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Protein

Retinoic acid receptor RXR-gamma-A

Gene

rxrga

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript 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. The high affinity ligand for rxrs is 9-cis retinoic acid (By similarity).By similarity1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi117 – 18266Nuclear receptorPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri117 – 13721NR C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri153 – 17725NR C4-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Activator, Receptor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Retinoic acid receptor RXR-gamma-A
Alternative name(s):
Nuclear receptor subfamily 2 group B member 3-A
Retinoic acid receptor RXR-alpha
Retinoid X receptor alpha
Retinoid X receptor gamma-A
Gene namesi
Name:rxrga
Synonyms:nr2b1, nr2b3a, rxr, rxra, rxrg
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
Proteomesi
  • UP000000437 Componenti: Unplaced

Organism-specific databases

ZFINiZDB-GENE-980526-36. rxrga.

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 – 441441Retinoic acid receptor RXR-gamma-APRO_0000053570Add
BLAST

Proteomic databases

PaxDbiQ90416.

Expressioni

Tissue specificityi

Uniformly expressed from the blastula to mid-gastrula stages. In late gastrula stages, there is specific expression in the presumptive hindbrain and spinal cord. At 16 hours post-fertilization (hpf), expressed in the hindbrain from rhombomere 7/8 to the anterior spinal cord; this expression continues until 42 hpf. At 24 hpf, also expressed in the lateral plate mesoderm flanking rhombomere 6 and in the cranial neural crest, but not in the migrating crest. At 26 hpf, also expressed in retina. At 48 hpf, strong retinal expression.2 Publications

Developmental stagei

Expressed both maternally and zygotically.3 Publications

Interactioni

Subunit structurei

Homodimer (By similarity). Heterodimer; with a rar molecule (By similarity). Binds DNA preferentially as a rar/rxr heterodimer (By similarity). Heterodimerizes with rarga.By similarity

Protein-protein interaction databases

STRINGi7955.ENSDARP00000021935.

Structurei

3D structure databases

ProteinModelPortaliQ90416.
SMRiQ90416. Positions 110-193, 209-441.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 116116ModulatingBy similarityAdd
BLAST
Regioni183 – 20624HingeAdd
BLAST
Regioni207 – 441235Ligand-bindingBy similarityAdd
BLAST

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 fingeri117 – 13721NR C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri153 – 17725NR C4-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG3575. Eukaryota.
ENOG410XRZC. LUCA.
HOGENOMiHOG000260821.
HOVERGENiHBG005606.
InParanoidiQ90416.
KOiK08524.
PhylomeDBiQ90416.

Family and domain databases

Gene3Di1.10.565.10. 1 hit.
3.30.50.10. 1 hit.
InterProiIPR021780. Nuc_recep-AF1.
IPR000536. Nucl_hrmn_rcpt_lig-bd.
IPR001723. Nuclear_hrmn_rcpt.
IPR000003. Retinoid-X_rcpt/HNF4.
IPR001628. Znf_hrmn_rcpt.
IPR013088. Znf_NHR/GATA.
[Graphical view]
PfamiPF00104. Hormone_recep. 1 hit.
PF11825. Nuc_recep-AF1. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view]
PRINTSiPR00545. RETINOIDXR.
PR00398. STRDHORMONER.
PR00047. STROIDFINGER.
SMARTiSM00430. HOLI. 1 hit.
SM00399. ZnF_C4. 1 hit.
[Graphical view]
SUPFAMiSSF48508. SSF48508. 1 hit.
PROSITEiPS00031. NUCLEAR_REC_DBD_1. 1 hit.
PS51030. NUCLEAR_REC_DBD_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q90416-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDNNDTYLHL SSSLQVAHGH LSSPPSQPPL SSMVSHHHPS IINGLGSPYS
60 70 80 90 100
VITSSSLGSP SASMPTTSNM GYGALNSPQM NSLNSVSSSE DIKPPPGLAG
110 120 130 140 150
LGSYPCGSPG SLSKHICAIC GDRSSGKHYG VYSCEGCKGF FKRTIRKDLT
160 170 180 190 200
YTCRDNKDCQ IDKRQRNRCQ YCRYQKCLAM GMKREAVQEE RQRGRERSDN
210 220 230 240 250
EVDSSSSFNE EMPVEKILDA ELAVEPKTEA YMESSMSNST NDPVTNICQA
260 270 280 290 300
ADKQLFTLVE WAKRIPHFSD LPLDDQVILL RAGWNELLIA SFSHRSVTVK
310 320 330 340 350
DGILLATGLH VHRSSAHSAG VGSIFDRVLT ELVSKMRDMQ MDKTELGCLR
360 370 380 390 400
AIVLFNPDAK GLSNPSEVEA LREKVYASLE GYTKHNYPDQ PGRFAKLLLR
410 420 430 440
LPALRSIGLK CLEHLFFFKL IGDTPIDTFL MEMLEAPHQI T
Length:441
Mass (Da):48,720
Last modified:September 27, 2004 - v2
Checksum:iF169ADE221F2F13C
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti31 – 311S → G in AAC59720 (PubMed:7565671).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29940 mRNA. Translation: AAC59720.1.
BC059576 mRNA. Translation: AAH59576.1.
PIRiI50515.
RefSeqiNP_571292.3. NM_131217.3.
UniGeneiDr.348.

