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ONTOLOGY REPORT - ANNOTATIONS


Term:formation of primary germ layer
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Accession:GO:0001704 term browser browse the term
Definition:The formation of the ectoderm, mesoderm and endoderm during gastrulation.


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formation of primary germ layer term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Arid1a AT-rich interaction domain 1A ISO (MGI:3789431|PMID:18448678) MGI PMID:18448678 MGI:3789431 NCBI chrNW_004955452:6,068,631...6,120,759
Ensembl chrNW_004955452:6,068,631...6,120,759
JBrowse link
G Atoh8 atonal bHLH transcription factor 8 ISO (MGI:3798332|PMID:18560595) UniProt PMID:18560595 MGI:3798332 NCBI chrNW_004955424:1,775,139...1,803,106
Ensembl chrNW_004955424:1,776,127...1,802,763
JBrowse link
G Kif16b kinesin family member 16B ISO (MGI:4889011|PMID:21238925) UniProt PMID:21238925 MGI:4889011 NCBI chrNW_004955415:25,449,734...25,740,697
Ensembl chrNW_004955415:25,447,539...25,740,775
JBrowse link
axial mesoderm formation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Axin1 axin 1 ISO (MGI:894149|PMID:9230313) MGI PMID:9230313 MGI:894149 NCBI chrNW_004955442:16,845,728...16,898,301
Ensembl chrNW_004955442:16,843,152...16,898,430
JBrowse link
G Epha2 EPH receptor A2 ISO (MGI:1934524|PMID:11287184) MGI PMID:11287184 MGI:1934524 NCBI chrNW_004955527:2,120,447...2,151,932
Ensembl chrNW_004955527:2,120,266...2,152,781
JBrowse link
axial mesodermal cell fate specification term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Nodal nodal growth differentiation factor ISO (MGI:2677178|PMID:14511481) MGI PMID:14511481 MGI:2677178 NCBI chrNW_004955437:20,828,448...20,835,486
Ensembl chrNW_004955437:20,828,448...20,835,628
JBrowse link
BMP signaling pathway involved in mesodermal cell fate specification term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Etv2 ETS variant transcription factor 2 ISO (MGI:4415813|PMID:18462699) MGI PMID:18462699 MGI:4415813 NCBI chrNW_004955468:4,857,023...4,859,926
Ensembl chrNW_004955468:4,857,595...4,860,531
JBrowse link
cell fate commitment involved in formation of primary germ layer term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Pou5f1 POU class 5 homeobox 1 ISO (PMID:19736317) BHF-UCL PMID:19736317 NCBI chrNW_004955583:995,707...1,003,202 JBrowse link
ectoderm formation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Foxa2 forkhead box A2 ISO (MGI:1344734|PMID:10498685) MGI PMID:10498685 MGI:1344734 NCBI chrNW_004955415:29,982,940...29,987,093
Ensembl chrNW_004955415:29,982,940...29,986,255
JBrowse link
G Lhx1 LIM homeobox 1 ISO (MGI:1344734|PMID:10498685) MGI PMID:10498685 MGI:1344734 NCBI chrNW_004955451:1,037,936...1,048,501
Ensembl chrNW_004955451:1,037,825...1,048,501
JBrowse link
ectodermal cell fate commitment term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Elf5 E74 like ETS transcription factor 5 ISO (MGI:5616945|PMID:25446535) MGI PMID:25446535 MGI:5616945 NCBI chrNW_004955422:11,751,073...11,779,313
Ensembl chrNW_004955422:11,750,774...11,780,310
JBrowse link
G Ets2 ETS proto-oncogene 2, transcription factor ISO (MGI:5616945|PMID:25446535) MGI PMID:25446535 MGI:5616945 NCBI chrNW_004955407:37,747,152...37,764,170
Ensembl chrNW_004955407:37,747,000...37,765,237
JBrowse link
G Pou5f1 POU class 5 homeobox 1 ISO (MGI:1355046|PMID:10742100) MGI PMID:10742100 MGI:1355046 NCBI chrNW_004955583:995,707...1,003,202 JBrowse link
endoderm formation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ctnnb1 catenin beta 1 ISO (MGI:3625553|PMID:12194849)
(MGI:5498579|PMID:23824574)
MGI PMID:12194849, PMID:23824574 MGI:3625553, MGI:5498579 NCBI chrNW_004955420:29,030,716...29,047,447
Ensembl chrNW_004955420:29,030,716...29,047,449
JBrowse link
G Dkk1 dickkopf WNT signaling pathway inhibitor 1 ISO (MGI:4415813|PMID:18462699) MGI PMID:18462699 MGI:4415813 NCBI chrNW_004955425:7,353,964...7,357,599 JBrowse link
