RARGA_DANRE
ID RARGA_DANRE Reviewed; 499 AA.
AC Q91392; A2BGD3; O42552; Q4KMK9; Q90273;
DT 15-JUL-1999, integrated into UniProtKB/Swiss-Prot.
DT 28-NOV-2006, sequence version 2.
DT 03-AUG-2022, entry version 170.
DE RecName: Full=Retinoic acid receptor gamma-A;
DE Short=RAR-gamma-A;
DE Short=zRAR gamma;
DE AltName: Full=Nuclear receptor subfamily 1 group B member 3-A;
DE AltName: Full=RAR-gamma-2;
GN Name=rarga; Synonyms=nr1b3a, rarg, rarg2; ORFNames=si:dkey-148f24.2;
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, AND
RP INDUCTION.
RC TISSUE=Embryo;
RX PubMed=7918098; DOI=10.1016/0925-4773(94)90082-5;
RA Joore J., van der Lans G.B.L.J., Lanser P.H., Vervaart J.M.A., Zivkovic D.,
RA Speksnijder J.E., Kruijer W.;
RT "Effects of retinoic acid on the expression of retinoic acid receptors
RT during zebrafish embryogenesis.";
RL Mech. Dev. 46:137-150(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen;
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=AB; TISSUE=Embryo;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 1-367, AND POSSIBLE FUNCTION.
RC TISSUE=Gastrula;
RA Stachel S.E., Kushner P.;
RT "The molecular characterization of three zebrafish retinoic acid receptor
RT genes suggests the retinoic acid pathway functions in embryonic hindbrain
RT development.";
RL Submitted (DEC-1992) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 113-146.
RX PubMed=9192646; DOI=10.1073/pnas.94.13.6803;
RA Escriva H., Safi R., Haenni C., Langlois M.-C., Saumitou-Laprade P.,
RA Stehelin D., Capron A., Pierce R., Laudet V.;
RT "Ligand binding was acquired during evolution of nuclear receptors.";
RL Proc. Natl. Acad. Sci. U.S.A. 94:6803-6808(1997).
RN [6]
RP HETERODIMERIZATION, AND DNA-BINDING.
RX PubMed=7565671; DOI=10.1128/mcb.15.10.5226;
RA Jones B.B., Ohno C.K., Allenby G., Boffa M.B., Levin A.A., Grippo J.F.,
RA Petkovich M.;
RT "New retinoid X receptor subtypes in zebra fish (Danio rerio)
RT differentially modulate transcription and do not bind 9-cis retinoic
RT acid.";
RL Mol. Cell. Biol. 15:5226-5234(1995).
RN [7]
RP DEVELOPMENTAL STAGE.
RX PubMed=16455309; DOI=10.1016/j.modgep.2005.10.007;
RA Hale L.A., Tallafuss A., Yan Y.-L., Dudley L., Eisen J.S.,
RA Postlethwait J.H.;
RT "Characterization of the retinoic acid receptor genes raraa, rarab and rarg
RT during zebrafish development.";
RL Gene Expr. Patterns 6:546-555(2006).
RN [8]
RP DEVELOPMENTAL STAGE.
RX PubMed=17195188; DOI=10.1002/dvdy.21049;
RA Waxman J.S., Yelon D.;
RT "Comparison of the expression patterns of newly identified zebrafish
RT retinoic acid and retinoid X receptors.";
RL Dev. Dyn. 236:587-595(2007).
RN [9]
RP DEVELOPMENTAL STAGE, INDUCTION, AND FUNCTION.
RX PubMed=18929555; DOI=10.1016/j.ydbio.2008.09.022;
RA Linville A., Radtke K., Waxman J.S., Yelon D., Schilling T.F.;
RT "Combinatorial roles for zebrafish retinoic acid receptors in the
RT hindbrain, limbs and pharyngeal arches.";
RL Dev. Biol. 325:60-70(2009).
CC -!- FUNCTION: Receptor for retinoic acid. Retinoic acid receptors bind as
CC heterodimers to their target response elements in response to their
CC ligands, all-trans or 9-cis retinoic acid, and regulate gene expression
CC in various biological processes. The rar/rxr heterodimers bind to the
CC retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3'
CC sites known as DR1-DR5 (By similarity). Required for hindbrain
CC development and for the development of pharyngeal arches. {ECO:0000250,
CC ECO:0000269|PubMed:18929555}.
