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ONTOLOGY REPORT - ANNOTATIONS


Term:midbrain development
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Accession:GO:0030901 term browser browse the term
Definition:The process whose specific outcome is the progression of the midbrain over time, from its formation to the mature structure. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles).
Synonyms:exact_synonym: mesencephalon development


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midbrain development term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Acvr1c activin A receptor type 1C JBrowse link 3 44,272,859 44,342,501 RGD:631880
G Aplp2 amyloid beta precursor like protein 2 JBrowse link 8 32,298,526 32,328,821 RGD:1624291
G Barhl1 BarH-like homeobox 1 JBrowse link 3 7,491,234 7,498,555 RGD:1624291
G Cma1 chymase 1 JBrowse link 15 34,601,037 34,603,819 RGD:5128663
G Ctnnb1 catenin beta 1 JBrowse link 8 129,601,511 129,628,378 RGD:1624291
G Cxcl6 C-X-C motif chemokine ligand 6 JBrowse link 14 18,860,201 18,920,839 RGD:4892032
G Cxcr2 C-X-C motif chemokine receptor 2 JBrowse link 9 81,427,275 81,435,065 RGD:4892032
G Dlg5 discs large MAGUK scaffold protein 5 JBrowse link 15 120,213 230,312 RGD:1624291
G En1 engrailed homeobox 1 JBrowse link 13 36,532,758 36,537,888 RGD:1624291
RGD:1600115
G En2 engrailed homeobox 2 JBrowse link 4 438,668 444,508 RGD:1624291
G Fgfr1 Fibroblast growth factor receptor 1 JBrowse link 16 71,265,390 71,319,046 RGD:1624291
RGD:1600115
G Fgfr2 fibroblast growth factor receptor 2 JBrowse link 1 200,590,951 200,696,946 RGD:1624291
G Foxb1 forkhead box B1 JBrowse link 8 75,992,751 75,995,371 RGD:1624291
RGD:1600115
G Fzd3 frizzled class receptor 3 JBrowse link 15 48,601,259 48,670,257 RGD:1624291
G Fzd6 frizzled class receptor 6 JBrowse link 7 77,898,329 77,931,034 RGD:1624291
G Gdf7 growth differentiation factor 7 JBrowse link 6 33,496,596 33,507,626 RGD:1624291
G Gdnf glial cell derived neurotrophic factor JBrowse link 2 56,884,181 56,912,964 RGD:2324945
G Hes1 hes family bHLH transcription factor 1 JBrowse link 11 74,312,837 74,315,249 RGD:1624291
RGD:1600115
G Hes3 hes family bHLH transcription factor 3 JBrowse link 5 169,463,196 169,469,795 RGD:1624291
G Kat2a lysine acetyltransferase 2A JBrowse link 10 88,611,586 88,619,558 RGD:1624291
G Kdm2b lysine demethylase 2B JBrowse link 12 39,021,924 39,161,954 RGD:1624291
G Lmx1a LIM homeobox transcription factor 1 alpha JBrowse link 13 85,916,753 86,061,534 RGD:1624291
G Lmx1b LIM homeobox transcription factor 1 beta JBrowse link 3 12,608,748 12,686,937 RGD:1624291
G Lrp6 LDL receptor related protein 6 JBrowse link 4 168,194,054 168,323,962 RGD:1624291
RGD:13792537
G Msx1 msh homeobox 1 JBrowse link 14 77,712,262 77,716,061 RGD:1624291
G Ndst1 N-deacetylase and N-sulfotransferase 1 JBrowse link 18 55,951,497 56,014,107 RGD:1624291
G Otx1 orthodenticle homeobox 1 JBrowse link 14 106,861,556 106,864,933 RGD:1624291
RGD:1600115
G Otx2 orthodenticle homeobox 2 JBrowse link 15 25,500,037 25,511,619 RGD:1624291
G Phox2a paired-like homeobox 2a JBrowse link 1 166,893,734 166,898,252 RGD:1624291
RGD:1600115
G Pitx3 paired-like homeodomain 3 JBrowse link 1 265,886,766 265,899,947 RGD:1600115
RGD:1624291
