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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 IEA Ensembl GO_REF:0000107 NCBI chr 6:84,049,729...84,124,302
Ensembl chr 6:84,049,365...84,123,384
JBrowse link
G ATOH8 atonal bHLH transcription factor 8 IEA Ensembl GO_REF:0000107 NCBI chr 3:58,964,541...59,001,620
Ensembl chr 3:58,964,541...59,001,146
JBrowse link
G KIF16B kinesin family member 16B ISO (MGI:4889011|PMID:21238925) UniProt PMID:21238925 MGI:4889011 NCBI chr17:24,882,139...25,188,990 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 chr 3:41,344,908...41,393,999
Ensembl chr 3:41,337,071...41,393,997
JBrowse link
G EPHA2 EPH receptor A2 IEA Ensembl GO_REF:0000107 NCBI chr 6:75,251,465...75,279,364
Ensembl chr 6:75,251,467...75,279,314
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 IEA Ensembl GO_REF:0000107 NCBI chr14:73,350,358...73,357,064
Ensembl chr14:73,349,965...73,360,618
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 IEA Ensembl GO_REF:0000107 NCBI chr 6:45,085,984...45,089,592
Ensembl chr 6:45,088,171...45,089,595
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 chr 7:23,564,654...23,570,691 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 chr17:29,997,397...30,001,704
Ensembl chr17:29,997,400...30,001,707
JBrowse link
G LHX1 LIM homeobox 1 IEA Ensembl GO_REF:0000107 NCBI chr12:38,450,708...38,457,583
Ensembl chr12:38,450,708...38,456,139
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 IEA Ensembl GO_REF:0000107 NCBI chr 2:26,443,979...26,486,802
Ensembl chr 2:26,443,963...26,485,903
JBrowse link
G ETS2 ETS proto-oncogene 2, transcription factor IEA Ensembl GO_REF:0000107 NCBI chr13:202,464,341...202,483,534
Ensembl chr13:202,468,721...202,484,610
JBrowse link
G POU5F1 POU class 5 homeobox 1 IEA Ensembl GO_REF:0000107 NCBI chr 7:23,564,654...23,570,691 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 chr13:25,163,550...25,208,314
Ensembl chr13:25,137,173...25,208,311
JBrowse link
G DKK1 dickkopf WNT signaling pathway inhibitor 1 IEA Ensembl GO_REF:0000107 NCBI chr14:97,487,854...97,490,118
Ensembl chr14:97,487,226...97,490,450
JBrowse link
G DUSP1 dual specificity phosphatase 1 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr16:51,457,924...51,461,095
Ensembl chr16:51,458,020...51,461,086
JBrowse link
G DUSP2 dual specificity phosphatase 2 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 3:47,052,443...47,054,816
Ensembl chr 3:47,052,457...47,054,816
JBrowse link
G DUSP4 dual specificity phosphatase 4 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr15:55,491,084...55,508,460
Ensembl chr15:55,490,468...55,509,459
JBrowse link
G DUSP5 dual specificity phosphatase 5 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr14:120,906,340...120,919,398
Ensembl chr14:120,906,343...120,919,395
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 chr13:14,209,590...14,216,184
Ensembl chr13:14,210,083...14,215,797
JBrowse link
G GATA4 GATA binding protein 4 ISO (MGI:77407|PMID:8582296) MGI PMID:8582296 MGI:77407 NCBI chr14:14,858,470...14,938,156
Ensembl chr14:14,858,159...14,939,941
JBrowse link
G LHX1 LIM homeobox 1 IEA Ensembl GO_REF:0000107 NCBI chr12:38,450,708...38,457,583
Ensembl chr12:38,450,708...38,456,139
JBrowse link
