mm10_v2_chr2_-_168767029_168767104	6.60243	Msx3	ENSMUST00000075044.3|Sall4|ENSMUSG00000027547.11|sal-like 4 (Drosophila)
mm10_v2_chr2_-_168767136_168767201	5.69671	Msx3	ENSMUST00000029061.5|Sall4|ENSMUSG00000027547.11|sal-like 4 (Drosophila) 	ENSMUST00000103074.1|Sall4|ENSMUSG00000027547.11|sal-like 4 (Drosophila)
mm10_v2_chr14_+_27000362_27000507	4.1536	Msx3	ENSMUST00000035433.8|Hesx1|ENSMUSG00000040726.8|homeobox gene expressed in ES cells
mm10_v2_chr1_-_52190901_52190915	2.8974	Msx3	ENSMUST00000156887.1|Gls|ENSMUSG00000026103.8|glutaminase 	ENSMUST00000129107.1|Gls|ENSMUSG00000026103.8|glutaminase
mm10_v2_chr9_+_96258697_96258711	2.87272	Msx3	ENSMUST00000179416.1|Tfdp2|ENSMUSG00000032411.9|transcription factor Dp 2
mm10_v2_chr10_-_76110956_76110962	2.64916	Msx3	ENSMUST00000120757.1|Slc5a4b|ENSMUSG00000020226.9|solute carrier family 5 (neutral amino acid transporters, system A), member 4b
mm10_v2_chr3_-_116253467_116253484	2.47011	Msx3	ENSMUST00000090473.5|Gpr88|ENSMUSG00000068696.5|G-protein coupled receptor 88
mm10_v2_chr8_+_57511833_57511869	2.44557	Msx3	ENSMUST00000067925.6|Hmgb2|ENSMUSG00000054717.6|high mobility group box 2
mm10_v2_chr12_+_102128718_102128739	1.99971	Msx3	ENSMUST00000159329.1|Slc24a4|ENSMUSG00000041771.7|solute carrier family 24 (sodium/potassium/calcium exchanger), member 4
mm10_v2_chr15_-_34356421_34356421	1.89283	Msx3	ENSMUST00000179647.1|9430069I07Rik|ENSMUSG00000094447.1|RIKEN cDNA 9430069I07 gene
mm10_v2_chr8_-_24725762_24725852	1.81314	Msx3	ENSMUST00000171438.1|Adam3|ENSMUSG00000031553.9|a disintegrin and metallopeptidase domain 3 (cyritestin) 	ENSMUST00000171611.1|Adam3|ENSMUSG00000031553.9|a disintegrin and metallopeptidase domain 3 (cyritestin) 	ENSMUST00000033958.7|Adam3|ENSMUSG00000031553.9|a disintegrin and metallopeptidase domain 3 (cyritestin)
mm10_v2_chrX_+_9885622_9885622	1.76617	Msx3	ENSMUST00000067529.2|Sytl5|ENSMUSG00000054453.5|synaptotagmin-like 5 	ENSMUST00000086165.3|Sytl5|ENSMUSG00000054453.5|synaptotagmin-like 5
mm10_v2_chr2_-_160619971_160619971	1.40391	Msx3	ENSMUST00000109473.1|Gm14221|ENSMUSG00000078956.2|predicted gene 14221
mm10_v2_chrX_+_101449078_101449089	1.38059	Msx3	ENSMUST00000033674.5|Itgb1bp2|ENSMUSG00000031312.5|integrin beta 1 binding protein 2
mm10_v2_chr17_-_24527925_24527938	1.37486	Msx3	ENSMUST00000176652.1|Traf7|ENSMUSG00000052752.9|TNF receptor-associated factor 7
mm10_v2_chr9_-_53975246_53975348	1.34324	Msx3	ENSMUST00000048409.7|Elmod1|ENSMUSG00000041986.9|ELMO/CED-12 domain containing 1
mm10_v2_chr17_-_24527830_24527884	1.31489	Msx3	ENSMUST00000176353.1|Traf7|ENSMUSG00000052752.9|TNF receptor-associated factor 7 	ENSMUST00000176237.1|Traf7|ENSMUSG00000052752.9|TNF receptor-associated factor 7
mm10_v2_chr16_+_49699198_49699304	1.26124	Msx3	ENSMUST00000046777.4|Ift57|ENSMUSG00000032965.4|intraflagellar transport 57 	ENSMUST00000142682.1|Ift57|ENSMUSG00000032965.4|intraflagellar transport 57
mm10_v2_chr10_+_81257277_81257309	1.11378	Msx3	ENSMUST00000117488.1|Matk|ENSMUSG00000004933.11|megakaryocyte-associated tyrosine kinase 	ENSMUST00000105328.3|Matk|ENSMUSG00000004933.11|megakaryocyte-associated tyrosine kinase 	ENSMUST00000121205.1|Matk|ENSMUSG00000004933.11|megakaryocyte-associated tyrosine kinase
