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Protein

Retinoic acid receptor gamma-A

Gene

rarga

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi77 – 14266Nuclear receptorPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri77 – 9721NR C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri113 – 13725NR C4-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • liver development Source: ZFIN
  • pharyngeal system development Source: UniProtKB
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Receptor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-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

  • Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 499499Retinoic acid receptor gamma-APRO_0000053477Add
BLAST

Proteomic databases

PaxDbiQ91392.

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.

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. Positions 71-149, 170-407.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 7676ModulatingAdd
BLAST
Regioni143 – 18846HingeAdd
BLAST
Regioni189 – 409221Ligand-bindingAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi65 – 717Poly-Pro
Compositional biasi153 – 1564Poly-Lys
Compositional biasi354 – 3574Poly-Arg
Compositional biasi421 – 43111Poly-ProAdd
BLAST
Compositional biasi461 – 4666Poly-Asp

Domaini

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

Sequence similaritiesi

Contains 1 nuclear receptor DNA-binding domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri77 – 9721NR C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri113 – 13725NR C4-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG3575. Eukaryota.
ENOG410XRZC. LUCA.
GeneTreeiENSGT00840000129681.
HOGENOMiHOG000010312.
HOVERGENiHBG005606.
InParanoidiQ91392.
KOiK08529.
OMAiNTAVRND.
OrthoDBiEOG091G0XCQ.
PhylomeDBiQ91392.
TreeFamiTF328382.

Family and domain databases

Gene3Di1.10.565.10. 1 hit.
3.30.50.10. 1 hit.
InterProiIPR000536. Nucl_hrmn_rcpt_lig-bd.
IPR001723. Nuclear_hrmn_rcpt.
IPR003078. Retinoic_acid_rcpt.
IPR001628. Znf_hrmn_rcpt.
IPR013088. Znf_NHR/GATA.
[Graphical view]
PfamiPF00104. Hormone_recep. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view]
PRINTSiPR01292. RETNOICACIDR.
PR00398. STRDHORMONER.
PR00047. STROIDFINGER.
SMARTiSM00430. HOLI. 1 hit.
SM00399. ZnF_C4. 1 hit.
[Graphical view]
SUPFAMiSSF48508. SSF48508. 2 hits.
PROSITEiPS00031. NUCLEAR_REC_DBD_1. 1 hit.
PS51030. NUCLEAR_REC_DBD_2. 1 hit.
[Graphical view]

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti20 – 201N → D in AAB59953 (Ref. 4) Curated
Sequence conflicti116 – 1183DKN → EKS in AAB68756 (PubMed:9192646).Curated
Sequence conflicti235 – 2351R → A in AAB59953 (Ref. 4) Curated
Sequence conflicti366 – 3672RM → KI in AAB59953 (Ref. 4) Curated
Sequence conflicti416 – 4161S → A in AAB32277 (PubMed:7918098).Curated

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.

Cross-referencesi

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.

3D structure databases

ProteinModelPortaliQ91392.
SMRiQ91392. Positions 71-149, 170-407.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000093932.

Proteomic databases

PaxDbiQ91392.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSDART00000049551; ENSDARP00000049550; ENSDARG00000034117.
GeneIDi30606.
KEGGidre:30606.

Organism-specific databases

CTDi30606.
ZFINiZDB-GENE-980526-531. rarga.

Phylogenomic databases

eggNOGiKOG3575. Eukaryota.
ENOG410XRZC. LUCA.
GeneTreeiENSGT00840000129681.
HOGENOMiHOG000010312.
HOVERGENiHBG005606.
InParanoidiQ91392.
KOiK08529.
OMAiNTAVRND.
OrthoDBiEOG091G0XCQ.
PhylomeDBiQ91392.
TreeFamiTF328382.

Enzyme and pathway databases

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

Miscellaneous databases

PROiQ91392.

Gene expression databases

BgeeiENSDARG00000034117.

Family and domain databases

Gene3Di1.10.565.10. 1 hit.
3.30.50.10. 1 hit.
InterProiIPR000536. Nucl_hrmn_rcpt_lig-bd.
IPR001723. Nuclear_hrmn_rcpt.
IPR003078. Retinoic_acid_rcpt.
IPR001628. Znf_hrmn_rcpt.
IPR013088. Znf_NHR/GATA.
[Graphical view]
PfamiPF00104. Hormone_recep. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view]
PRINTSiPR01292. RETNOICACIDR.
PR00398. STRDHORMONER.
PR00047. STROIDFINGER.
SMARTiSM00430. HOLI. 1 hit.
SM00399. ZnF_C4. 1 hit.
[Graphical view]
SUPFAMiSSF48508. SSF48508. 2 hits.
PROSITEiPS00031. NUCLEAR_REC_DBD_1. 1 hit.
PS51030. NUCLEAR_REC_DBD_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRARGA_DANRE
AccessioniPrimary (citable) accession number: Q91392
Secondary accession number(s): A2BGD3
, O42552, Q4KMK9, Q90273
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: November 28, 2006
Last modified: September 7, 2016
This is version 137 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.