G MIXL1 Mix paired-like homeobox ISO (MGI:3695524|PMID:17151016) MGI PMID:17151016 MGI:3695524 NCBI chr10:14,102,273...14,105,544
Ensembl chr10:14,102,395...14,104,982
JBrowse link
G NOG noggin IEA Ensembl GO_REF:0000107 NCBI chr12:32,891,321...32,892,206
Ensembl chr12:32,891,321...32,892,206
JBrowse link
G SMAD2 SMAD family member 2 IEA Ensembl GO_REF:0000107 NCBI chr 1:97,415,360...97,511,388
Ensembl chr 1:97,415,716...97,511,358
JBrowse link
G SOX17 SRY-box transcription factor 17 ISO (PMID:18682240) UniProtKB PMID:18682240 NCBI chr 4:76,854,218...76,857,143
Ensembl chr 4:76,852,230...76,857,139
JBrowse link
G SOX7 SRY-box transcription factor 7 IEA Ensembl GO_REF:0000107 NCBI chr14:13,938,381...13,945,324
Ensembl chr14:13,938,385...13,945,166
JBrowse link
G TNRC6C trinucleotide repeat containing adaptor 6C ISO (MGI:5315650|PMID:22187428) MGI PMID:22187428 MGI:5315650 NCBI chr12:3,847,522...3,939,054
Ensembl chr12:3,846,428...3,935,391
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 IEA Ensembl GO_REF:0000107 NCBI chr 4:115,638,381...115,841,679
Ensembl chr 4:115,540,950...115,840,708
JBrowse link
G COL12A1 collagen type XII alpha 1 chain IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 1:90,744,409...90,875,127
Ensembl chr 1:90,744,429...90,875,118
JBrowse link
G COL4A2 collagen type IV alpha 2 chain IEA Ensembl GO_REF:0000107 NCBI chr11:76,996,885...77,161,617
Ensembl chr11:76,997,516...77,161,615
JBrowse link
G COL7A1 collagen type VII alpha 1 chain ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chr13:31,262,750...31,295,112 JBrowse link
G COL8A1 collagen type VIII alpha 1 chain IEA Ensembl GO_REF:0000107 NCBI chr13:159,216,138...159,374,718
Ensembl chr13:159,216,138...159,374,504
JBrowse link
G FN1 fibronectin 1 IEA Ensembl GO_REF:0000107 NCBI chr15:117,658,158...117,737,145
Ensembl chr15:117,658,099...117,731,014
JBrowse link
G GATA6 GATA binding protein 6 ISO (MGI:1315079|PMID:9832509) MGI PMID:9832509 MGI:1315079 NCBI chr 6:107,282,709...107,314,725
Ensembl chr 6:107,282,847...107,314,634
JBrowse link
G HMGA2 high mobility group AT-hook 2 ISO (PMID:17624332) UniProtKB PMID:17624332 NCBI chr 5:30,188,521...30,329,635 JBrowse link
G HSBP1 heat shock factor binding protein 1 ISO (MGI:5553204|PMID:24380799) MGI PMID:24380799 MGI:5553204 NCBI chr 6:4,795,203...4,798,158
Ensembl chr 6:4,793,920...4,798,191
JBrowse link
G INHBA inhibin subunit beta A IEA Ensembl GO_REF:0000107 NCBI chr12:53,115,379...53,117,128
NCBI chr18:52,889,684...52,909,260
Ensembl chr18:52,889,684...52,900,967
JBrowse link
G ITGA4 integrin subunit alpha 4 IEA Ensembl GO_REF:0000107 NCBI chr15:86,942,054...87,028,428
Ensembl chr15:86,947,021...87,029,777
JBrowse link
G ITGA5 integrin subunit alpha 5 IEA Ensembl GO_REF:0000107 NCBI chr 5:19,587,361...19,610,580
Ensembl chr 5:19,586,746...19,610,362
JBrowse link
G ITGA7 integrin subunit alpha 7 IEA Ensembl GO_REF:0000107 NCBI chr 5:21,126,565...21,150,875
Ensembl chr 5:21,126,565...21,148,776
JBrowse link
G ITGAV integrin subunit alpha V IEA Ensembl GO_REF:0000107 NCBI chr15:91,604,666...91,711,843
Ensembl chr15:91,604,676...91,711,840
JBrowse link
G ITGB2 integrin subunit beta 2 IEA Ensembl GO_REF:0000107 NCBI chr13:207,514,281...207,544,108