G Rfx4 regulatory factor X4 JBrowse link 7 25,831,358 25,909,976 RGD:1624291
G Shh sonic hedgehog signaling molecule JBrowse link 4 718,538 727,691 RGD:1624291
RGD:1600115
G Smad1 SMAD family member 1 JBrowse link 19 32,182,942 32,248,694 RGD:1624291
RGD:1600115
G Smad9 SMAD family member 9 JBrowse link 2 143,951,725 144,002,025 RGD:1624291
G Taf1 TATA-box binding protein associated factor 1 JBrowse link X 71,412,291 71,486,456 RGD:1624291
G Tal2 TAL bHLH transcription factor 2 JBrowse link 5 70,592,871 70,599,428 RGD:1624291
G Uchl5 ubiquitin C-terminal hydrolase L5 JBrowse link 13 60,568,102 60,603,812 RGD:1624291
G Uqcrq ubiquinol-cytochrome c reductase, complex III subunit VII JBrowse link 10 38,779,132 38,782,489 RGD:1624291
G Wls Wnt ligand secretion mediator JBrowse link 2 266,315,036 266,431,220 RGD:1624291
G Wnt1 Wnt family member 1 JBrowse link 7 140,464,999 140,469,046 RGD:1624291
G Wnt3a Wnt family member 3A JBrowse link 10 45,598,898 45,643,151 RGD:1624291
G Wnt5a Wnt family member 5A JBrowse link 16 4,469,451 4,490,271 RGD:1624291
canonical Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Wnt1 Wnt family member 1 JBrowse link 7 140,464,999 140,469,046 RGD:1624291
G Wnt2 Wnt family member 2 JBrowse link 4 45,286,845 45,332,899 RGD:1624291
G Wnt3 Wnt family member 3 JBrowse link 10 91,830,709 91,874,907 RGD:1624291
cell proliferation in midbrain term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Fzd3 frizzled class receptor 3 JBrowse link 15 48,601,259 48,670,257 RGD:1624291
G Fzd6 frizzled class receptor 6 JBrowse link 7 77,898,329 77,931,034 RGD:1624291
G Wnt1 Wnt family member 1 JBrowse link 7 140,464,999 140,469,046 RGD:1624291
G Wnt2 Wnt family member 2 JBrowse link 4 45,286,845 45,332,899 RGD:1624291
G Wnt3a Wnt family member 3A JBrowse link 10 45,598,898 45,643,151 RGD:1624291
inferior colliculus development term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Foxb1 forkhead box B1 JBrowse link 8 75,992,751 75,995,371 RGD:1624291
RGD:1600115
G Tfap2d transcription factor AP-2 delta JBrowse link 9 25,304,876 25,365,151 RGD:1624291
midbrain dopaminergic neuron differentiation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Ctnnb1 catenin beta 1 JBrowse link 8 129,601,511 129,628,378 RGD:1624291
RGD:1600115
G Lmx1a LIM homeobox transcription factor 1 alpha JBrowse link 13 85,916,753 86,061,534 RGD:1624291
G Rac1 Rac family small GTPase 1 JBrowse link 12 13,090,316 13,111,841 RGD:1624291
G Ryk receptor-like tyrosine kinase JBrowse link 8 111,326,339 111,398,640 RGD:1624291
G Wnt1 Wnt family member 1 JBrowse link 7 140,464,999 140,469,046 RGD:1624291
G Wnt2 Wnt family member 2 JBrowse link 4 45,286,845 45,332,899 RGD:1624291
G Wnt5a Wnt family member 5A JBrowse link 16 4,469,451 4,490,271 RGD:1624291
G Wnt9b Wnt family member 9B JBrowse link 10 91,785,892 91,808,061 RGD:1624291
midbrain morphogenesis term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Sos1 SOS Ras/Rac guanine nucleotide exchange factor 1 JBrowse link 6 3,105,443 3,182,977 RGD:1624291
negative regulation of cell proliferation in midbrain term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Wnt5a Wnt family member 5A JBrowse link 16 4,469,451 4,490,271 RGD:1624291
RGD:1600115
