2_chrM_+_7005_7022	0.195714	Msx3	ENSMUST00000082405.1|mt-Co2|ENSMUSG00000064354.1|mitochondrially encoded cytochrome c oxidase II
mm10_v2_chr1_-_172027269_172027313	0.18414	Msx3	ENSMUST00000027837.6|Vangl2|ENSMUSG00000026556.9|vang-like 2 (van gogh, Drosophila) 	ENSMUST00000111264.1|Vangl2|ENSMUSG00000026556.9|vang-like 2 (van gogh, Drosophila)
mm10_v2_chr2_+_121956651_121956664	0.183812	Msx3	ENSMUST00000110574.1|Ctdspl2|ENSMUSG00000033411.10|CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2
mm10_v2_chr10_-_85127977_85128035	0.16983	Msx3	ENSMUST00000050813.2|Mterfd3|ENSMUSG00000049038.2|MTERF domain containing 3
mm10_v2_chr13_-_58354862_58354862	0.165114	Msx3	ENSMUST00000043605.5|Kif27|ENSMUSG00000060176.3|kinesin family member 27
mm10_v2_chr12_+_71136848_71136848	0.164365	Msx3	ENSMUST00000149564.1|2700049A03Rik|ENSMUSG00000034601.10|RIKEN cDNA 2700049A03 gene 	ENSMUST00000045907.8|2700049A03Rik|ENSMUSG00000034601.10|RIKEN cDNA 2700049A03 gene
mm10_v2_chr10_-_76110956_76110962	0.152182	Msx3	ENSMUST00000120757.1|Slc5a4b|ENSMUSG00000020226.9|solute carrier family 5 (neutral amino acid transporters, system A), member 4b
mm10_v2_chr9_-_15301555_15301607	0.141149	Msx3	ENSMUST00000034414.8|4931406C07Rik|ENSMUSG00000031938.8|RIKEN cDNA 4931406C07 gene
mm10_v2_chrX_+_16619698_16619758	0.140467	Msx3	ENSMUST00000026013.5|Maoa|ENSMUSG00000025037.6|monoamine oxidase A
mm10_v2_chr5_+_88583527_88583590	0.134697	Msx3	ENSMUST00000031229.6|Rufy3|ENSMUSG00000029291.7|RUN and FYVE domain containing 3
mm10_v2_chr4_-_14621805_14621819	0.132201	Msx3	ENSMUST00000042221.7|Slc26a7|ENSMUSG00000040569.7|solute carrier family 26, member 7
mm10_v2_chr9_-_53975246_53975348	0.131471	Msx3	ENSMUST00000048409.7|Elmod1|ENSMUSG00000041986.9|ELMO/CED-12 domain containing 1
mm10_v2_chr12_-_84617326_84617466	0.126252	Msx3	ENSMUST00000021666.4|Abcd4|ENSMUSG00000021240.5|ATP-binding cassette, sub-family D (ALD), member 4
mm10_v2_chr4_-_58912678_58912776	0.12514	Msx3	ENSMUST00000144512.1|AI314180|ENSMUSG00000050812.12|expressed sequence AI314180 	ENSMUST00000102889.3|AI314180|ENSMUSG00000050812.12|expressed sequence AI314180 	ENSMUST00000055822.8|AI314180|ENSMUSG00000050812.12|expressed sequence AI314180
mm10_v2_chrX_-_60893430_60893440	0.11438	Msx3	ENSMUST00000135107.2|Sox3|ENSMUSG00000045179.8|SRY-box containing gene 3
mm10_v2_chr2_+_121956411_121956480	0.111225	Msx3	ENSMUST00000110578.1|Ctdspl2|ENSMUSG00000033411.10|CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2
mm10_v2_chr3_-_116253467_116253484	0.106345	Msx3	ENSMUST00000090473.5|Gpr88|ENSMUSG00000068696.5|G-protein coupled receptor 88
mm10_v2_chr10_+_88379127_88379169	0.10406	Msx3	ENSMUST00000127615.1|Gnptab|ENSMUSG00000035311.10|N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits
mm10_v2_chr3_+_138374121_138374163	0.0931152	Msx3	ENSMUST00000171054.1|Adh6-ps1|ENSMUSG00000090306.1|alcohol dehydrogenase 6 (class V), pseudogene 1
mm10_v2_chr16_-_75766758_75766821	0.0894472	Msx3	ENSMUST00000114244.1|Hspa13|ENSMUSG00000032932.8|heat shock protein 70 family, member 13 	ENSMUST00000046283.8|Hspa13|ENSMUSG00000032932.8|heat shock protein 70 family, member 13
mm10_v2_chr9_+_100597686_100597798	0.0806188	Msx3	ENSMUST00000124487.1|Stag1|ENSMUSG00000037286.9|stromal antigen 1
mm10_v2_chr7_+_103550368_103550368	0.0793364	Msx3	ENSMUST00000106888.1|Olfr613|ENSMUSG00000078624.2|olfactory receptor 613