Ensembl chr13:207,512,954...207,544,108
JBrowse link
G ITGB5 integrin subunit beta 5 IEA Ensembl GO_REF:0000107 NCBI chr13:135,468,111...135,587,483
Ensembl chr13:135,467,798...135,587,483
JBrowse link
G LAMA3 laminin subunit alpha 3 IEA Ensembl GO_REF:0000107 NCBI chr 6:108,548,818...108,805,700
Ensembl chr 6:108,548,837...108,805,693
JBrowse link
G LAMB1 laminin subunit beta 1 IEA Ensembl GO_REF:0000107 NCBI chr 9:107,670,120...107,747,242
Ensembl chr 9:107,671,152...107,772,269
JBrowse link
G LAMB3 laminin subunit beta 3 IEA Ensembl GO_REF:0000107 NCBI chr 9:133,298,009...133,351,162
Ensembl chr 9:133,311,834...133,351,197
JBrowse link
G LOC100623720 collagen alpha-1(VI) chain IEA Ensembl GO_REF:0000107 NCBI chr13:208,295,245...208,321,789
Ensembl chr13:208,295,240...208,313,127
JBrowse link
G MIXL1 Mix paired-like homeobox IEA Ensembl GO_REF:0000107 NCBI chr10:14,102,273...14,105,544
Ensembl chr10:14,102,395...14,104,982
JBrowse link
G MMP14 matrix metallopeptidase 14 IEA Ensembl GO_REF:0000107 NCBI chr 7:76,174,502...76,185,931
Ensembl chr 7:76,174,500...76,185,923
JBrowse link
G MMP15 matrix metallopeptidase 15 IEA Ensembl GO_REF:0000107 NCBI chr 6:19,890,867...19,912,941
Ensembl chr 6:19,890,884...19,918,244
JBrowse link
G MMP2 matrix metallopeptidase 2 IEA Ensembl GO_REF:0000107 NCBI chr 6:30,059,247...30,087,031
Ensembl chr 6:30,058,594...30,086,982
JBrowse link
G MMP8 matrix metallopeptidase 8 IEA Ensembl GO_REF:0000107 NCBI chr 9:33,384,034...33,397,637
Ensembl chr 9:33,384,028...33,396,947
JBrowse link
G MMP9 matrix metallopeptidase 9 IEA Ensembl GO_REF:0000107 NCBI chr17:48,179,690...48,186,782
Ensembl chr17:48,175,056...48,188,264
JBrowse link
G NODAL nodal growth differentiation factor IEA Ensembl GO_REF:0000107 NCBI chr14:73,350,358...73,357,064
Ensembl chr14:73,349,965...73,360,618
JBrowse link
G SETD2 SET domain containing 2, histone lysine methyltransferase IEA Ensembl GO_REF:0000107 NCBI chr13:29,884,708...29,996,285
Ensembl chr13:29,884,712...29,996,360
JBrowse link
G VTN vitronectin ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chr12:44,650,532...44,653,916
Ensembl chr12:44,617,499...44,660,271
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 IEA Ensembl GO_REF:0000107 NCBI chr10:575,075...667,618
Ensembl chr10:575,074...667,434
JBrowse link
G CTNNB1 catenin beta 1 IEA Ensembl GO_REF:0000107 NCBI chr13:25,163,550...25,208,314
Ensembl chr13:25,137,173...25,208,311
JBrowse link
G CTR9 CTR9 homolog, Paf1/RNA polymerase II complex component IEA Ensembl GO_REF:0000107 NCBI chr 2:48,700,629...48,729,480
Ensembl chr 2:48,697,972...48,729,307
JBrowse link
G LEO1 LEO1 homolog, Paf1/RNA polymerase II complex component IEA Ensembl GO_REF:0000107 NCBI chr 1:119,804,992...119,842,343
Ensembl chr 1:119,805,039...119,897,073
JBrowse link
G PAF1 PAF1 homolog, Paf1/RNA polymerase II complex component IEA Ensembl GO_REF:0000107 NCBI chr 6:48,046,487...48,053,631
Ensembl chr 6:48,046,691...48,059,035
JBrowse link
G POU5F1 POU class 5 homeobox 1 IEA Ensembl GO_REF:0000107 NCBI chr 7:23,564,654...23,570,691 JBrowse link
G RTF1 RTF1 homolog, Paf1/RNA polymerase II complex component IEA Ensembl GO_REF:0000107 NCBI chr 1:129,886,798...129,942,845
Ensembl chr 1:129,886,800...129,942,982
JBrowse link
