mm39_v1_chr9_+_96140781_96140838	3.30215	Msx3	ENSMUST00000190104.7|Tfdp2|ENSMUSG00000032411.16|transcription factor Dp 2	ENSMUST00000179416.8|Tfdp2|ENSMUSG00000032411.16|transcription factor Dp 2	ENSMUST00000189606.7|Tfdp2|ENSMUSG00000032411.16|transcription factor Dp 2
mm39_v1_chr8_+_57964921_57964947	2.49151	Msx3	ENSMUST00000067925.8|Hmgb2|ENSMUSG00000054717.8|high mobility group box 2
mm39_v1_chr17_-_24746911_24746924	1.90532	Msx3	ENSMUST00000176652.8|Traf7|ENSMUSG00000052752.16|TNF receptor-associated factor 7
mm39_v1_chr8_+_57964956_57965008	1.88446	Msx3	ENSMUST00000210871.2|Hmgb2|ENSMUSG00000054717.8|high mobility group box 2
mm39_v1_chr17_-_24746804_24746858	1.8686	Msx3	ENSMUST00000176353.8|Traf7|ENSMUSG00000052752.16|TNF receptor-associated factor 7	ENSMUST00000176237.8|Traf7|ENSMUSG00000052752.16|TNF receptor-associated factor 7
mm39_v1_chr9_+_96140750_96140764	1.66572	Msx3	ENSMUST00000186609.7|Tfdp2|ENSMUSG00000032411.16|transcription factor Dp 2
mm39_v1_chr17_+_56920389_56920425	1.62199	Msx3	ENSMUST00000080492.7|Rpl36|ENSMUSG00000057863.7|ribosomal protein L36
mm39_v1_chr2_-_168609110_168609126	1.55915	Msx3	ENSMUST00000029061.12|Sall4|ENSMUSG00000027547.18|spalt like transcription factor 4	ENSMUST00000103074.2|Sall4|ENSMUSG00000027547.18|spalt like transcription factor 4
mm39_v1_chr14_+_26722319_26722463	1.34276	Msx3	ENSMUST00000035433.10|Hesx1|ENSMUSG00000040726.11|homeobox gene expressed in ES cells
mm39_v1_chr12_-_114443071_114443116	1.32858	Msx3	ENSMUST00000103492.2|Ighv10-1|ENSMUSG00000095981.2|immunoglobulin heavy variable 10-1
mm39_v1_chr19_+_13208692_13208692	1.23992	Msx3	ENSMUST00000207246.4|Olfr1463|ENSMUSG00000096365.5|olfactory receptor 1463
mm39_v1_chr2_-_168608949_168608965	1.22874	Msx3	ENSMUST00000075044.10|Sall4|ENSMUSG00000027547.18|spalt like transcription factor 4
mm39_v1_chr3_-_88317601_88317656	1.22026	Msx3	ENSMUST00000193338.6|Pmf1|ENSMUSG00000028066.16|polyamine-modulated factor 1	ENSMUST00000056370.13|Pmf1|ENSMUSG00000028066.16|polyamine-modulated factor 1
mm39_v1_chr19_-_39875192_39875243	1.20355	Msx3	ENSMUST00000168838.3|Cyp2c69|ENSMUSG00000092008.3|cytochrome P450, family 2, subfamily c, polypeptide 69
mm39_v1_chr1_-_52230062_52230090	1.13739	Msx3	ENSMUST00000156887.8|Gls|ENSMUSG00000026103.15|glutaminase	ENSMUST00000129107.2|Gls|ENSMUSG00000026103.15|glutaminase
mm39_v1_chr2_+_163500290_163500430	1.06915	Msx3	ENSMUST00000164399.8|Pkig|ENSMUSG00000035268.15|protein kinase inhibitor, gamma	ENSMUST00000064703.13|Pkig|ENSMUSG00000035268.15|protein kinase inhibitor, gamma	ENSMUST00000099105.9|Pkig|ENSMUSG00000035268.15|protein kinase inhibitor, gamma	ENSMUST00000152418.8|Pkig|ENSMUSG00000035268.15|protein kinase inhibitor, gamma	ENSMUST00000126182.8|Pkig|ENSMUSG00000035268.15|protein kinase inhibitor, gamma	ENSMUST00000131228.8|Pkig|ENSMUSG00000035268.15|protein kinase inhibitor, gamma