CC -!- SUBUNIT: Heterodimer; with an rxr molecule. Binds DNA preferentially as
CC a rar/rxr heterodimer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00407}.
CC -!- DEVELOPMENTAL STAGE: Expressed zygotically, with greatest expression at
CC 24 hours post-fertilization (hpf). At 9 hpf, shows ubiquitous
CC expression in the epiblast. At 10 hpf, expressed in anterior and
CC posterior regions; not expressed in the presumptive hindbrain, and
CC anterior expression is limited to mesoderm adjacent to the head.
CC Between 11-15 hpf restricted expression in the cranial mesoderm and
CC tailbud. At 12 hpf, expressed in anterior lateral mesenchyme, with
CC strongest expression lateral to the future hindbrain, and in tailbud.
CC At 24 hpf, also expressed in the hindbrain, neural crest cells and
CC tail; not detected in spinal cord. At 48 hpf, hindbrain expression
CC increases with an anterior border at rhombomere 3 and a posterior
CC border at the spinal cord/hindbrain junction; expressed in stripes one
CC rhombomere wide in dorsal hindbrain. At 48 hpf, also expressed in
CC pharangeal arches 1-7, anterior neurocranium, cells separating the eyes
CC and forebrain, pectoral fin buds and tailbud. Embryonic zygotic
CC expression overlaps that of raraa and rarab, but there is stronger
CC expression in the posterior hindbrain beginning in late somitogenesis,
CC and in neural crest cells in the pharangeal arches. In the adult,
CC strongly expressed in the ovary, brain and muscle, and weakly expressed
CC in the liver and digestive tract. {ECO:0000269|PubMed:16455309,
CC ECO:0000269|PubMed:17195188, ECO:0000269|PubMed:18929555,
CC ECO:0000269|PubMed:7918098}.
CC -!- INDUCTION: By retinoic acid, in embryonic anterior brain and eye.
CC {ECO:0000269|PubMed:18929555, ECO:0000269|PubMed:7918098}.
CC -!- DOMAIN: Composed of three domains: a modulating N-terminal domain, a
CC DNA-binding domain and a C-terminal ligand-binding domain.
CC -!- SIMILARITY: Belongs to the nuclear hormone receptor family. NR1
CC subfamily. {ECO:0000305}.
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DR EMBL; S74156; AAB32277.1; -; mRNA.
DR EMBL; BX465864; CAM14485.1; -; Genomic_DNA.
DR EMBL; BX546466; CAM14485.1; JOINED; Genomic_DNA.
DR EMBL; BX546466; CAM16092.1; -; Genomic_DNA.
DR EMBL; BX465864; CAM16092.1; JOINED; Genomic_DNA.
DR EMBL; BC098519; AAH98519.1; -; mRNA.
DR EMBL; L03400; AAB59953.1; -; mRNA.
DR EMBL; U93479; AAB68756.1; -; Genomic_DNA.
DR PIR; I51257; I51257.
DR RefSeq; NP_571414.1; NM_131339.1.
DR AlphaFoldDB; Q91392; -.
DR SMR; Q91392; -.
DR STRING; 7955.ENSDARP00000093932; -.
DR PaxDb; Q91392; -.
DR Ensembl; ENSDART00000049551; ENSDARP00000049550; ENSDARG00000034117.
DR GeneID; 30606; -.
DR KEGG; dre:30606; -.
DR CTD; 30606; -.
DR ZFIN; ZDB-GENE-980526-531; rarga.
DR eggNOG; KOG3575; Eukaryota.
DR GeneTree; ENSGT00940000156458; -.
DR HOGENOM; CLU_007368_18_2_1; -.
DR InParanoid; Q91392; -.
DR OMA; TVSPFCA; -.
DR OrthoDB; 1165737at2759; -.
DR PhylomeDB; Q91392; -.
DR TreeFam; TF328382; -.
DR Reactome; R-DRE-383280; Nuclear Receptor transcription pathway.
DR Reactome; R-DRE-5362517; Signaling by Retinoic Acid.
DR SignaLink; Q91392; -.
DR PRO; PR:Q91392; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 23.
DR Bgee; ENSDARG00000034117; Expressed in zone of skin and 43 other tissues.
DR ExpressionAtlas; Q91392; baseline and differential.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IDA:UniProtKB.
DR GO; GO:0004879; F:nuclear receptor activity; IBA:GO_Central.