endodermal cell fate determination term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G GATA6 GATA binding protein 6 IEA Ensembl GO_REF:0000107 NCBI chr 6:107,282,709...107,314,725
Ensembl chr 6:107,282,847...107,314,634
JBrowse link
G SOX17 SRY-box transcription factor 17 IEA Ensembl GO_REF:0000107 NCBI chr 4:76,854,218...76,857,143
Ensembl chr 4:76,852,230...76,857,139
JBrowse link
endodermal cell fate specification term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G EOMES eomesodermin IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr13:14,209,590...14,216,184
Ensembl chr13:14,210,083...14,215,797
JBrowse link
G HNF1B HNF1 homeobox B IEA Ensembl GO_REF:0000107 NCBI chr12:39,143,119...39,201,631
Ensembl chr12:39,143,121...39,313,511
JBrowse link
G NANOG Nanog homeobox ISO (PMID:20713518) MGI PMID:20713518 NCBI chr 5:62,931,642...62,939,086
Ensembl chr 5:62,932,382...62,939,082
JBrowse link
G POU5F1 POU class 5 homeobox 1 ISO (PMID:20713518) MGI PMID:20713518 NCBI chr 7:23,564,654...23,570,691 JBrowse link
G SOX2 SRY-box transcription factor 2 ISO (PMID:21245162) MGI PMID:21245162 NCBI chr13:119,668,476...119,669,435 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 IEA Ensembl GO_REF:0000107 NCBI chr 6:164,282,242...164,297,636
Ensembl chr 6:164,281,737...164,297,637
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 IEA Ensembl GO_REF:0000107 NCBI chr 1:183,415,989...183,422,888
Ensembl chr 1:183,416,134...183,792,417
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 IEA Ensembl GO_REF:0000107 NCBI chr 6:2,579,348...2,598,122
Ensembl chr 6:2,592,993...2,597,659
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 IEA Ensembl GO_REF:0000107 NCBI chr15:64,749,478...64,891,653
Ensembl chr15:64,748,761...64,892,153
JBrowse link
G ARMC5 armadillo repeat containing 5 IEA Ensembl GO_REF:0000107 NCBI chr 3:17,100,612...17,108,523
Ensembl chr 3:17,100,624...17,108,365
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 chr 1:183,415,989...183,422,888
Ensembl chr 1:183,416,134...183,792,417
JBrowse link
G BMP7 bone morphogenetic protein 7 IEA Ensembl GO_REF:0000107 NCBI chr17:57,567,770...57,676,516
Ensembl chr17:57,584,091...57,676,944
JBrowse link
G BMPR1A bone morphogenetic protein receptor type 1A IEA Ensembl GO_REF:0000107 NCBI chr14:87,743,270...87,891,790
Ensembl chr14:87,742,459...87,891,793
JBrowse link
G BMPR2 bone morphogenetic protein receptor type 2 IEA Ensembl GO_REF:0000107 NCBI chr15:105,971,577...106,132,496
Ensembl chr15:105,970,427...106,135,730
JBrowse link
G CHRD chordin IEA Ensembl GO_REF:0000107 NCBI chr13:122,266,632...122,277,513
Ensembl chr13:122,266,615...122,277,509
JBrowse link
G CRB2 crumbs cell polarity complex component 2 ISS UniProt GO_REF:0000024 NCBI chr 1:264,277,549...264,301,731
Ensembl chr 1:264,276,572...264,301,725
JBrowse link
G DKK1 dickkopf WNT signaling pathway inhibitor 1 IEA Ensembl GO_REF:0000107 NCBI chr14:97,487,854...97,490,118
Ensembl chr14:97,487,226...97,490,450
JBrowse link
G ECSIT ECSIT signaling integrator ISO (MGI:2682456|PMID:14633973) MGI PMID:14633973 MGI:2682456 NCBI chr 2:70,154,861...70,170,762
Ensembl chr 2:70,136,778...70,170,696
JBrowse link
G EOMES eomesodermin IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr13:14,209,590...14,216,184