mm10_v2_chr9_+_35423582_35423589	0.0683329	Msx3	ENSMUST00000154652.1|Cdon|ENSMUSG00000038119.8|cell adhesion molecule-related/down-regulated by oncogenes
mm10_v2_chr2_-_168767136_168767201	0.0681601	Msx3	ENSMUST00000029061.5|Sall4|ENSMUSG00000027547.11|sal-like 4 (Drosophila) 	ENSMUST00000103074.1|Sall4|ENSMUSG00000027547.11|sal-like 4 (Drosophila)
mm10_v2_chr2_-_20943413_20943424	0.0578539	Msx3	ENSMUST00000140230.1|Arhgap21|ENSMUSG00000036591.9|Rho GTPase activating protein 21
mm10_v2_chr7_-_99141068_99141149	0.0519259	Msx3	ENSMUST00000037968.8|Uvrag|ENSMUSG00000035354.8|UV radiation resistance associated gene
mm10_v2_chr10_+_39612934_39612934	0.0496719	Msx3	ENSMUST00000019987.6|Traf3ip2|ENSMUSG00000019842.6|TRAF3 interacting protein 2
mm10_v2_chrX_+_107255878_107256064	0.0490744	Msx3	ENSMUST00000101294.2|Gpr174|ENSMUSG00000073008.5|G protein-coupled receptor 174 	ENSMUST00000118820.1|Gpr174|ENSMUSG00000073008.5|G protein-coupled receptor 174 	ENSMUST00000120971.1|Gpr174|ENSMUSG00000073008.5|G protein-coupled receptor 174
mm10_v2_chr1_-_34439672_34439672	0.0485724	Msx3	ENSMUST00000042493.8|Ccdc115|ENSMUSG00000042111.8|coiled-coil domain containing 115
mm10_v2_chr15_+_38661904_38661981	0.0477754	Msx3	ENSMUST00000022904.6|Atp6v1c1|ENSMUSG00000022295.7|ATPase, H+ transporting, lysosomal V1 subunit C1
mm10_v2_chr13_+_83732438_83732566	0.0465965	Msx3	ENSMUST00000182701.1|C130071C03Rik|ENSMUSG00000050334.6|RIKEN cDNA C130071C03 gene
mm10_v2_chr12_-_71136611_71136701	0.0452468	Msx3	ENSMUST00000021486.8|Timm9|ENSMUSG00000021079.9|translocase of inner mitochondrial membrane 9 	ENSMUST00000166120.1|Timm9|ENSMUSG00000021079.9|translocase of inner mitochondrial membrane 9
mm10_v2_chr3_+_32515295_32515295	0.0394878	Msx3	ENSMUST00000029203.7|Zfp639|ENSMUSG00000027667.8|zinc finger protein 639
mm10_v2_chr1_+_34439851_34439910	0.024197	Msx3	ENSMUST00000027303.7|Imp4|ENSMUSG00000026127.7|IMP4, U3 small nucleolar ribonucleoprotein, homolog (yeast)
mm10_v2_chr15_+_82252397_82252475	0.0231766	Msx3	ENSMUST00000136948.1|1500009C09Rik|ENSMUSG00000068099.4|RIKEN cDNA 1500009C09 gene
mm10_v2_chr10_+_88379217_88379299	0.0118772	Msx3	ENSMUST00000130301.1|Gnptab|ENSMUSG00000035311.10|N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits 	ENSMUST00000020251.8|Gnptab|ENSMUSG00000035311.10|N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits
mm10_v2_chr3_+_66985947_66985986	0.0117004	Msx3	ENSMUST00000161726.1|Rsrc1|ENSMUSG00000034544.11|arginine/serine-rich coiled-coil 1 	ENSMUST00000160504.1|Rsrc1|ENSMUSG00000034544.11|arginine/serine-rich coiled-coil 1
mm10_v2_chr13_-_102958084_102958173	0.00688141	Msx3	ENSMUST00000099202.3|Mast4|ENSMUSG00000034751.9|microtubule associated serine/threonine kinase family member 4 	ENSMUST00000172264.1|Mast4|ENSMUSG00000034751.9|microtubule associated serine/threonine kinase family member 4
mm10_v2_chrX_+_9885622_9885622	0.00661331	Msx3	ENSMUST00000067529.2|Sytl5|ENSMUSG00000054453.5|synaptotagmin-like 5 	ENSMUST00000086165.3|Sytl5|ENSMUSG00000054453.5|synaptotagmin-like 5
mm10_v2_chr3_+_94837533_94837567	0.00634804	Msx3	ENSMUST00000107270.2|Pogz|ENSMUSG00000038902.8|pogo transposable element with ZNF domain
mm10_v2_chr3_+_66985680_66985692	0.00018073	Msx3	ENSMUST00000065047.6|Rsrc1|ENSMUSG00000034544.11|arginine/serine-rich coiled-coil 1