mm39_v1_chr12_-_114487525_114487579	0.982263	Msx3	ENSMUST00000103495.3|Ighv10-3|ENSMUSG00000095700.3|immunoglobulin heavy variable V10-3
mm39_v1_chr7_+_101545547_101545638	0.937836	Msx3	ENSMUST00000035395.14|Anapc15|ENSMUSG00000030649.19|anaphase promoting complex C subunit 15	ENSMUST00000106973.8|Anapc15|ENSMUSG00000030649.19|anaphase promoting complex C subunit 15	ENSMUST00000144207.9|Anapc15|ENSMUSG00000030649.19|anaphase promoting complex C subunit 15
mm39_v1_chrX_+_152506577_152506642	0.871418	Msx3	ENSMUST00000140575.8|Nbdy|ENSMUSG00000086316.9|negative regulator of P-body association	ENSMUST00000208373.2|Nbdy|ENSMUSG00000086316.9|negative regulator of P-body association	ENSMUST00000185492.7|Nbdy|ENSMUSG00000086316.9|negative regulator of P-body association	ENSMUST00000149514.8|Nbdy|ENSMUSG00000086316.9|negative regulator of P-body association
mm39_v1_chr8_+_107757847_107757862	0.849001	Msx3	ENSMUST00000034388.10|Vps4a|ENSMUSG00000031913.10|vacuolar protein sorting 4A
mm39_v1_chr10_+_81093110_81093144	0.815282	Msx3	ENSMUST00000117488.8|Matk|ENSMUSG00000004933.18|megakaryocyte-associated tyrosine kinase	ENSMUST00000105328.10|Matk|ENSMUSG00000004933.18|megakaryocyte-associated tyrosine kinase	ENSMUST00000121205.8|Matk|ENSMUSG00000004933.18|megakaryocyte-associated tyrosine kinase
mm39_v1_chr10_-_75946790_75946796	0.797314	Msx3	ENSMUST00000120757.2|Slc5a4b|ENSMUSG00000020226.10|solute carrier family 5 (neutral amino acid transporters, system A), member 4b
mm39_v1_chr7_+_89814713_89814756	0.784188	Msx3	ENSMUST00000207084.2|Picalm|ENSMUSG00000039361.12|phosphatidylinositol binding clathrin assembly protein
mm39_v1_chr16_+_49519561_49519667	0.762227	Msx3	ENSMUST00000046777.11|Ift57|ENSMUSG00000032965.12|intraflagellar transport 57	ENSMUST00000142682.9|Ift57|ENSMUSG00000032965.12|intraflagellar transport 57
mm39_v1_chr7_+_101546059_101546168	0.76031	Msx3	ENSMUST00000143835.8|Anapc15|ENSMUSG00000030649.19|anaphase promoting complex C subunit 15
mm39_v1_chr6_+_68279392_68279411	0.746554	Msx3	ENSMUST00000103322.3|Igkv2-109|ENSMUSG00000105606.2|immunoglobulin kappa variable 2-109
mm39_v1_chr3_-_129834788_129834855	0.682901	Msx3	ENSMUST00000168644.3|Sec24b|ENSMUSG00000001052.16|Sec24 related gene family, member B (S. cerevisiae)
mm39_v1_chr4_+_134658209_134658221	0.670511	Msx3	ENSMUST00000030622.3|Syf2|ENSMUSG00000028821.9|SYF2 homolog, RNA splicing factor (S. cerevisiae)
mm39_v1_chr12_-_113649535_113649665	0.644867	Msx3	ENSMUST00000103449.4|Ighv2-5|ENSMUSG00000096498.4|immunoglobulin heavy variable 2-5	ENSMUST00000195707.3|Ighv2-5|ENSMUSG00000096498.4|immunoglobulin heavy variable 2-5
mm39_v1_chr2_-_174188505_174188505	0.628021	Msx3	ENSMUST00000168292.2|Gm20721|ENSMUSG00000090625.2|predicted gene, 20721