Ensembl chr13:14,210,083...14,215,797
JBrowse link
G ETV2 ETS variant transcription factor 2 ISO (MGI:4415813|PMID:18462699) MGI PMID:18462699 MGI:4415813 NCBI chr 6:45,085,984...45,089,592
Ensembl chr 6:45,088,171...45,089,595
JBrowse link
G EXT2 exostosin glycosyltransferase 2 IEA Ensembl GO_REF:0000107 NCBI chr 2:18,099,790...18,239,229
Ensembl chr 2:18,100,379...18,232,025
JBrowse link
G GPI glucose-6-phosphate isomerase IEA Ensembl GO_REF:0000107 NCBI chr 6:44,038,374...44,069,331
Ensembl chr 6:43,933,759...44,069,330
JBrowse link
G HAND1 heart and neural crest derivatives expressed 1 IEA Ensembl GO_REF:0000107 NCBI chr16:68,679,977...68,683,346
Ensembl chr16:68,677,963...68,683,342
JBrowse link
G INHBA inhibin subunit beta A ISO (MGI:70235|PMID:7799920) MGI PMID:7799920 MGI:70235 NCBI chr12:53,115,379...53,117,128
NCBI chr18:52,889,684...52,909,260
Ensembl chr18:52,889,684...52,900,967
JBrowse link
G MACF1 microtubule actin crosslinking factor 1 ISO (MGI:3640889|PMID:16815997) MGI PMID:16815997 MGI:3640889 NCBI chr 6:94,960,385...95,318,126
Ensembl chr 6:94,960,457...95,317,145
JBrowse link
G MESP1 mesoderm posterior bHLH transcription factor 1 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 7:55,322,016...55,327,600
Ensembl chr 7:55,322,010...55,325,732
JBrowse link
G MESP2 mesoderm posterior bHLH transcription factor 2 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 7:55,341,941...55,345,824
Ensembl chr 7:55,343,134...55,345,904
JBrowse link
G MSGN1 mesogenin 1 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 3:120,033,980...120,034,624
Ensembl chr 3:120,034,043...120,034,624
JBrowse link
G NF2 neurofibromin 2 IEA Ensembl GO_REF:0000107 NCBI chr14:46,653,869...46,726,421
Ensembl chr14:46,653,902...46,731,999
JBrowse link
G NODAL nodal growth differentiation factor ISO (MGI:2155575|PMID:11311163) MGI PMID:11311163 MGI:2155575 NCBI chr14:73,350,358...73,357,064
Ensembl chr14:73,349,965...73,360,618
JBrowse link
G NOG noggin IEA Ensembl GO_REF:0000107 NCBI chr12:32,891,321...32,892,206
Ensembl chr12:32,891,321...32,892,206
JBrowse link
G NR4A3 nuclear receptor subfamily 4 group A member 3 IEA Ensembl GO_REF:0000107 NCBI chr 1:241,569,867...241,611,735
Ensembl chr 1:241,569,905...241,611,734
JBrowse link
G POFUT2 protein O-fucosyltransferase 2 IEA Ensembl GO_REF:0000107 NCBI chr13:207,801,101...207,818,138 JBrowse link
G PRKACA protein kinase cAMP-activated catalytic subunit alpha IEA Ensembl GO_REF:0000107 NCBI chr 2:65,074,876...65,095,564
Ensembl chr 2:65,074,870...65,095,553
JBrowse link
G PRKAR1A protein kinase cAMP-dependent type I regulatory subunit alpha IEA Ensembl GO_REF:0000107 NCBI chr12:11,662,344...11,681,490
Ensembl chr12:11,662,347...11,681,202
JBrowse link
G SCX scleraxis bHLH transcription factor ISO (MGI:1343990|PMID:10477299) UniProt PMID:10477299 MGI:1343990 NCBI chr 4:500,884...503,276
Ensembl chr 4:501,172...502,994
JBrowse link
G SMAD2 SMAD family member 2 IEA Ensembl GO_REF:0000107 NCBI chr 1:97,415,360...97,511,388
Ensembl chr 1:97,415,716...97,511,358
JBrowse link
G SMAD3 SMAD family member 3 IEA Ensembl GO_REF:0000107 NCBI chr 1:164,998,457...165,124,455
Ensembl chr 1:164,998,083...165,124,454
JBrowse link