G Eomes eomesodermin ISO (MGI:3772748|PMID:18171685)
(MGI:4887279|PMID:21245162), (MGI:5293253|PMID:21822279)
UniProt
MGI
PMID:18171685, PMID:21245162, PMID:21822279 MGI:3772748, MGI:4887279, MGI:5293253 NCBI chrNW_004955430:19,280,460...19,287,060
Ensembl chrNW_004955430:19,281,602...19,286,867
JBrowse link
G Gata4 GATA binding protein 4 ISO (MGI:77407|PMID:8582296) MGI PMID:8582296 MGI:77407 NCBI chrNW_004955403:52,958,318...53,029,267
Ensembl chrNW_004955403:52,987,644...53,029,267
JBrowse link
G Lhx1 LIM homeobox 1 ISO (MGI:3487194|PMID:15355796) MGI PMID:15355796 MGI:3487194 NCBI chrNW_004955451:1,037,936...1,048,501
Ensembl chrNW_004955451:1,037,825...1,048,501
JBrowse link
G Mixl1 Mix paired-like homeobox ISO (MGI:3695524|PMID:17151016) MGI PMID:17151016 MGI:3695524 NCBI chrNW_004955489:418,650...422,428 JBrowse link
G Nog noggin ISO (MGI:4415813|PMID:18462699) MGI PMID:18462699 MGI:4415813 NCBI chrNW_004955451:6,192,368...6,193,766
Ensembl chrNW_004955451:6,193,042...6,193,740
JBrowse link
G Smad2 SMAD family member 2 ISO (MGI:5293253|PMID:21822279) MGI PMID:21822279 MGI:5293253 NCBI chrNW_004955402:33,131,760...33,217,144
Ensembl chrNW_004955402:33,136,778...33,216,844
JBrowse link
G Sox17 SRY-box transcription factor 17 ISO (PMID:18682240) UniProtKB PMID:18682240 NCBI chrNW_004955454:13,689,403...13,690,019 JBrowse link
G Sox7 SRY-box transcription factor 7 ISO (PMID:18682240) UniProtKB PMID:18682240 NCBI chrNW_004955403:52,253,816...52,259,884
Ensembl chrNW_004955403:52,253,482...52,259,884
JBrowse link
G Tnrc6c trinucleotide repeat containing adaptor 6C ISO (MGI:5315650|PMID:22187428) MGI PMID:22187428 MGI:5315650 NCBI chrNW_004955506:4,440,555...4,579,642
Ensembl chrNW_004955506:4,440,555...4,559,070
JBrowse link
endodermal cell differentiation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Col11a1 collagen type XI alpha 1 chain ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955435:7,352,617...7,545,235
Ensembl chrNW_004955435:7,352,617...7,545,235
JBrowse link
G Col12a1 collagen type XII alpha 1 chain ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955488:8,128,816...8,240,714
Ensembl chrNW_004955488:8,131,846...8,240,777
JBrowse link
G Col4a2 collagen type IV alpha 2 chain ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955404:2,092,184...2,178,079
Ensembl chrNW_004955404:2,092,184...2,178,079
JBrowse link
G Col6a1 collagen type VI alpha 1 chain ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955407:42,461,837...42,479,048
Ensembl chrNW_004955407:42,461,952...42,478,261
JBrowse link
G Col7a1 collagen type VII alpha 1 chain ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955532:650,913...681,186 JBrowse link
G Col8a1 collagen type VIII alpha 1 chain ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955427:1,187,550...1,335,794
Ensembl chrNW_004955427:1,187,550...1,335,794
JBrowse link
G Fn1 fibronectin 1 ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955457:629,599...694,948
Ensembl chrNW_004955457:629,518...696,975
JBrowse link
G Hmga2 high mobility group AT-hook 2 ISO (PMID:17624332) UniProtKB PMID:17624332 NCBI chrNW_004955458:12,493,790...12,624,805 JBrowse link
G Hsbp1 heat shock factor binding protein 1 ISO (MGI:5553204|PMID:24380799) MGI PMID:24380799 MGI:5553204 NCBI chrNW_004955564:396,985...400,975 JBrowse link
G Inhba inhibin subunit beta A ISO (PMID:21828274) BHF-UCL PMID:21828274 NCBI chrNW_004955460:2,054,879...2,066,628
Ensembl chrNW_004955460:2,046,588...2,066,609
JBrowse link
G Itga4 integrin subunit alpha 4 ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955403:15,726,296...15,807,055
Ensembl chrNW_004955403:15,723,785...15,807,111
JBrowse link
G Itga5 integrin subunit alpha 5 ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955458:1,635,554...1,657,609
Ensembl chrNW_004955458:1,632,282...1,658,295