mm39_v1_chr3_+_57332735_57332873	0.568561	Msx3	ENSMUST00000029377.8|Tm4sf4|ENSMUSG00000027801.8|transmembrane 4 superfamily member 4
mm39_v1_chr17_-_37523969_37524009	0.55138	Msx3	ENSMUST00000060728.7|Olfr95|ENSMUSG00000049561.10|olfactory receptor 95	ENSMUST00000216318.2|Olfr95|ENSMUSG00000049561.10|olfactory receptor 95
mm39_v1_chr2_+_87696836_87696836	0.545335	Msx3	ENSMUST00000213308.3|Olfr1152|ENSMUSG00000045225.5|olfactory receptor 1152
mm39_v1_chr9_+_44309727_44309771	0.538179	Msx3	ENSMUST00000213268.2|Slc37a4|ENSMUSG00000032114.10|solute carrier family 37 (glucose-6-phosphate transporter), member 4
mm39_v1_chr4_+_94627513_94627537	0.522301	Msx3	ENSMUST00000073939.13|Tek|ENSMUSG00000006386.16|TEK receptor tyrosine kinase	ENSMUST00000102798.8|Tek|ENSMUSG00000006386.16|TEK receptor tyrosine kinase
mm39_v1_chrX_+_132751729_132751878	0.484976	Msx3	ENSMUST00000033602.9|Tnmd|ENSMUSG00000031250.9|tenomodulin
mm39_v1_chr15_+_82136598_82136676	0.476899	Msx3	ENSMUST00000136948.3|1500009C09Rik|ENSMUSG00000068099.6|RIKEN cDNA 1500009C09 gene
mm39_v1_chr9_+_35334878_35334885	0.474305	Msx3	ENSMUST00000154652.8|Cdon|ENSMUSG00000038119.16|cell adhesion molecule-related/down-regulated by oncogenes
mm39_v1_chr4_-_43710231_43710255	0.459673	Msx3	ENSMUST00000217544.2|Olfr71|ENSMUSG00000046450.4|olfactory receptor 71	ENSMUST00000107862.3|Olfr71|ENSMUSG00000046450.4|olfactory receptor 71
mm39_v1_chr1_-_34478753_34478753	0.455712	Msx3	ENSMUST00000042493.10|Ccdc115|ENSMUSG00000042111.10|coiled-coil domain containing 115
mm39_v1_chr19_-_24178000_24178016	0.433474	Msx3	ENSMUST00000233658.3|Tjp2|ENSMUSG00000024812.12|tight junction protein 2
mm39_v1_chrX_+_9751861_9751861	0.433138	Msx3	ENSMUST00000067529.9|Sytl5|ENSMUSG00000054453.12|synaptotagmin-like 5	ENSMUST00000086165.4|Sytl5|ENSMUSG00000054453.12|synaptotagmin-like 5
mm39_v1_chr3_+_82962823_82962893	0.385275	Msx3	ENSMUST00000150268.8|Plrg1|ENSMUSG00000027998.12|pleiotropic regulator 1	ENSMUST00000122128.2|Plrg1|ENSMUSG00000027998.12|pleiotropic regulator 1
mm39_v1_chrX_+_100492684_100492697	0.38467	Msx3	ENSMUST00000033674.6|Itgb1bp2|ENSMUSG00000031312.6|integrin beta 1 binding protein 2
mm39_v1_chr11_+_6366259_6366319	0.370482	Msx3	ENSMUST00000213200.2|Ppia|ENSMUSG00000071866.13|peptidylprolyl isomerase A
mm39_v1_chr11_-_73382303_73382429	0.368277	Msx3	ENSMUST00000119863.2|Olfr381|ENSMUSG00000072708.4|olfactory receptor 381	ENSMUST00000215358.2|Olfr381|ENSMUSG00000072708.4|olfactory receptor 381	ENSMUST00000214623.2|Olfr381|ENSMUSG00000072708.4|olfactory receptor 381
mm39_v1_chr2_-_111843053_111843053	0.36552	Msx3	ENSMUST00000213559.3|Olfr1310|ENSMUSG00000108827.4|olfactory receptor 1310
mm39_v1_chr7_+_45271229_45271249	0.361677	Msx3	ENSMUST00000033100.5|Izumo1|ENSMUSG00000064158.7|izumo sperm-egg fusion 1
