Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Retinoic acid receptor gamma-A

Gene

rarga

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The rar/rxr heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5 (By similarity). Required for hindbrain development and for the development of pharyngeal arches.By similarity1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi77 – 142Nuclear receptorPROSITE-ProRule annotationAdd BLAST66
Zinc fingeri77 – 97NR C4-typePROSITE-ProRule annotationAdd BLAST21
Zinc fingeri113 – 137NR C4-typePROSITE-ProRule annotationAdd BLAST25

GO - Molecular functioni

GO - Biological processi

  • liver development Source: ZFIN
  • pharyngeal system development Source: UniProtKB
  • transcription, DNA-templated Source: UniProtKB-KW

Keywordsi

Molecular functionDNA-binding, Receptor
Biological processTranscription, Transcription regulation
LigandMetal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-DRE-383280 Nuclear Receptor transcription pathway
R-DRE-5362517 Signaling by Retinoic Acid

Names & Taxonomyi

Protein namesi
Recommended name:
Retinoic acid receptor gamma-A
Short name:
RAR-gamma-A
Short name:
zRAR gamma
Alternative name(s):
Nuclear receptor subfamily 1 group B member 3-A
RAR-gamma-2
Gene namesi
Name:rarga
Synonyms:nr1b3a, rarg, rarg2
ORF Names:si:dkey-148f24.2
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
Proteomesi
  • UP000000437 Componenti: Chromosome 23

Organism-specific databases

ZFINiZDB-GENE-980526-531 rarga

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000534771 – 499Retinoic acid receptor gamma-AAdd BLAST499

Proteomic databases

PaxDbiQ91392
PRIDEiQ91392

Expressioni

Developmental stagei

Expressed zygotically, with greatest expression at 24 hours post-fertilization (hpf). At 9 hpf, shows ubiquitous expression in the epiblast. At 10 hpf, expressed in anterior and posterior regions; not expressed in the presumptive hindbrain, and anterior expression is limited to mesoderm adjacent to the head. Between 11-15 hpf restricted expression in the cranial mesoderm and tailbud. At 12 hpf, expressed in anterior lateral mesenchyme, with strongest expression lateral to the future hindbrain, and in tailbud. At 24 hpf, also expressed in the hindbrain, neural crest cells and tail; not detected in spinal cord. At 48 hpf, hindbrain expression increases with an anterior border at rhombomere 3 and a posterior border at the spinal cord/hindbrain junction; expressed in stripes one rhombomere wide in dorsal hindbrain. At 48 hpf, also expressed in pharangeal arches 1-7, anterior neurocranium, cells separating the eyes and forebrain, pectoral fin buds and tailbud. Embryonic zygotic expression overlaps that of raraa and rarab, but there is stronger expression in the posterior hindbrain beginning in late somitogenesis, and in neural crest cells in the pharangeal arches. In the adult, strongly expressed in the ovary, brain and muscle, and weakly expressed in the liver and digestive tract.4 Publications

Inductioni

By retinoic acid, in embryonic anterior brain and eye.2 Publications

Gene expression databases

BgeeiENSDARG00000034117
ExpressionAtlasiQ91392 baseline

Interactioni

Subunit structurei

Heterodimer; with an rxr molecule. Binds DNA preferentially as a rar/rxr heterodimer.By similarity

Protein-protein interaction databases

STRINGi7955.ENSDARP00000093932

Structurei

3D structure databases

ProteinModelPortaliQ91392
SMRiQ91392
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini173 – 407NR LBDPROSITE-ProRule annotationAdd BLAST235

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 76ModulatingAdd BLAST76
Regioni143 – 172HingeAdd BLAST30

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi65 – 71Poly-Pro7
Compositional biasi153 – 156Poly-Lys4
Compositional biasi354 – 357Poly-Arg4
Compositional biasi421 – 431Poly-ProAdd BLAST11
Compositional biasi461 – 466Poly-Asp6

Domaini

Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain.