JBrowse link
G Itga7 integrin subunit alpha 7 ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955458:3,322,735...3,343,275
Ensembl chrNW_004955458:3,321,259...3,343,275
JBrowse link
G Itgav integrin subunit alpha V ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955403:11,588,536...11,669,809
Ensembl chrNW_004955403:11,592,339...11,659,297
JBrowse link
G Itgb2 integrin subunit beta 2 ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955407:41,779,849...41,805,637
Ensembl chrNW_004955407:41,777,777...41,800,201
JBrowse link
G Itgb5 integrin subunit beta 5 ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955427:23,851,475...23,952,211
Ensembl chrNW_004955427:23,850,261...23,939,950
JBrowse link
G Lama3 laminin subunit alpha 3 ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955402:11,980,980...12,362,143 JBrowse link
G Lamb1 laminin subunit beta 1 ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955410:12,241,235...12,305,433
Ensembl chrNW_004955410:12,241,235...12,305,433
JBrowse link
G Lamb3 laminin subunit beta 3 ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955489:2,547,611...2,603,079
Ensembl chrNW_004955489:2,568,650...2,607,595
JBrowse link
G Mixl1 Mix paired-like homeobox ISO (MGI:5447921|PMID:19038793) BHF-UCL PMID:19038793 MGI:5447921 NCBI chrNW_004955489:418,650...422,428 JBrowse link
G Mmp14 matrix metallopeptidase 14 ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955409:37,438,924...37,448,704
Ensembl chrNW_004955409:37,440,541...37,448,437
JBrowse link
G Mmp15 matrix metallopeptidase 15 ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955433:15,584,206...15,603,162
Ensembl chrNW_004955433:15,584,780...15,601,739
JBrowse link
G Mmp2 matrix metallopeptidase 2 ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955433:13,024,844...13,050,041
Ensembl chrNW_004955433:13,024,418...13,052,775
JBrowse link
G Mmp8 matrix metallopeptidase 8 ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955412:5,928,997...5,939,012
Ensembl chrNW_004955412:5,928,997...5,939,012
JBrowse link
G Mmp9 matrix metallopeptidase 9 ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955445:11,295,500...11,303,322
Ensembl chrNW_004955445:11,295,448...11,303,288
JBrowse link
G Nodal nodal growth differentiation factor ISO (PMID:21741376) BHF-UCL PMID:21741376 NCBI chrNW_004955437:20,828,448...20,835,486
Ensembl chrNW_004955437:20,828,448...20,835,628
JBrowse link
G Setd2 SET domain containing 2, histone lysine methyltransferase ISO (MGI:5908786|PMID:25242323) UniProt PMID:25242323 MGI:5908786 NCBI chrNW_004955420:25,070,626...25,178,410
Ensembl chrNW_004955420:25,090,798...25,177,760
JBrowse link
G Vtn vitronectin ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955481:4,765,078...4,768,027 JBrowse link
endodermal cell fate commitment term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cdc73 cell division cycle 73 ISO (MGI:3849235|PMID:19345177) UniProt PMID:19345177 MGI:3849235 NCBI chrNW_004955406:30,533,919...30,665,812
Ensembl chrNW_004955406:30,533,060...30,665,812
JBrowse link
G Ctnnb1 catenin beta 1 ISO (MGI:3625553|PMID:12194849) MGI PMID:12194849 MGI:3625553 NCBI chrNW_004955420:29,030,716...29,047,447
Ensembl chrNW_004955420:29,030,716...29,047,449
JBrowse link
G Ctr9 CTR9 homolog, Paf1/RNA polymerase II complex component ISO (MGI:3849235|PMID:19345177) UniProt PMID:19345177 MGI:3849235 NCBI chrNW_004955414:26,347,508...26,373,726
Ensembl chrNW_004955414:26,347,508...26,373,785
JBrowse link
G Leo1 LEO1 homolog, Paf1/RNA polymerase II complex component ISO (MGI:3849235|PMID:19345177) UniProt PMID:19345177 MGI:3849235 NCBI chrNW_004955409:2,711,475...2,727,879
Ensembl chrNW_004955409:2,711,564...2,727,755
JBrowse link
G Paf1 PAF1 homolog, Paf1/RNA polymerase II complex component ISO (MGI:3849235|PMID:19345177) UniProt PMID:19345177 MGI:3849235 NCBI chrNW_004955468:166,477...172,200 JBrowse link