mm10_v2_chr2_-_33087169_33087253	1.07997	Msx3	ENSMUST00000102810.3|Garnl3|ENSMUSG00000038860.9|GTPase activating RANGAP domain-like 3
mm10_v2_chr1_-_172027269_172027313	1.07403	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_chr10_-_88379051_88379080	1.05559	Msx3	ENSMUST00000138159.1|Dram1|ENSMUSG00000020057.2|DNA-damage regulated autophagy modulator 1
mm10_v2_chr2_-_45117349_45117395	1.03095	Msx3	ENSMUST00000176438.2|Zeb2|ENSMUSG00000026872.10|zinc finger E-box binding homeobox 2
mm10_v2_chr9_+_72806874_72806874	0.988717	Msx3	ENSMUST00000055535.8|Prtg|ENSMUSG00000036030.9|protogenin homolog (Gallus gallus)
mm10_v2_chr7_+_101896817_101896961	0.889112	Msx3	ENSMUST00000143835.1|Anapc15|ENSMUSG00000030649.11|anaphase prompoting complex C subunit 15
mm10_v2_chr7_+_45621805_45621825	0.867306	Msx3	ENSMUST00000033100.4|Izumo1|ENSMUSG00000064158.4|izumo sperm-egg fusion 1
mm10_v2_chr7_+_101896340_101896431	0.837601	Msx3	ENSMUST00000035395.7|Anapc15|ENSMUSG00000030649.11|anaphase prompoting complex C subunit 15 	ENSMUST00000106973.1|Anapc15|ENSMUSG00000030649.11|anaphase prompoting complex C subunit 15 	ENSMUST00000144207.1|Anapc15|ENSMUSG00000030649.11|anaphase prompoting complex C subunit 15
mm10_v2_chr13_-_58354862_58354862	0.771855	Msx3	ENSMUST00000043605.5|Kif27|ENSMUSG00000060176.3|kinesin family member 27
mm10_v2_chr17_+_56613392_56613425	0.760589	Msx3	ENSMUST00000080492.5|Rpl36|ENSMUSG00000057863.5|ribosomal protein L36
mm10_v2_chr17_+_21383725_21383766	0.730052	Msx3	ENSMUST00000056107.4|Zfp677|ENSMUSG00000062743.3|zinc finger protein 677 	ENSMUST00000162659.1|Zfp677|ENSMUSG00000062743.3|zinc finger protein 677
mm10_v2_chr5_-_105051047_105051047	0.715356	Msx3	ENSMUST00000112718.4|Gbp8|ENSMUSG00000034438.10|guanylate-binding protein 8
mm10_v2_chr12_+_71136848_71136848	0.693451	Msx3	ENSMUST00000149564.1|2700049A03Rik|ENSMUSG00000034601.10|RIKEN cDNA 2700049A03 gene 	ENSMUST00000045907.8|2700049A03Rik|ENSMUSG00000034601.10|RIKEN cDNA 2700049A03 gene
mm10_v2_chr2_-_20943413_20943424	0.672311	Msx3	ENSMUST00000140230.1|Arhgap21|ENSMUSG00000036591.9|Rho GTPase activating protein 21
mm10_v2_chr11_+_70018421_70018484	0.655917	Msx3	ENSMUST00000108588.1|Dlg4|ENSMUSG00000020886.10|discs, large homolog 4 (Drosophila)
mm10_v2_chr9_+_35423582_35423589	0.638978	Msx3	ENSMUST00000154652.1|Cdon|ENSMUSG00000038119.8|cell adhesion molecule-related/down-regulated by oncogenes
mm10_v2_chr19_+_5474681_5474775	0.615187	Msx3	ENSMUST00000165485.1|Efemp2|ENSMUSG00000024909.8|epidermal growth factor-containing fibulin-like extracellular matrix protein 2 	ENSMUST00000166253.1|Efemp2|ENSMUSG00000024909.8|epidermal growth factor-containing fibulin-like extracellular matrix protein 2 	ENSMUST00000167371.1|Efemp2|ENSMUSG00000024909.8|epidermal growth factor-containing fibulin-like extracellular matrix protein 2 	ENSMUST00000167855.1|Efemp2|ENSMUSG00000024909.8|epidermal growth factor-containing fibulin-like extracellular matrix protein 2 	ENSMUST00000070118.7|Efemp2|ENSMUSG00000024909.8|epidermal growth factor-containing fibulin-like extracellular matrix protein 2