non-canonical Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Wnt9b Wnt family member 9B JBrowse link 10 91,785,892 91,808,061 RGD:1624291
positive regulation of cell proliferation in midbrain term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Pitx3 paired-like homeodomain 3 JBrowse link 1 265,886,766 265,899,947 RGD:11535083
positive regulation of midbrain dopaminergic neuron differentiation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Dkk1 dickkopf WNT signaling pathway inhibitor 1 JBrowse link 1 248,952,896 248,956,579 RGD:1624291
positive regulation of Wnt-mediated midbrain dopaminergic neuron differentiation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Csnk1e casein kinase 1, epsilon JBrowse link 7 120,651,976 120,675,559 RGD:10448953
regulation of midbrain dopaminergic neuron differentiation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Sfrp1 secreted frizzled-related protein 1 JBrowse link 16 73,372,007 73,410,777 RGD:1624291
RGD:1600115
G Sfrp2 secreted frizzled-related protein 2 JBrowse link 2 182,723,732 182,731,277 RGD:1624291
substantia nigra development term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Actb actin, beta JBrowse link 12 13,715,843 13,718,813 RGD:9068941
G Atp5pb ATP synthase peripheral stalk-membrane subunit b JBrowse link 2 208,566,385 208,577,147 RGD:9068941
G Atp5pf ATP synthase peripheral stalk subunit F6 JBrowse link 11 24,286,806 24,294,419 RGD:9068941
G Basp1 brain abundant, membrane attached signal protein 1 JBrowse link 2 77,586,424 77,632,626 RGD:9068941
G Calm1 calmodulin 1 JBrowse link 6 124,217,241 124,225,292 RGD:9068941
G Calm2 calmodulin 2 JBrowse link 6 11,067,675 11,080,078 RGD:9068941
G Calm3 calmodulin 3 JBrowse link 1 78,844,520 78,851,628 RGD:9068941
G Ccdc14 coiled-coil domain containing 14 JBrowse link 11 69,281,000 69,316,897 RGD:9068941
G Cdc42 cell division cycle 42 JBrowse link 5 155,690,267 155,728,385 RGD:9068941
G Ckb creatine kinase B JBrowse link 6 136,142,956 136,145,838 RGD:9068941
G Cnp 2',3'-cyclic nucleotide 3' phosphodiesterase JBrowse link 10 88,490,798 88,497,357 RGD:9068941
G Cox6b1 cytochrome c oxidase subunit 6B1 JBrowse link 1 89,075,987 89,084,834 RGD:9068941
G Dynll1 dynein light chain LC8-type 1 JBrowse link 12 47,074,200 47,076,573 RGD:9068941
G Eno3 enolase 3 JBrowse link 10 57,278,271 57,283,661 RGD:9068941
G Fgf2 fibroblast growth factor 2 JBrowse link 2 124,081,072 124,134,133 RGD:1624291
G Fgf9 fibroblast growth factor 9 JBrowse link 15 38,341,657 38,386,945 RGD:9068941
G Fgfr3 fibroblast growth factor receptor 3 JBrowse link 14 82,272,322 82,287,739 RGD:1624291
G G6pd glucose-6-phosphate dehydrogenase JBrowse link X 156,274,800 156,293,935 RGD:9068941
G Glud1 glutamate dehydrogenase 1 JBrowse link 16 10,661,486 10,695,557 RGD:9068941
G Gnb4 G protein subunit beta 4 JBrowse link 2 118,978,965 119,007,877 RGD:9068941
G Hspa5 heat shock protein family A (Hsp70) member 5 JBrowse link 3 13,838,304 13,842,763 RGD:9068941
G Ina internexin neuronal intermediate filament protein, alpha JBrowse link 1 266,782,835 266,794,389 RGD:9068941
G Ldha lactate dehydrogenase A JBrowse link 1 102,900,288 102,909,713 RGD:9068941
G LOC100361457 actin, gamma 1 propeptide-like JBrowse link 3 75,643,053 75,644,978 RGD:9068941