G Pou5f1 POU class 5 homeobox 1 ISO (MGI:1355046|PMID:10742100) MGI PMID:10742100 MGI:1355046 NCBI chrNW_004955583:995,707...1,003,202 JBrowse link
G Rtf1 RTF1 homolog, Paf1/RNA polymerase II complex component ISO (MGI:3849235|PMID:19345177) UniProt PMID:19345177 MGI:3849235 NCBI chrNW_004955416:8,237,439...8,293,802
Ensembl chrNW_004955416:8,237,439...8,293,802
JBrowse link
endodermal cell fate determination term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Sox17 SRY-box transcription factor 17 ISO (MGI:4442295|PMID:20308546) MGI PMID:20308546 MGI:4442295 NCBI chrNW_004955454:13,689,403...13,690,019 JBrowse link
endodermal cell fate specification term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Eomes eomesodermin ISO (MGI:4887279|PMID:21245162) MGI PMID:21245162 MGI:4887279 NCBI chrNW_004955430:19,280,460...19,287,060
Ensembl chrNW_004955430:19,281,602...19,286,867
JBrowse link
G Hnf1b HNF1 homeobox B ISO (MGI:3807614|PMID:18635606) MGI PMID:18635606 MGI:3807614 NCBI chrNW_004955451:320,283...371,420
Ensembl chrNW_004955451:320,283...371,420
JBrowse link
G Nanog Nanog homeobox ISO (PMID:20713518) MGI PMID:20713518 NCBI chrNW_004955413:6,561,323...6,565,770 JBrowse link
G Pou5f1 POU class 5 homeobox 1 ISO (PMID:20713518) MGI PMID:20713518 NCBI chrNW_004955583:995,707...1,003,202 JBrowse link
G Sox2 SRY-box transcription factor 2 ISO (PMID:21245162) MGI PMID:21245162 NCBI chrNW_004955420:10,671,888...10,674,080
Ensembl chrNW_004955420:10,671,978...10,672,934
JBrowse link
hemangioblast cell differentiation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Tal1 TAL bHLH transcription factor 1, erythroid differentiation factor ISO (MGI:3580923|PMID:15677567), (MGI:3807430|PMID:18550854)
(MGI:3838687|PMID:19182774)
MGI PMID:15677567, PMID:18550854, PMID:19182774 MGI:3580923, MGI:3807430, MGI:3838687 NCBI chrNW_004955464:11,304,611...11,317,420
Ensembl chrNW_004955464:11,310,628...11,315,924
JBrowse link
intermediate mesodermal cell differentiation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Bmp4 bone morphogenetic protein 4 ISO (PMID:10021330) UniProtKB PMID:10021330 NCBI chrNW_004955409:9,432,835...9,439,680
Ensembl chrNW_004955409:9,432,841...9,440,303
JBrowse link
lateral mesodermal cell differentiation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Foxf1 forkhead box F1 ISO (MGI:1928688|PMID:11124112) MGI PMID:11124112 MGI:1928688 NCBI chrNW_004955541:1,341,715...1,345,397
Ensembl chrNW_004955541:1,317,114...1,346,590
JBrowse link
mesoderm formation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Acvr1 activin A receptor type 1 ISO (MGI:1345529|PMID:10479450)
(MGI:3695845|PMID:17117439)
MGI PMID:10479450, PMID:17117439 MGI:1345529, MGI:3695845 NCBI chrNW_004955449:15,587,958...15,706,432
Ensembl chrNW_004955449:15,640,230...15,708,694
JBrowse link
G Armc5 armadillo repeat containing 5 ISO (MGI:5913685|PMID:28911199) MGI PMID:28911199 MGI:5913685 NCBI chrNW_004955493:8,295,868...8,302,638
Ensembl chrNW_004955493:8,295,868...8,304,520
JBrowse link
G Bmp4 bone morphogenetic protein 4 ISO (MGI:4415813|PMID:18462699), (MGI:70235|PMID:7799920) MGI PMID:7799920, PMID:18462699 MGI:4415813, MGI:70235 NCBI chrNW_004955409:9,432,835...9,439,680
Ensembl chrNW_004955409:9,432,841...9,440,303
JBrowse link
G Bmp7 bone morphogenetic protein 7 ISO (MGI:3578079|PMID:15843411) MGI PMID:15843411 MGI:3578079 NCBI chrNW_004955445:2,154,057...2,235,594
Ensembl chrNW_004955445:2,153,170...2,235,795
JBrowse link
G Bmpr1a bone morphogenetic protein receptor type 1A ISO (MGI:3722226|PMID:17699604) MGI PMID:17699604 MGI:3722226 NCBI chrNW_004955510:5,812,571...5,936,312
Ensembl chrNW_004955510:5,905,008...5,936,312
JBrowse link
G Bmpr2 bone morphogenetic protein receptor type 2 ISO (MGI:1855789|PMID:10772805) MGI PMID:10772805 MGI:1855789 NCBI chrNW_004955457:12,235,780...12,315,680
Ensembl chrNW_004955457:12,235,780...12,316,727
JBrowse link