mm39_v1_chr11_+_69909245_69909310	0.361616	Msx3	ENSMUST00000231415.2|Dlg4|ENSMUSG00000020886.18|discs large MAGUK scaffold protein 4	ENSMUST00000108588.9|Dlg4|ENSMUSG00000020886.18|discs large MAGUK scaffold protein 4
mm39_v1_chr5_-_105198913_105198913	0.356711	Msx3	ENSMUST00000112718.5|Gbp8|ENSMUSG00000034438.17|guanylate-binding protein 8
mm39_v1_chr19_+_12257218_12257303	0.346758	Msx3	ENSMUST00000207186.4|Olfr1434|ENSMUSG00000095640.5|olfactory receptor 1434	ENSMUST00000207915.2|Olfr1434|ENSMUSG00000095640.5|olfactory receptor 1434
mm39_v1_chr2_-_87504008_87504008	0.335478	Msx3	ENSMUST00000213835.2|Olfr1135|ENSMUSG00000075153.3|olfactory receptor 1135
mm39_v1_chr13_-_22289994_22289994	0.334185	Msx3	ENSMUST00000227357.2|Vmn1r189|ENSMUSG00000099611.3|vomeronasal 1 receptor 189	ENSMUST00000228428.2|Vmn1r189|ENSMUSG00000099611.3|vomeronasal 1 receptor 189
mm39_v1_chr1_-_4430481_4430537	0.325267	Msx3	ENSMUST00000027032.6|Rp1|ENSMUSG00000025900.14|retinitis pigmentosa 1 (human)
mm39_v1_chr11_-_99134885_99134964	0.322144	Msx3	ENSMUST00000103132.10|Krt222|ENSMUSG00000035849.15|keratin 222	ENSMUST00000038214.7|Krt222|ENSMUSG00000035849.15|keratin 222
mm39_v1_chr2_+_85648823_85648823	0.320425	Msx3	ENSMUST00000214416.2|Olfr1018|ENSMUSG00000043892.4|olfactory receptor 1018
mm39_v1_chr1_+_34478932_34478991	0.303758	Msx3	ENSMUST00000027303.14|Imp4|ENSMUSG00000026127.14|IMP4, U3 small nucleolar ribonucleoprotein
mm39_v1_chr2_-_45007407_45007421	0.300301	Msx3	ENSMUST00000176438.9|Zeb2|ENSMUSG00000026872.19|zinc finger E-box binding homeobox 2
mm39_v1_chr13_-_78344492_78344561	0.287854	Msx3	ENSMUST00000125176.3|Nr2f1|ENSMUSG00000069171.15|nuclear receptor subfamily 2, group F, member 1
mm39_v1_chr2_-_87570322_87570322	0.27114	Msx3	ENSMUST00000214573.2|Olfr1138|ENSMUSG00000075149.3|olfactory receptor 1138
mm39_v1_chr17_+_34457868_34457938	0.269754	Msx3	ENSMUST00000095342.11|H2-Ob|ENSMUSG00000041538.17|histocompatibility 2, O region beta locus	ENSMUST00000167280.8|H2-Ob|ENSMUSG00000041538.17|histocompatibility 2, O region beta locus	ENSMUST00000236838.2|H2-Ob|ENSMUSG00000041538.17|histocompatibility 2, O region beta locus
mm39_v1_chr14_+_60615128_60615153	0.255139	Msx3	ENSMUST00000022561.9|Amer2|ENSMUSG00000021986.10|APC membrane recruitment 2
mm39_v1_chr2_-_85632888_85632888	0.238096	Msx3	ENSMUST00000217410.3|Olfr1016|ENSMUSG00000075209.4|olfactory receptor 1016	ENSMUST00000216425.3|Olfr1016|ENSMUSG00000075209.4|olfactory receptor 1016
mm39_v1_chr11_-_99265721_99265735	0.218501	Msx3	ENSMUST00000006963.3|Krt28|ENSMUSG00000055937.2|keratin 28
mm39_v1_chr3_+_94745009_94745034	0.214225	Msx3	ENSMUST00000107266.8|Pogz|ENSMUSG00000038902.15|pogo transposable element with ZNF domain	ENSMUST00000042402.12|Pogz|ENSMUSG00000038902.15|pogo transposable element with ZNF domain	ENSMUST00000107269.2|Pogz|ENSMUSG00000038902.15|pogo transposable element with ZNF domain