Genome annotation databases

GeneIDi30464.
KEGGidre:30464.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29940 mRNA. Translation: AAC59720.1.
BC059576 mRNA. Translation: AAH59576.1.
PIRiI50515.
RefSeqiNP_571292.3. NM_131217.3.
UniGeneiDr.348.

3D structure databases

ProteinModelPortaliQ90416.
SMRiQ90416. Positions 110-193, 209-441.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000021935.

Proteomic databases

PaxDbiQ90416.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi30464.
KEGGidre:30464.

Organism-specific databases

CTDi30464.
ZFINiZDB-GENE-980526-36. rxrga.

Phylogenomic databases

eggNOGiKOG3575. Eukaryota.
ENOG410XRZC. LUCA.
HOGENOMiHOG000260821.
HOVERGENiHBG005606.
InParanoidiQ90416.
KOiK08524.
PhylomeDBiQ90416.

Miscellaneous databases

PROiQ90416.

Family and domain databases

Gene3Di1.10.565.10. 1 hit.
3.30.50.10. 1 hit.
InterProiIPR021780. Nuc_recep-AF1.
IPR000536. Nucl_hrmn_rcpt_lig-bd.
IPR001723. Nuclear_hrmn_rcpt.
IPR000003. Retinoid-X_rcpt/HNF4.
IPR001628. Znf_hrmn_rcpt.
IPR013088. Znf_NHR/GATA.
[Graphical view]
PfamiPF00104. Hormone_recep. 1 hit.
PF11825. Nuc_recep-AF1. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view]
PRINTSiPR00545. RETINOIDXR.
PR00398. STRDHORMONER.
PR00047. STROIDFINGER.
SMARTiSM00430. HOLI. 1 hit.
SM00399. ZnF_C4. 1 hit.
[Graphical view]
SUPFAMiSSF48508. SSF48508. 1 hit.
PROSITEiPS00031. NUCLEAR_REC_DBD_1. 1 hit.
PS51030. NUCLEAR_REC_DBD_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "New retinoid X receptor subtypes in zebra fish (Danio rerio) differentially modulate transcription and do not bind 9-cis retinoic acid."
    Jones B.B., Ohno C.K., Allenby G., Boffa M.B., Levin A.A., Grippo J.F., Petkovich M.
    Mol. Cell. Biol. 15:5226-5234(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, HETERODIMERIZATION WITH RARGA, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
  2. NIH - Zebrafish Gene Collection (ZGC) project
    Submitted (OCT-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Retina.
  3. "Characterization of retinoid-X receptor genes rxra, rxrba, rxrbb and rxrg during zebrafish development."
    Tallafuss A., Hale L.A., Yan Y.-L., Dudley L., Eisen J.S., Postlethwait J.H.
    Gene Expr. Patterns 6:556-565(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: DEVELOPMENTAL STAGE.
  4. "Comparison of the expression patterns of newly identified zebrafish retinoic acid and retinoid X receptors."
    Waxman J.S., Yelon D.
    Dev. Dyn. 236:587-595(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.

Entry informationi

Entry nameiRXRGA_DANRE
AccessioniPrimary (citable) accession number: Q90416
Secondary accession number(s): Q6PBU9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: September 27, 2004
Last modified: July 6, 2016
This is version 121 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.