G Chrd chordin ISO (MGI:2662951|PMID:12810603) MGI PMID:12810603 MGI:2662951 NCBI chrNW_004955420:23,111,690...23,120,038
Ensembl chrNW_004955420:23,112,093...23,120,036
JBrowse link
G Crb2 crumbs cell polarity complex component 2 ISO (MGI:5296388|PMID:22072575), (MGI:5823085|PMID:27870829) UniProt PMID:22072575, PMID:27870829 MGI:5296388, MGI:5823085 NCBI chrNW_004955419:4,604,883...4,626,675
Ensembl chrNW_004955419:4,607,507...4,626,608
JBrowse link
G Dkk1 dickkopf WNT signaling pathway inhibitor 1 ISO (MGI:4415813|PMID:18462699) MGI PMID:18462699 MGI:4415813 NCBI chrNW_004955425:7,353,964...7,357,599 JBrowse link
G Ecsit ECSIT signaling integrator ISO (MGI:2682456|PMID:14633973) MGI PMID:14633973 MGI:2682456 NCBI chrNW_004955495:2,375,992...2,385,962
Ensembl chrNW_004955495:2,375,602...2,382,035
JBrowse link
G Eomes eomesodermin ISO (MGI:1354065|PMID:10716450) MGI PMID:10716450 MGI:1354065 NCBI chrNW_004955430:19,280,460...19,287,060
Ensembl chrNW_004955430:19,281,602...19,286,867
JBrowse link
G Etv2 ETS variant transcription factor 2 ISO (MGI:4415813|PMID:18462699) MGI PMID:18462699 MGI:4415813 NCBI chrNW_004955468:4,857,023...4,859,926
Ensembl chrNW_004955468:4,857,595...4,860,531
JBrowse link
G Ext2 exostosin glycosyltransferase 2 ISO (MGI:3608483|PMID:16236767) MGI PMID:16236767 MGI:3608483 NCBI chrNW_004955422:3,303,948...3,438,381
Ensembl chrNW_004955422:3,304,842...3,447,908
JBrowse link
G Gpi glucose-6-phosphate isomerase ISO (MGI:84014|PMID:8922529) MGI PMID:8922529 MGI:84014 NCBI chrNW_004955468:3,980,999...4,007,553
Ensembl chrNW_004955468:3,980,999...4,008,652
JBrowse link
G Hand1 heart and neural crest derivatives expressed 1 ISO (MGI:1197801|PMID:9500550) MGI PMID:9500550 MGI:1197801 NCBI chrNW_004955408:8,848,723...8,851,804
Ensembl chrNW_004955408:8,848,559...8,851,994
JBrowse link
G Inhba inhibin subunit beta A ISO (MGI:70235|PMID:7799920) MGI PMID:7799920 MGI:70235 NCBI chrNW_004955460:2,054,879...2,066,628
Ensembl chrNW_004955460:2,046,588...2,066,609
JBrowse link
G Macf1 microtubule actin crosslinking factor 1 ISO (MGI:3640889|PMID:16815997) MGI PMID:16815997 MGI:3640889 NCBI chrNW_004955452:16,684,784...17,025,940
Ensembl chrNW_004955452:16,798,911...17,024,732
JBrowse link
G Nf2 neurofibromin 2 ISO (MGI:707944|PMID:9171370) MGI PMID:9171370 MGI:707944 NCBI chrNW_004955455:3,862,804...3,950,669
Ensembl chrNW_004955455:3,862,347...3,951,891
JBrowse link
G Nodal nodal growth differentiation factor ISO (MGI:2155575|PMID:11311163) MGI PMID:11311163 MGI:2155575 NCBI chrNW_004955437:20,828,448...20,835,486
Ensembl chrNW_004955437:20,828,448...20,835,628
JBrowse link
G Nog noggin ISO (MGI:4415813|PMID:18462699) MGI PMID:18462699 MGI:4415813 NCBI chrNW_004955451:6,192,368...6,193,766
Ensembl chrNW_004955451:6,193,042...6,193,740
JBrowse link
G Nr4a3 nuclear receptor subfamily 4 group A member 3 ISO (MGI:3042044|PMID:13129926) MGI PMID:13129926 MGI:3042044 NCBI chrNW_004955419:25,779,368...25,817,445
Ensembl chrNW_004955419:25,779,178...25,818,706
JBrowse link
G Pofut2 protein O-fucosyltransferase 2 ISO (MGI:4838381|PMID:20637190) MGI PMID:20637190 MGI:4838381 NCBI chrNW_004955407:41,972,833...41,984,095
Ensembl chrNW_004955407:41,972,717...41,984,095
JBrowse link
G Prkaca protein kinase cAMP-activated catalytic subunit alpha ISO (MGI:2183097|PMID:12004056) MGI PMID:12004056 MGI:2183097 NCBI chrNW_004955415:32,794,172...32,807,944
Ensembl chrNW_004955415:32,793,718...32,812,930
JBrowse link
G Prkar1a protein kinase cAMP-dependent type I regulatory subunit alpha ISO (MGI:2183097|PMID:12004056) MGI PMID:12004056 MGI:2183097 NCBI chrNW_004955478:4,241,283...4,262,119
Ensembl chrNW_004955478:4,241,283...4,263,087
JBrowse link
G Scx scleraxis bHLH transcription factor ISO (MGI:1343990|PMID:10477299) UniProt PMID:10477299 MGI:1343990 NCBI chrNW_004955454:2,886,981...2,888,829
Ensembl chrNW_004955454:2,886,981...2,888,829
JBrowse link