mm39_v1_chr14_+_65612788_65612842	0.207292	Msx3	ENSMUST00000224687.2|Zfp395|ENSMUSG00000034522.11|zinc finger protein 395
mm39_v1_chr8_+_66964401_66964417	0.1818	Msx3	ENSMUST00000002025.5|Tktl2|ENSMUSG00000025519.6|transketolase-like 2	ENSMUST00000183187.2|Tktl2|ENSMUSG00000025519.6|transketolase-like 2
mm39_v1_chr7_+_84562283_84562297	0.180971	Msx3	ENSMUST00000216367.2|Olfr290|ENSMUSG00000070459.7|olfactory receptor 290	ENSMUST00000214501.3|Olfr290|ENSMUSG00000070459.7|olfactory receptor 290
mm39_v1_chr7_-_106341650_106341650	0.166814	Msx3	ENSMUST00000217734.2|Olfr697|ENSMUSG00000051591.5|olfactory receptor 697
mm39_v1_chr9_+_43222104_43222145	0.153752	Msx3	ENSMUST00000034511.7|Trim29|ENSMUSG00000032013.7|tripartite motif-containing 29
mm39_v1_chrX_-_74621828_74621854	0.145645	Msx3	ENSMUST00000033545.6|Rab39b|ENSMUSG00000031202.6|RAB39B, member RAS oncogene family
mm39_v1_chrX_-_48980360_48980360	0.143312	Msx3	ENSMUST00000217355.3|Olfr1322|ENSMUSG00000056281.5|olfactory receptor 1322
mm39_v1_chr7_-_107633196_107633196	0.14236	Msx3	ENSMUST00000210173.3|Olfr478|ENSMUSG00000094426.4|olfactory receptor 478
mm39_v1_chr13_+_22268610_22268610	0.139875	Msx3	ENSMUST00000228243.2|Vmn1r188|ENSMUSG00000069299.3|vomeronasal 1 receptor 188	ENSMUST00000226680.2|Vmn1r188|ENSMUSG00000069299.3|vomeronasal 1 receptor 188
mm39_v1_chr9_+_38516398_38516398	0.136986	Msx3	ENSMUST00000217057.2|Olfr914|ENSMUSG00000047050.3|olfactory receptor 914
mm39_v1_chr13_+_19394484_19394513	0.116903	Msx3	ENSMUST00000200495.2|Trgj1|ENSMUSG00000104962.2|T cell receptor gamma joining 1
mm39_v1_chr1_-_171854818_171854880	0.113385	Msx3	ENSMUST00000138714.2|Vangl2|ENSMUSG00000026556.16|VANGL planar cell polarity 2	ENSMUST00000027837.13|Vangl2|ENSMUSG00000026556.16|VANGL planar cell polarity 2	ENSMUST00000111264.8|Vangl2|ENSMUSG00000026556.16|VANGL planar cell polarity 2
mm39_v1_chr10_+_32959472_32959563	0.107184	Msx3	ENSMUST00000095762.5|Trdn|ENSMUSG00000019787.10|triadin	ENSMUST00000218281.2|Trdn|ENSMUSG00000019787.10|triadin	ENSMUST00000217779.2|Trdn|ENSMUSG00000019787.10|triadin	ENSMUST00000219665.2|Trdn|ENSMUSG00000019787.10|triadin	ENSMUST00000219931.2|Trdn|ENSMUSG00000019787.10|triadin
mm39_v1_chr15_-_101422054_101422054	0.10126	Msx3	ENSMUST00000230067.3|Gm49425|ENSMUSG00000116336.3|predicted gene, 49425
mm39_v1_chr3_+_66892979_66893026	0.0950314	Msx3	ENSMUST00000162362.8|Rsrc1|ENSMUSG00000034544.18|arginine/serine-rich coiled-coil 1	ENSMUST00000065074.14|Rsrc1|ENSMUSG00000034544.18|arginine/serine-rich coiled-coil 1	ENSMUST00000065047.13|Rsrc1|ENSMUSG00000034544.18|arginine/serine-rich coiled-coil 1
mm39_v1_chr19_-_11261177_11261249	0.0898407	Msx3	ENSMUST00000186937.7|Ms4a5|ENSMUSG00000054523.14|membrane-spanning 4-domains, subfamily A, member 5	ENSMUST00000067673.13|Ms4a5|ENSMUSG00000054523.14|membrane-spanning 4-domains, subfamily A, member 5