G SNAI1 snail family transcriptional repressor 1 IEA Ensembl GO_REF:0000107 NCBI chr17:51,546,446...51,552,498
Ensembl chr17:51,546,393...51,552,504
JBrowse link
G SRF serum response factor IEA Ensembl GO_REF:0000107 NCBI chr 7:38,213,300...38,223,686
Ensembl chr 7:38,213,063...38,222,140
JBrowse link
G TBX19 T-box transcription factor 19 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 4:82,663,121...82,699,261
Ensembl chr 4:82,663,581...82,697,813
JBrowse link
G TBX6 T-box transcription factor 6 IEA Ensembl GO_REF:0000107 NCBI chr 3:18,271,983...18,277,864
Ensembl chr 3:18,271,984...18,277,573
JBrowse link
G TBXT T-box transcription factor T IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 1:2,717,165...2,725,561
Ensembl chr 1:2,717,165...2,724,976
JBrowse link
G TGFB2 transforming growth factor beta 2 TAS (PMID:8133057) UniProt PMID:8133057 NCBI chr10:8,306,136...8,435,307
Ensembl chr10:8,305,424...8,405,771
JBrowse link
G TLX2 T cell leukemia homeobox 2 IEA Ensembl GO_REF:0000107 NCBI chr 3:68,532,111...68,537,385
Ensembl chr 3:68,532,963...68,534,344
JBrowse link
G TWSG1 twisted gastrulation BMP signaling modulator 1 IEA Ensembl GO_REF:0000107 NCBI chr 6:98,629,116...98,678,322
Ensembl chr 6:98,623,439...98,678,258
JBrowse link
G TXNRD1 thioredoxin reductase 1 IEA Ensembl GO_REF:0000107 NCBI chr 5:80,170,334...80,213,889
Ensembl chr 5:80,168,523...80,288,075
JBrowse link
G WLS Wnt ligand secretion mediator IEA Ensembl GO_REF:0000107 NCBI chr 6:144,242,639...144,529,659
Ensembl chr 6:144,242,656...144,555,880
JBrowse link
G WNT3 Wnt family member 3 IEA Ensembl GO_REF:0000107 NCBI chr12:17,627,291...17,681,197
Ensembl chr12:17,628,726...17,681,572
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 IEA Ensembl GO_REF:0000107 NCBI chr15:31,159,214...31,295,891
Ensembl chr15:31,159,217...31,295,896
JBrowse link
G TBXT T-box transcription factor T IEA Ensembl GO_REF:0000107 NCBI chr 1:2,717,165...2,725,561
Ensembl chr 1:2,717,165...2,724,976
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 chr 1:183,415,989...183,422,888
Ensembl chr 1:183,416,134...183,792,417
JBrowse link
G FGFR2 fibroblast growth factor receptor 2 ISO RGD PMID:7803853 RGD:632663 NCBI chr14:131,183,095...131,285,001
Ensembl chr14:131,181,710...131,579,703
JBrowse link
G HMGA2 high mobility group AT-hook 2 ISO (PMID:17624332) UniProtKB PMID:17624332 NCBI chr 5:30,188,521...30,329,635 JBrowse link
G INHBA inhibin subunit beta A IEA Ensembl GO_REF:0000107 NCBI chr12:53,115,379...53,117,128
NCBI chr18:52,889,684...52,909,260
Ensembl chr18:52,889,684...52,900,967
JBrowse link
G ITGA2 integrin subunit alpha 2 IEA Ensembl GO_REF:0000107 NCBI chr16:32,336,240...32,440,311
Ensembl chr16:32,336,292...32,437,103
JBrowse link
G ITGA3 integrin subunit alpha 3 IEA Ensembl GO_REF:0000107 NCBI chr12:26,234,769...26,269,327
Ensembl chr12:26,234,753...26,271,561
JBrowse link
G ITGA8 integrin subunit alpha 8 IEA Ensembl GO_REF:0000107 NCBI chr10:46,132,887...46,303,659
Ensembl chr10:46,132,914...46,303,365
JBrowse link
G ITGB1 integrin subunit beta 1 IEA Ensembl GO_REF:0000107 NCBI chr10:56,078,393...56,130,608
Ensembl chr10:56,078,398...56,173,795
JBrowse link
G ITGB3 integrin subunit beta 3 ISO (PMID:23154389) UniProtKB PMID:23154389 NCBI chr12:16,694,466...16,752,228