mm10_v2_chr2_+_163658370_163658510	0.601133	Msx3	ENSMUST00000164399.1|Pkig|ENSMUSG00000035268.8|protein kinase inhibitor, gamma 	ENSMUST00000064703.6|Pkig|ENSMUSG00000035268.8|protein kinase inhibitor, gamma 	ENSMUST00000099105.2|Pkig|ENSMUSG00000035268.8|protein kinase inhibitor, gamma 	ENSMUST00000152418.1|Pkig|ENSMUSG00000035268.8|protein kinase inhibitor, gamma 	ENSMUST00000126182.1|Pkig|ENSMUSG00000035268.8|protein kinase inhibitor, gamma 	ENSMUST00000131228.1|Pkig|ENSMUSG00000035268.8|protein kinase inhibitor, gamma
mm10_v2_chr9_+_43310763_43310806	0.578831	Msx3	ENSMUST00000034511.5|Trim29|ENSMUSG00000032013.5|tripartite motif-containing 29
mm10_v2_chr2_-_33086366_33086447	0.566789	Msx3	ENSMUST00000049618.2|Garnl3|ENSMUSG00000038860.9|GTPase activating RANGAP domain-like 3
mm10_v2_chr15_+_82252397_82252475	0.561345	Msx3	ENSMUST00000136948.1|1500009C09Rik|ENSMUSG00000068099.4|RIKEN cDNA 1500009C09 gene
mm10_v2_chr6_-_135254326_135254359	0.497284	Msx3	ENSMUST00000111911.2|Gsg1|ENSMUSG00000030206.7|germ cell-specific gene 1 	ENSMUST00000111910.2|Gsg1|ENSMUSG00000030206.7|germ cell-specific gene 1
mm10_v2_chr3_-_41742471_41742548	0.47215	Msx3	ENSMUST00000026866.8|Sclt1|ENSMUSG00000059834.6|sodium channel and clathrin linker 1
mm10_v2_chr11_-_99244058_99244136	0.439404	Msx3	ENSMUST00000103132.3|Krt222|ENSMUSG00000035849.8|keratin 222 	ENSMUST00000038214.6|Krt222|ENSMUSG00000035849.8|keratin 222
mm10_v2_chr17_+_49615104_49615172	0.422077	Msx3	ENSMUST00000162854.1|Kif6|ENSMUSG00000023999.8|kinesin family member 6
mm10_v2_chr7_+_27486910_27486960	0.421838	Msx3	ENSMUST00000008528.7|Sertad1|ENSMUSG00000008384.8|SERTA domain containing 1
mm10_v2_chr9_-_40984460_40984474	0.416311	Msx3	ENSMUST00000180872.1|Crtam|ENSMUSG00000032021.7|cytotoxic and regulatory T cell molecule
mm10_v2_chr12_+_72441852_72441866	0.41481	Msx3	ENSMUST00000162159.1|Lrrc9|ENSMUSG00000021090.9|leucine rich repeat containing 9
mm10_v2_chr1_-_34439672_34439672	0.396548	Msx3	ENSMUST00000042493.8|Ccdc115|ENSMUSG00000042111.8|coiled-coil domain containing 115
mm10_v2_chr13_-_102958084_102958173	0.322447	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_chr4_+_94739276_94739300	0.319777	Msx3	ENSMUST00000073939.6|Tek|ENSMUSG00000006386.9|endothelial-specific receptor tyrosine kinase 	ENSMUST00000102798.1|Tek|ENSMUSG00000006386.9|endothelial-specific receptor tyrosine kinase
mm10_v2_chrX_+_133850980_133851129	0.317073	Msx3	ENSMUST00000033602.8|Tnmd|ENSMUSG00000031250.8|tenomodulin
mm10_v2_chr4_-_129378116_129378116	0.31466	Msx3	ENSMUST00000030610.2|Zbtb8a|ENSMUSG00000028807.2|zinc finger and BTB domain containing 8a
mm10_v2_chr3_+_106034661_106034692	0.294236	Msx3	ENSMUST00000170669.2|Gm4540|ENSMUSG00000092072.2|predicted gene 4540
mm10_v2_chr11_+_53433299_53433357	0.285458	Msx3	ENSMUST00000018382.6|Gdf9|ENSMUSG00000018238.6|growth differentiation factor 9
mm10_v2_chr4_-_14621805_14621819	0.28386	Msx3	ENSMUST00000042221.7|Slc26a7|ENSMUSG00000040569.7|solute carrier family 26, member 7