G Mag myelin-associated glycoprotein JBrowse link 1 89,345,325 89,360,905 RGD:9068941
G Maob monoamine oxidase B JBrowse link X 6,430,694 6,533,520 RGD:9068941
G Mapkap1 MAPK associated protein 1 JBrowse link 3 13,484,952 13,701,772 RGD:9068941
G Mbp myelin basic protein JBrowse link 18 79,326,738 79,437,310 RGD:9068941
G Ndrg2 NDRG family member 2 JBrowse link 15 28,305,820 28,314,459 RGD:9068941
G Ndufs3 NADH:ubiquinone oxidoreductase core subunit S3 JBrowse link 3 79,721,686 79,728,863 RGD:9068941
G Padi2 peptidyl arginine deiminase 2 JBrowse link 5 159,428,479 159,471,113 RGD:9068941
G Plp1 proteolipid protein 1 JBrowse link X 107,494,326 107,511,355 RGD:9068941
G Rad1 RAD1 checkpoint DNA exonuclease JBrowse link 2 60,461,513 60,469,646 RGD:9068941
G Rhoa ras homolog family member A JBrowse link 8 117,082,440 117,116,244 RGD:9068941
G S100a1 S100 calcium binding protein A1 JBrowse link 2 189,900,505 189,905,348 RGD:9068941
G Sec16a SEC16 homolog A, endoplasmic reticulum export factor JBrowse link 3 3,856,218 3,890,785 RGD:9068941
G Sirt2 sirtuin 2 JBrowse link 1 86,948,866 86,971,954 RGD:9068941
G Suds3 SDS3 homolog, SIN3A corepressor complex component JBrowse link 12 45,199,012 45,221,507 RGD:9068941
G Syngr3 synaptogyrin 3 JBrowse link 10 14,051,413 14,056,169 RGD:9068941
G Sypl2 synaptophysin-like 2 JBrowse link 2 211,003,046 211,017,778 RGD:9068941
G Ttbk1 tau tubulin kinase 1 JBrowse link 9 16,862,305 16,899,399 RGD:9068941
G Ywhae tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon JBrowse link 10 63,884,338 63,921,709 RGD:9068941
G Ywhah tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta JBrowse link 14 83,053,041 83,062,424 RGD:9068941
G Ywhaq tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta JBrowse link 6 43,463,294 43,493,816 RGD:9068941
G Zfp148 zinc finger protein 148 JBrowse link 11 70,509,909 70,618,422 RGD:9068941
Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Wnt5a Wnt family member 5A JBrowse link 16 4,469,451 4,490,271 RGD:1600115
RGD:1624291

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 19858
    developmental process 6734
      anatomical structure development 6180
        midbrain development 98
          cell proliferation in midbrain + 7
          corpora quadrigemina development + 2
          midbrain dopaminergic neuron differentiation + 13
          midbrain morphogenesis 1
          substantia nigra development 45
          ventral tegmental area development 0
Path 2
Term Annotations click to browse term
  biological_process 19858
    developmental process 6734
      anatomical structure development 6180
        multicellular organism development 5638
          system development 5213
            nervous system development 2702
              central nervous system development 1251
                brain development 963
                  midbrain development 98
                    cell proliferation in midbrain + 7
                    corpora quadrigemina development + 2
                    midbrain dopaminergic neuron differentiation + 13
                    midbrain morphogenesis 1
                    substantia nigra development 45
                    ventral tegmental area development 0
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.