Ensembl chr12:16,693,505...16,752,292
JBrowse link
G ITGB4 integrin subunit beta 4 IEA Ensembl GO_REF:0000107 NCBI chr12:5,651,292...5,685,601
Ensembl chr12:5,651,292...5,685,611
JBrowse link
G KDM6A lysine demethylase 6A ISO (MGI:5448135|PMID:22949634) MGI PMID:22949634 MGI:5448135 NCBI chr  X:39,953,764...40,154,197
Ensembl chr  X:39,953,759...40,154,194
JBrowse link
G KDM6B lysine demethylase 6B IEA Ensembl GO_REF:0000107 NCBI chr12:53,087,072...53,108,949
Ensembl chr12:53,091,334...53,108,214
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 IEA Ensembl GO_REF:0000107 NCBI chr 5:62,931,642...62,939,086
Ensembl chr 5:62,932,382...62,939,082
JBrowse link
G POU5F1 POU class 5 homeobox 1 IEA Ensembl GO_REF:0000107 NCBI chr 7:23,564,654...23,570,691 JBrowse link
G SMAD1 SMAD family member 1 IEA Ensembl GO_REF:0000107 NCBI chr 8:82,907,557...82,987,909
Ensembl chr 8:82,908,527...82,968,994
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 IEA Ensembl GO_REF:0000107 NCBI chr 1:183,415,989...183,422,888
Ensembl chr 1:183,416,134...183,792,417
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 IEA Ensembl GO_REF:0000107 NCBI chr 4:63,970,939...64,328,107
Ensembl chr 4:63,970,511...64,328,105
JBrowse link
G HOXA11 homeobox A11 IEA Ensembl GO_REF:0000107 NCBI chr18:45,388,523...45,392,190
Ensembl chr18:45,388,574...45,392,573
JBrowse link
G PAX2 paired box 2 ISO (MGI:3768605|PMID:17785448) UniProt PMID:17785448 MGI:3768605 NCBI chr14:111,822,334...111,914,950
Ensembl chr14:111,834,168...111,914,304
JBrowse link
G SIX2 SIX homeobox 2 IEA Ensembl GO_REF:0000107 NCBI chr 3:95,460,046...95,463,428
Ensembl chr 3:95,459,937...95,464,066
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 IEA Ensembl GO_REF:0000107 NCBI chr15:105,644,164...105,648,860
Ensembl chr15:105,644,188...105,648,854
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 IEA Ensembl GO_REF:0000107 NCBI chr 1:273,934,219...274,083,264
Ensembl chr 1:273,971,971...274,085,426
JBrowse link
G COL5A2 collagen type V alpha 2 chain IEA Ensembl GO_REF:0000107 NCBI chr15:93,611,856...93,981,131
Ensembl chr15:93,611,856...93,981,110
JBrowse link
negative regulation of endodermal cell fate specification term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G MESP1 mesoderm posterior bHLH transcription factor 1 IEA Ensembl GO_REF:0000107 NCBI chr 7:55,322,016...55,327,600
Ensembl chr 7:55,322,010...55,325,732
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 IEA Ensembl GO_REF:0000107 NCBI chr14:97,487,854...97,490,118
Ensembl chr14:97,487,226...97,490,450
JBrowse link
G MESP1 mesoderm posterior bHLH transcription factor 1 IEA Ensembl GO_REF:0000107 NCBI chr 7:55,322,016...55,327,600
Ensembl chr 7:55,322,010...55,325,732
JBrowse link
G SFRP2 secreted frizzled related protein 2 IEA Ensembl GO_REF:0000107 NCBI chr 8:75,337,311...75,345,926
Ensembl chr 8:75,337,133...75,345,926
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 IEA Ensembl GO_REF:0000107 NCBI chr18:15,105,152...15,906,734
Ensembl chr18:15,105,138...15,906,707
JBrowse link
G FOXC1 forkhead box C1 IEA Ensembl GO_REF:0000107 NCBI chr 7:837,088...840,593
Ensembl chr 7:837,171...838,805
JBrowse link