mm10_v2_chr19_-_11283813_11283879	0.251988	Msx3	ENSMUST00000067673.6|Ms4a5|ENSMUSG00000054523.7|membrane-spanning 4-domains, subfamily A, member 5
mm10_v2_chr19_+_29951808_29951819	0.238544	Msx3	ENSMUST00000136850.1|Il33|ENSMUSG00000024810.10|interleukin 33
mm10_v2_chr9_+_100597686_100597798	0.224376	Msx3	ENSMUST00000124487.1|Stag1|ENSMUSG00000037286.9|stromal antigen 1
mm10_v2_chr13_+_67863324_67863328	0.22334	Msx3	ENSMUST00000078471.5|BC048507|ENSMUSG00000064063.5|cDNA sequence BC048507
mm10_v2_chr16_-_29544852_29544869	0.222262	Msx3	ENSMUST00000039090.8|Atp13a4|ENSMUSG00000038094.9|ATPase type 13A4
mm10_v2_chr12_+_72441933_72441970	0.212275	Msx3	ENSMUST00000161284.1|Lrrc9|ENSMUSG00000021090.9|leucine rich repeat containing 9
mm10_v2_chr8_+_107031218_107031229	0.200416	Msx3	ENSMUST00000034388.9|Vps4a|ENSMUSG00000031913.9|vacuolar protein sorting 4a (yeast)
mm10_v2_chr3_+_83055516_83055565	0.199746	Msx3	ENSMUST00000150268.1|Plrg1|ENSMUSG00000027998.5|pleiotropic regulator 1, PRL1 homolog (Arabidopsis) 	ENSMUST00000122128.1|Plrg1|ENSMUSG00000027998.5|pleiotropic regulator 1, PRL1 homolog (Arabidopsis)
mm10_v2_chr2_-_174346712_174346712	0.182733	Msx3	ENSMUST00000168292.1|Gm20721|ENSMUSG00000090625.1|predicted gene, 20721
mm10_v2_chr3_+_32515295_32515295	0.131028	Msx3	ENSMUST00000029203.7|Zfp639|ENSMUSG00000027667.8|zinc finger protein 639
mm10_v2_chr4_+_134930898_134930997	0.122836	Msx3	ENSMUST00000030622.2|Syf2|ENSMUSG00000028821.2|SYF2 homolog, RNA splicing factor (S. cerevisiae)
mm10_v2_chr12_-_11208948_11208948	0.116546	Msx3	ENSMUST00000049877.1|Msgn1|ENSMUSG00000047002.1|mesogenin 1
mm10_v2_chr2_-_150255591_150255591	0.110023	Msx3	ENSMUST00000063463.5|Gm21994|ENSMUSG00000074735.2|predicted gene 21994
mm10_v2_chr1_-_4360256_4360314	0.0940734	Msx3	ENSMUST00000027032.4|Rp1|ENSMUSG00000025900.5|retinitis pigmentosa 1 (human)
mm10_v2_chr6_-_135254170_135254289	0.0868962	Msx3	ENSMUST00000111909.1|Gsg1|ENSMUSG00000030206.7|germ cell-specific gene 1
mm10_v2_chr1_+_34439851_34439910	0.0644274	Msx3	ENSMUST00000027303.7|Imp4|ENSMUSG00000026127.7|IMP4, U3 small nucleolar ribonucleoprotein, homolog (yeast)
mm10_v2_chr8_+_66511732_66511743	0.0582006	Msx3	ENSMUST00000002025.3|Tktl2|ENSMUSG00000025519.4|transketolase-like 2
mm10_v2_chr14_+_122034660_122034677	0.0526509	Msx3	ENSMUST00000045976.6|Timm8a2|ENSMUSG00000071229.3|translocase of inner mitochondrial membrane 8A2
mm10_v2_chr1_-_127840290_127840290	0.0455385	Msx3	ENSMUST00000061512.2|Map3k19|ENSMUSG00000051590.2|mitogen-activated protein kinase kinase kinase 19
mm10_v2_chr3_+_66985680_66985692	0.0381303	Msx3	ENSMUST00000065047.6|Rsrc1|ENSMUSG00000034544.11|arginine/serine-rich coiled-coil 1
mm10_v2_chr10_-_116896879_116896956	0.037976	Msx3	ENSMUST00000048229.7|Myrfl|ENSMUSG00000034057.7|myelin regulatory factor-like
mm10_v2_chr3_+_41742615_41742725	0.00879994	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_chr14_-_118735143_118735160	0.00556267	Msx3	ENSMUST00000184172.1|RP24-241I19.1|ENSMUSG00000098630.1|RP24-241I19.1