Sequence similaritiesi

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri77 – 97NR C4-typePROSITE-ProRule annotationAdd BLAST21
Zinc fingeri113 – 137NR C4-typePROSITE-ProRule annotationAdd BLAST25

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG3575 Eukaryota
ENOG410XRZC LUCA
GeneTreeiENSGT00870000136372
HOGENOMiHOG000010312
HOVERGENiHBG005606
InParanoidiQ91392
KOiK08529
OMAiTIACKIC
OrthoDBiEOG091G0XCQ
PhylomeDBiQ91392
TreeFamiTF328382

Family and domain databases

Gene3Di3.30.50.10, 1 hit
InterProiView protein in InterPro
IPR035500 NHR_like_dom_sf
IPR000536 Nucl_hrmn_rcpt_lig-bd
IPR001723 Nuclear_hrmn_rcpt
IPR003078 Retinoic_acid_rcpt
IPR001628 Znf_hrmn_rcpt
IPR013088 Znf_NHR/GATA
PfamiView protein in Pfam
PF00104 Hormone_recep, 1 hit
PF00105 zf-C4, 1 hit
PRINTSiPR01292 RETNOICACIDR
PR00398 STRDHORMONER
PR00047 STROIDFINGER
SMARTiView protein in SMART
SM00430 HOLI, 1 hit
SM00399 ZnF_C4, 1 hit
SUPFAMiSSF48508 SSF48508, 2 hits
PROSITEiView protein in PROSITE
PS51843 NR_LBD, 1 hit
PS00031 NUCLEAR_REC_DBD_1, 1 hit
PS51030 NUCLEAR_REC_DBD_2, 1 hit

Sequencei

Sequence statusi: Complete.

Q91392-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFDCMEALGM GPRQLYDVTN RGACMLRKAS PFYAGLDPFA WTGTASVRSV
60 70 80 90 100
ETQSTSSEEM VPSSPSPPPP PRVYKPCFVC QDKSSGYHYG VSSCEGCKGF
110 120 130 140 150
FRRSIQKNMV YTCHRDKNCQ INKVTRNRCQ YCRLQKCFEV GMSKEAVRND
160 170 180 190 200
RNKKKKDVKD EVIPPESYEL SGELEELVNK VSKAHQETFP SLCQLGKYTT
210 220 230 240 250
NSSSDHRIQL DLGLWDKFSE LSTKCIIKIV EFAKRLPGFT TLTIADQITL
260 270 280 290 300
LKSACLDILM LRICTRYTPE QDTMTFSDGL TLNRTQMHNA GFGPLTDLVF
310 320 330 340 350
AFAGQLLPLE MDDTETGLLS AICLICGDRM DLEEPERVDR LQEPLLEALK
360 370 380 390 400
IYARRRRPNK PHMFPRMLMK ITDLRGISTK GAERAITLKM EIPGPMPPLI
410 420 430 440 450
REMLENPEAF EDQSESTEKK PEPEPPAPPP PALLTMKKEQ EDEDDSWATE
460 470 480 490
NGSEPSPEEE DDDDEDGEEE RGTDSDGEAW GGQEPNADVS RKSHGGRAQ
Length:499
Mass (Da):56,195
Last modified:November 28, 2006 - v2
Checksum:i00660607E4A45B28
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti20N → D in AAB59953 (Ref. 4) Curated1
Sequence conflicti116 – 118DKN → EKS in AAB68756 (PubMed:9192646).Curated3
Sequence conflicti235R → A in AAB59953 (Ref. 4) Curated1
Sequence conflicti366 – 367RM → KI in AAB59953 (Ref. 4) Curated2
Sequence conflicti416S → A in AAB32277 (PubMed:7918098).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S74156 mRNA Translation: AAB32277.1
BX465864, BX546466 Genomic DNA Translation: CAM14485.1
BX546466, BX465864 Genomic DNA Translation: CAM16092.1
BC098519 mRNA Translation: AAH98519.1
L03400 mRNA Translation: AAB59953.1
U93479 Genomic DNA Translation: AAB68756.1
PIRiI51257
RefSeqiNP_571414.1, NM_131339.1
UniGeneiDr.23544

Genome annotation databases

EnsembliENSDART00000049551; ENSDARP00000049550; ENSDARG00000034117
GeneIDi30606
KEGGidre:30606

Similar proteinsi

Entry informationi

Entry nameiRARGA_DANRE
AccessioniPrimary (citable) accession number: Q91392
Secondary accession number(s): A2BGD3
, O42552, Q4KMK9, Q90273
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: November 28, 2006
Last modified: May 23, 2018
This is version 151 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health