G FOXC2 forkhead box C2 ISO (MGI:2150572|PMID:11562355) MGI PMID:11562355 MGI:2150572 NCBI chr 6:2,552,141...2,555,041
Ensembl chr 6:2,552,862...2,554,367
JBrowse link
G HNF1A HNF1 homeobox A IEA Ensembl GO_REF:0000107 NCBI chr14:40,868,819...40,888,322
Ensembl chr14:40,868,676...40,888,328
JBrowse link
G HTT huntingtin ISO (MGI:3609520|PMID:16109169) MGI PMID:16109169 MGI:3609520 NCBI chr 8:1,809,768...1,934,002
Ensembl chr 8:1,809,785...1,934,024
JBrowse link
G LEF1 lymphoid enhancer binding factor 1 IEA Ensembl GO_REF:0000107 NCBI chr 8:113,824,511...113,944,078
Ensembl chr 8:113,824,547...113,944,078
JBrowse link
G WNT11 Wnt family member 11 IEA Ensembl GO_REF:0000107 NCBI chr 9:10,413,182...10,435,158
Ensembl chr 9:10,413,187...10,435,100
JBrowse link
G WNT5A Wnt family member 5A IEA Ensembl GO_REF:0000107 NCBI chr13:37,344,684...37,367,215
Ensembl chr13:37,344,699...37,367,207
JBrowse link
paraxial mesodermal cell fate commitment term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G FOXC2 forkhead box C2 IEA Ensembl GO_REF:0000107 NCBI chr 6:2,552,141...2,555,041
Ensembl chr 6:2,552,862...2,554,367
JBrowse link
G WNT3A Wnt family member 3A IEA Ensembl GO_REF:0000107 NCBI chr 2:51,153,978...51,203,678
Ensembl chr 2:51,154,086...51,202,176
JBrowse link
positive regulation of endodermal cell differentiation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G H2AFY H2A histone family, member Y IEA Ensembl GO_REF:0000107 NCBI chr 2:137,535,128...137,623,886
Ensembl chr 2:137,535,131...137,623,889
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 IEA Ensembl GO_REF:0000107 NCBI chr 1:40,988,818...41,002,129
Ensembl chr 1:40,988,515...41,002,137
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 IEA Ensembl GO_REF:0000107 NCBI chr 2:51,153,978...51,203,678
Ensembl chr 2:51,154,086...51,202,176
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 IEA Ensembl GO_REF:0000107 NCBI chr14:97,487,854...97,490,118
Ensembl chr14:97,487,226...97,490,450
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 IEA Ensembl GO_REF:0000107 NCBI chr14:87,743,270...87,891,790
Ensembl chr14:87,742,459...87,891,793
JBrowse link
G FGFR1 fibroblast growth factor receptor 1 IEA Ensembl GO_REF:0000107 NCBI chr15:48,053,895...48,106,634
Ensembl chr15:48,053,340...48,106,746
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 16548
    developmental process 6302
      anatomical structure formation involved in morphogenesis 1185
        formation of primary germ layer 128
          cell fate commitment involved in formation of primary germ layer + 31
          ectoderm formation + 6
          endoderm formation + 56
          mesoderm formation + 75
Path 2
Term Annotations click to browse term
  biological_process 16548
    developmental process 6302
      anatomical structure development 5842
        multicellular organism development 5340
          embryo development 1254
            embryonic morphogenesis 665
              gastrulation 193
                formation of primary germ layer 128
                  cell fate commitment involved in formation of primary germ layer + 31
                  ectoderm formation + 6
                  endoderm formation + 56
                  mesoderm formation + 75
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.