G Smad2 SMAD family member 2 ISO (MGI:3039049|PMID:15084457) MGI PMID:15084457 MGI:3039049 NCBI chrNW_004955402:33,131,760...33,217,144
Ensembl chrNW_004955402:33,136,778...33,216,844
JBrowse link
G Smad3 SMAD family member 3 ISO (MGI:3039049|PMID:15084457) MGI PMID:15084457 MGI:3039049 NCBI chrNW_004955450:8,747,651...8,842,003
Ensembl chrNW_004955450:8,747,651...8,842,136
JBrowse link
G Snai1 snail family transcriptional repressor 1 ISO (MGI:2153695|PMID:11689706) UniProt PMID:11689706 MGI:2153695 NCBI chrNW_004955445:8,232,084...8,237,893
Ensembl chrNW_004955445:8,231,924...8,237,996
JBrowse link
G Srf serum response factor ISO (MGI:1312998|PMID:9799237), (MGI:1927031|PMID:11060034) MGI PMID:9799237, PMID:11060034 MGI:1312998, MGI:1927031 NCBI chrNW_004955437:9,100,546...9,109,305
Ensembl chrNW_004955437:9,098,968...9,107,057
JBrowse link
G Tbx6 T-box transcription factor 6 ISO (MGI:2447720|PMID:9490412)
(MGI:3577662|PMID:15755804)
MGI PMID:9490412, PMID:15755804 MGI:2447720, MGI:3577662 NCBI chrNW_004955493:6,888,832...6,894,840
Ensembl chrNW_004955493:6,888,832...6,894,831
JBrowse link
G Tlx2 T cell leukemia homeobox 2 ISO (MGI:1267265|PMID:9550720) MGI PMID:9550720 MGI:1267265 NCBI chrNW_004955424:11,269,426...11,275,200
Ensembl chrNW_004955424:11,269,426...11,275,200
JBrowse link
G Twsg1 twisted gastrulation BMP signaling modulator 1 ISO (MGI:3578079|PMID:15843411) MGI PMID:15843411 MGI:3578079 NCBI chrNW_004955402:2,652,020...2,685,350
Ensembl chrNW_004955402:2,652,020...2,686,117
JBrowse link
G Txnrd1 thioredoxin reductase 1 ISO (MGI:3721365|PMID:17697936) MGI PMID:17697936 MGI:3721365 NCBI chrNW_004955405:38,863,762...38,928,615
Ensembl chrNW_004955405:38,903,918...38,927,410
JBrowse link
G Wls Wnt ligand secretion mediator ISO (MGI:4397730|PMID:19841259) UniProt PMID:19841259 MGI:4397730 NCBI chrNW_004955423:23,374,401...23,465,308
Ensembl chrNW_004955423:23,374,401...23,466,475
JBrowse link
mesoderm migration involved in gastrulation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Epb41l5 erythrocyte membrane protein band 4.1 like 5 ISO (MGI:3821807|PMID:18794329) MGI PMID:18794329 MGI:3821807 NCBI chrNW_004955459:9,641,926...9,783,718
Ensembl chrNW_004955459:9,641,884...9,784,173
JBrowse link
G Tbxt T-box transcription factor T ISO (MGI:71468|PMID:7720590) MGI PMID:7720590 MGI:71468 NCBI chrNW_004955439:15,675,680...15,683,542
Ensembl chrNW_004955439:15,676,095...15,683,554
JBrowse link
mesodermal cell differentiation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Bmp4 bone morphogenetic protein 4 ISO (MGI:70235|PMID:7799920) MGI PMID:7799920 MGI:70235 NCBI chrNW_004955409:9,432,835...9,439,680
Ensembl chrNW_004955409:9,432,841...9,440,303
JBrowse link
G Fgfr2 fibroblast growth factor receptor 2 ISO RGD PMID:7803853 RGD:632663 NCBI chrNW_004955551:2,321,190...2,427,000 JBrowse link
G Hmga2 high mobility group AT-hook 2 ISO (PMID:17624332) UniProtKB PMID:17624332 NCBI chrNW_004955458:12,493,790...12,624,805 JBrowse link
G Inhba inhibin subunit beta A ISO (MGI:70235|PMID:7799920) MGI PMID:7799920 MGI:70235 NCBI chrNW_004955460:2,054,879...2,066,628
Ensembl chrNW_004955460:2,046,588...2,066,609
JBrowse link
G Itga2 integrin subunit alpha 2 ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955446:14,309,516...14,421,991
Ensembl chrNW_004955446:14,309,349...14,422,170
JBrowse link
G Itga3 integrin subunit alpha 3 ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955451:11,563,120...11,590,119
Ensembl chrNW_004955451:11,561,704...11,589,727
JBrowse link
G Itga8 integrin subunit alpha 8 ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955429:11,932,764...12,120,757
Ensembl chrNW_004955429:11,932,570...12,120,821
JBrowse link
G Itgb1 integrin subunit beta 1 ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955462:4,454,809...4,483,227
Ensembl chrNW_004955462:4,454,809...4,484,842
JBrowse link
G Itgb3 integrin subunit beta 3 ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955478:9,788,192...9,830,254 JBrowse link