mm39_v1_chr13_-_118523760_118523812	0.089551	Msx3	ENSMUST00000022245.10|Mrps30|ENSMUSG00000021731.11|mitochondrial ribosomal protein S30
mm39_v1_chr9_-_53882530_53882632	0.0873233	Msx3	ENSMUST00000048409.14|Elmod1|ENSMUSG00000041986.17|ELMO/CED-12 domain containing 1
mm39_v1_chr4_+_102111936_102111959	0.0813732	Msx3	ENSMUST00000106907.9|Pde4b|ENSMUSG00000028525.17|phosphodiesterase 4B, cAMP specific
mm39_v1_chr7_+_3648264_3648351	0.0668096	Msx3	ENSMUST00000206287.2|Cnot3|ENSMUSG00000035632.17|CCR4-NOT transcription complex, subunit 3	ENSMUST00000038913.16|Cnot3|ENSMUSG00000035632.17|CCR4-NOT transcription complex, subunit 3
mm39_v1_chr18_+_37827413_37827444	0.0634391	Msx3	ENSMUST00000193414.2|Pcdhga5|ENSMUSG00000103567.2|protocadherin gamma subfamily A, 5
mm39_v1_chr13_+_68011442_68011447	0.0618729	Msx3	ENSMUST00000078471.7|BC048507|ENSMUSG00000064063.7|cDNA sequence BC048507
mm39_v1_chr12_+_102094977_102094997	0.061096	Msx3	ENSMUST00000159329.8|Slc24a4|ENSMUSG00000041771.15|solute carrier family 24 (sodium/potassium/calcium exchanger), member 4
mm39_v1_chr19_+_29929208_29929219	0.0532996	Msx3	ENSMUST00000136850.2|Il33|ENSMUSG00000024810.17|interleukin 33
mm39_v1_chr9_-_40895756_40895769	0.032681	Msx3	ENSMUST00000180872.9|Crtam|ENSMUSG00000032021.15|cytotoxic and regulatory T cell molecule
mm39_v1_chr11_+_53324126_53324184	0.0316613	Msx3	ENSMUST00000018382.7|Gdf9|ENSMUSG00000018238.7|growth differentiation factor 9
mm39_v1_chr12_-_11258973_11258973	0.0305181	Msx3	ENSMUST00000049877.3|Msgn1|ENSMUSG00000047002.3|mesogenin 1
mm39_v1_chr3_-_41696906_41696984	0.0278353	Msx3	ENSMUST00000026866.15|Sclt1|ENSMUSG00000059834.13|sodium channel and clathrin linker 1
mm39_v1_chr6_-_145379805_145379816	0.0174138	Msx3	ENSMUST00000149666.2|Lmntd1|ENSMUSG00000054966.14|lamin tail domain containing 1
mm39_v1_chr13_+_23191826_23191826	0.00792557	Msx3	ENSMUST00000228758.2|Vmn1r213|ENSMUSG00000060024.3|vomeronasal 1 receptor 213	ENSMUST00000228031.2|Vmn1r213|ENSMUSG00000060024.3|vomeronasal 1 receptor 213	ENSMUST00000227573.2|Vmn1r213|ENSMUSG00000060024.3|vomeronasal 1 receptor 213
mm39_v1_chr6_-_41749300_41749300	0.00694105	Msx3	ENSMUST00000050412.5|Olfr459|ENSMUSG00000045479.8|olfactory receptor 459
mm39_v1_chr2_-_150097511_150097511	0.00642599	Msx3	ENSMUST00000063463.6|Gm21994|ENSMUSG00000074735.3|predicted gene 21994
mm39_v1_chr2_-_111820618_111820626	0.00524046	Msx3	ENSMUST00000216948.2|Olfr1309|ENSMUSG00000109528.3|olfactory receptor 1309	ENSMUST00000214935.2|Olfr1309|ENSMUSG00000109528.3|olfactory receptor 1309	ENSMUST00000217452.2|Olfr1309|ENSMUSG00000109528.3|olfactory receptor 1309	ENSMUST00000215045.2|Olfr1309|ENSMUSG00000109528.3|olfactory receptor 1309