DR GO; GO:0000978; F:RNA polymerase II cis-regulatory region sequence-specific DNA binding; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0030154; P:cell differentiation; IBA:GO_Central.
DR GO; GO:0009755; P:hormone-mediated signaling pathway; IBA:GO_Central.
DR GO; GO:0001889; P:liver development; IMP:ZFIN.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0060037; P:pharyngeal system development; IDA:UniProtKB.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0048384; P:retinoic acid receptor signaling pathway; IBA:GO_Central.
DR Gene3D; 1.10.565.10; -; 1.
DR Gene3D; 3.30.50.10; -; 1.
DR InterPro; IPR035500; NHR-like_dom_sf.
DR InterPro; IPR000536; Nucl_hrmn_rcpt_lig-bd.
DR InterPro; IPR001723; Nuclear_hrmn_rcpt.
DR InterPro; IPR003078; Retinoic_acid_rcpt.
DR InterPro; IPR001628; Znf_hrmn_rcpt.
DR InterPro; IPR013088; Znf_NHR/GATA.
DR Pfam; PF00104; Hormone_recep; 1.
DR Pfam; PF00105; zf-C4; 1.
DR PRINTS; PR01292; RETNOICACIDR.
DR PRINTS; PR00398; STRDHORMONER.
DR PRINTS; PR00047; STROIDFINGER.
DR SMART; SM00430; HOLI; 1.
DR SMART; SM00399; ZnF_C4; 1.
DR SUPFAM; SSF48508; SSF48508; 1.
DR PROSITE; PS51843; NR_LBD; 1.
DR PROSITE; PS00031; NUCLEAR_REC_DBD_1; 1.
DR PROSITE; PS51030; NUCLEAR_REC_DBD_2; 1.
PE 1: Evidence at protein level;
KW DNA-binding; Metal-binding; Nucleus; Receptor; Reference proteome;
KW Transcription; Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..499
FT /note="Retinoic acid receptor gamma-A"
FT /id="PRO_0000053477"
FT DOMAIN 173..407
FT /note="NR LBD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01189"
FT DNA_BIND 77..142
FT /note="Nuclear receptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00407"
FT ZN_FING 77..97
FT /note="NR C4-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00407"
FT ZN_FING 113..137
FT /note="NR C4-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00407"
FT REGION 1..76
FT /note="Modulating"
FT REGION 51..70
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 143..172
FT /note="Hinge"
FT REGION 409..499
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 445..473
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 20
FT /note="N -> D (in Ref. 4; AAB59953)"
FT /evidence="ECO:0000305"
FT CONFLICT 116..118
FT /note="DKN -> EKS (in Ref. 5; AAB68756)"
FT /evidence="ECO:0000305"
FT CONFLICT 235
FT /note="R -> A (in Ref. 4; AAB59953)"
FT /evidence="ECO:0000305"
FT CONFLICT 366..367
FT /note="RM -> KI (in Ref. 4; AAB59953)"
FT /evidence="ECO:0000305"
FT CONFLICT 416
FT /note="S -> A (in Ref. 1; AAB32277)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 499 AA; 56195 MW; 00660607E4A45B28 CRC64;
MFDCMEALGM GPRQLYDVTN RGACMLRKAS PFYAGLDPFA WTGTASVRSV ETQSTSSEEM
VPSSPSPPPP PRVYKPCFVC QDKSSGYHYG VSSCEGCKGF FRRSIQKNMV YTCHRDKNCQ
INKVTRNRCQ YCRLQKCFEV GMSKEAVRND RNKKKKDVKD EVIPPESYEL SGELEELVNK
VSKAHQETFP SLCQLGKYTT NSSSDHRIQL DLGLWDKFSE LSTKCIIKIV EFAKRLPGFT
TLTIADQITL LKSACLDILM LRICTRYTPE QDTMTFSDGL TLNRTQMHNA GFGPLTDLVF
AFAGQLLPLE MDDTETGLLS AICLICGDRM DLEEPERVDR LQEPLLEALK IYARRRRPNK
PHMFPRMLMK ITDLRGISTK GAERAITLKM EIPGPMPPLI REMLENPEAF EDQSESTEKK
PEPEPPAPPP PALLTMKKEQ EDEDDSWATE NGSEPSPEEE DDDDEDGEEE RGTDSDGEAW
GGQEPNADVS RKSHGGRAQ