G Itgb4 integrin subunit beta 4 ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955506:6,493,466...6,526,778
Ensembl chrNW_004955506:6,493,466...6,526,778
JBrowse link
G Kdm6a lysine demethylase 6A ISO (MGI:5448135|PMID:22949634) MGI PMID:22949634 MGI:5448135 NCBI chrNW_004955516:3,151,350...3,346,832
Ensembl chrNW_004955516:3,149,948...3,346,832
JBrowse link
G Kdm6b lysine demethylase 6B ISO (MGI:5574281|PMID:23856522) BHF-UCL PMID:23856522 MGI:5574281 NCBI chrNW_004955467:9,085,239...9,106,658
Ensembl chrNW_004955467:9,086,204...9,094,404
JBrowse link
mesodermal cell fate commitment term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Nanog Nanog homeobox ISO (MGI:3654744|PMID:16801560) MGI PMID:16801560 MGI:3654744 NCBI chrNW_004955413:6,561,323...6,565,770 JBrowse link
G Pou5f1 POU class 5 homeobox 1 ISO (MGI:1355046|PMID:10742100) MGI PMID:10742100 MGI:1355046 NCBI chrNW_004955583:995,707...1,003,202 JBrowse link
G Smad1 SMAD family member 1 ISO (MGI:3654744|PMID:16801560) MGI PMID:16801560 MGI:3654744 NCBI chrNW_004955428:1,357,398...1,429,521
Ensembl chrNW_004955428:1,361,085...1,429,948
JBrowse link
mesodermal cell fate determination term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Bmp4 bone morphogenetic protein 4 ISO (MGI:76261|PMID:7657163) MGI PMID:7657163 MGI:76261 NCBI chrNW_004955409:9,432,835...9,439,680
Ensembl chrNW_004955409:9,432,841...9,440,303
JBrowse link
mesodermal cell fate specification term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Eya1 EYA transcriptional coactivator and phosphatase 1 ISO (MGI:3768605|PMID:17785448) UniProt PMID:17785448 MGI:3768605 NCBI chrNW_004955444:8,336,071...8,655,041
Ensembl chrNW_004955444:8,495,530...8,655,100
JBrowse link
G Hoxa11 homeobox A11 ISO (MGI:3768605|PMID:17785448) UniProt PMID:17785448 MGI:3768605 NCBI chrNW_004955410:28,875,780...28,879,643
Ensembl chrNW_004955410:28,877,055...28,879,465
JBrowse link
G Pax2 paired box 2 ISO (MGI:3768605|PMID:17785448) UniProt PMID:17785448 MGI:3768605 NCBI chrNW_004955485:9,351,913...9,430,607
Ensembl chrNW_004955485:9,350,087...9,430,607
JBrowse link
G Six2 SIX homeobox 2 ISO (MGI:3768605|PMID:17785448) UniProt PMID:17785448 MGI:3768605 NCBI chrNW_004955441:12,029,530...12,033,214
Ensembl chrNW_004955441:12,029,480...12,033,214
JBrowse link
negative regulation of ectodermal cell fate specification term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Fzd7 frizzled class receptor 7 ISO (PMID:18681827) BHF-UCL PMID:18681827 NCBI chrNW_004955457:12,729,277...12,733,057
Ensembl chrNW_004955457:12,731,279...12,732,979
JBrowse link
negative regulation of endodermal cell differentiation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Col5a1 collagen type V alpha 1 chain ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955513:3,533,612...3,660,605
Ensembl chrNW_004955513:3,533,614...3,658,161
JBrowse link
G Col5a2 collagen type V alpha 2 chain ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chrNW_004955403:9,562,401...9,703,828
Ensembl chrNW_004955403:9,562,401...9,703,828
JBrowse link
negative regulation of mesodermal cell fate specification term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Dkk1 dickkopf WNT signaling pathway inhibitor 1 ISO (PMID:20559569) BHF-UCL PMID:20559569 NCBI chrNW_004955425:7,353,964...7,357,599 JBrowse link
G Sfrp2 secreted frizzled related protein 2 ISO (MGI:3711603|PMID:17462603) MGI PMID:17462603 MGI:3711603 NCBI chrNW_004955471:8,103,937...8,112,596
Ensembl chrNW_004955471:8,103,783...8,112,321
JBrowse link
paraxial mesoderm formation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Exoc4 exocyst complex component 4 ISO (MGI:1195048|PMID:9441674) MGI PMID:9441674 MGI:1195048 NCBI chrNW_004955410:33,937,825...34,672,790
Ensembl chrNW_004955410:33,935,320...34,673,764
JBrowse link
G Hnf1a HNF1 homeobox A ISO (MGI:1334099|PMID:10090727) MGI PMID:10090727 MGI:1334099 NCBI chrNW_004955455:10,694,102...10,717,613
Ensembl chrNW_004955455:10,694,102...10,717,613
JBrowse link
G Htt huntingtin ISO (MGI:3609520|PMID:16109169) MGI PMID:16109169 MGI:3609520 NCBI chrNW_004955514:1,906,189...2,042,357
Ensembl chrNW_004955514:1,906,502...2,038,889
JBrowse link
G Lef1 lymphoid enhancer binding factor 1 ISO (MGI:1334099|PMID:10090727) MGI PMID:10090727 MGI:1334099 NCBI chrNW_004955496:1,728,840...1,827,749
Ensembl chrNW_004955496:1,728,840...1,828,698
JBrowse link
G Wnt11 Wnt family member 11 ISO (MGI:5634837|PMID:25813538) MGI PMID:25813538 MGI:5634837 NCBI chrNW_004955414:15,674,478...15,694,758
Ensembl chrNW_004955414:15,674,940...15,694,883
JBrowse link
G Wnt5a Wnt family member 5A ISO (MGI:5634837|PMID:25813538) MGI PMID:25813538 MGI:5634837 NCBI chrNW_004955430:5,304,817...5,325,684
Ensembl chrNW_004955430:5,304,745...5,325,684
JBrowse link
paraxial mesodermal cell fate commitment term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Wnt3a Wnt family member 3A ISO (MGI:86727|PMID:9126297) MGI PMID:9126297 MGI:86727 NCBI chrNW_004955581:351,375...382,541
Ensembl chrNW_004955581:350,889...382,541
JBrowse link
positive regulation of endodermal cell differentiation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G LOC102008188 core histone macro-H2A.1 ISO (PMID:23595991) UniProt PMID:23595991 NCBI chrNW_004955408:30,497,531...30,550,095
Ensembl chrNW_004955408:30,497,531...30,550,118
JBrowse link
positive regulation of mesodermal cell differentiation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Gja1 gap junction protein alpha 1 ISO (PMID:30599359) ARUK-UCL PMID:30599359 NCBI chrNW_004955436:3,612,533...3,618,095
Ensembl chrNW_004955436:3,612,533...3,618,095
JBrowse link
positive regulation of mesodermal cell fate specification term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Wnt3a Wnt family member 3A ISO (PMID:20559569) BHF-UCL PMID:20559569 NCBI chrNW_004955581:351,375...382,541
Ensembl chrNW_004955581:350,889...382,541
JBrowse link
regulation of endodermal cell fate specification term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Dkk1 dickkopf WNT signaling pathway inhibitor 1 ISO (PMID:20559569) BHF-UCL PMID:20559569 NCBI chrNW_004955425:7,353,964...7,357,599 JBrowse link
regulation of lateral mesodermal cell fate specification term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Bmpr1a bone morphogenetic protein receptor type 1A ISO (MGI:3702797|PMID:16943278) MGI PMID:16943278 MGI:3702797 NCBI chrNW_004955510:5,812,571...5,936,312
Ensembl chrNW_004955510:5,905,008...5,936,312
JBrowse link
G Fgfr1 fibroblast growth factor receptor 1 ISO (MGI:3702797|PMID:16943278) MGI PMID:16943278 MGI:3702797 NCBI chrNW_004955463:14,013,247...14,064,354
Ensembl chrNW_004955463:14,013,247...14,064,111
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 11892
    developmental process 5616
      anatomical structure formation involved in morphogenesis 1090
        formation of primary germ layer 115
          cell fate commitment involved in formation of primary germ layer + 28
          ectoderm formation + 6
          endoderm formation + 50
          mesoderm formation + 67
Path 2
Term Annotations click to browse term
  biological_process 11892
    developmental process 5616
      anatomical structure development 5254
        multicellular organism development 4812
          embryo development 1169
            embryonic morphogenesis 626
              gastrulation 176
                formation of primary germ layer 115
                  cell fate commitment involved in formation of primary germ layer + 28
                  ectoderm formation + 6
                  endoderm formation + 50
                  mesoderm formation + 67
paths to the root

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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.