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Protein

Retinoic acid receptor RXR-alpha-A

Gene

rxraa

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: Annotation score: 3 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 similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi100 – 17576Nuclear receptorPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri103 – 12321NR C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri139 – 15820NR C4-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Receptor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Retinoic acid receptor RXR-alpha-A
Alternative name(s):
Nuclear receptor subfamily 2 group B member 1-A
RXRalpha-B
Retinoid X receptor alpha-A
Gene namesi
Name:rxraaImported
Synonyms:nr2b1a
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
ProteomesiUP000000437 Componenti: Unplaced

Organism-specific databases

ZFINiZDB-GENE-070314-2. rxraa.

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 – 430430Retinoic acid receptor RXR-alpha-APRO_0000287896Add
BLAST

Expressioni

Developmental stagei

Expressed both maternally and zygotically. In the embryo, expressed in the posterior hindbrain and anterior spinal cord at the 5-somite stage, with expression increasing through to the 15-somite stage. At the 15-somite stage, also expressed in the tail bud region. At the 18-somite stage, also found in the third neural crest stream.2 Publications

Interactioni

Subunit structurei

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

Protein-protein interaction databases

STRINGi7955.ENSDARP00000104454.

Structurei

3D structure databases

ProteinModelPortaliA2T929.
SMRiA2T929. Positions 97-179, 193-430.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 9999ModulatingBy similarityAdd
BLAST
Regioni176 – 19217HingeBy similarityAdd
BLAST
Regioni193 – 430238Ligand-bindingBy similarityAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi4 – 7269Ser-richSequence AnalysisAdd
BLAST

Domaini

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

Sequence similaritiesi

Belongs to the nuclear hormone receptor family. NR2 subfamily.Sequence Analysis
Contains 1 nuclear receptor DNA-binding domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri103 – 12321NR C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri139 – 15820NR C4-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiNOG327099.
HOGENOMiHOG000260821.
HOVERGENiHBG005606.
InParanoidiA2T929.
PhylomeDBiA2T929.

Family and domain databases

Gene3Di1.10.565.10. 1 hit.
3.30.50.10. 1 hit.
InterProiIPR021780. Nuc_recep-AF1.
IPR008946. Nucl_hormone_rcpt_ligand-bd.
IPR000536. Nucl_hrmn_rcpt_lig-bd_core.
IPR000003. Retinoid-X_rcpt/HNF4.
IPR001723. Str_hrmn_rcpt.
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.

A2T929-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHPSLLSPTS LGPSGSLHSP ISTLSSPMNG LGSPFSVISS PMGPHSMASP
60 70 80 90 100
GVGYGPSISP QLNSHMNSVS SSEDIKPPLG LNGVMKVPAQ PSGTPLSLTK
110 120 130 140 150
HICAICGDRS SGKHYGVYSC EGCKGFFKRT VRKDLTYTCR DNKDCVIDKR
160 170 180 190 200
QRNRCQYCRY QKCLAMGMKR EAVQEERQRA KERSENEVES TSSANEDMPV
210 220 230 240 250
EKILEAELAV EPKTETYIET NVPMPSNSPN DPVTNICQAA DKQLFTLVEW
260 270 280 290 300
AKRIPHFSEL PLDDQVILLR AGWNELLIAS FSHRSIAVKD GILLATGLHV
310 320 330 340 350
HRNSAHSAGV GAIFDRVLTE LVSKMRDMQM DKTELGCLRA IVLFNPDSKG
360 370 380 390 400
LSNPGEVEAL REKVYASLEA YCKHKYPEQP GRFAKLLLRL PALRSIGLKC
410 420 430
LEHLFFFKLI GDTPIDTFLM EMLEAPHQMT
Length:430
Mass (Da):47,471
Last modified:May 15, 2007 - v2
Checksum:i362DBD748A24191F
GO

Sequence cautioni

The sequence ABM89229.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EF028132 mRNA. Translation: ABM89229.1. Different initiation.
DQ017629 mRNA. Translation: AAY85284.1.
UniGeneiDr.87467.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EF028132 mRNA. Translation: ABM89229.1. Different initiation.
DQ017629 mRNA. Translation: AAY85284.1.
UniGeneiDr.87467.

3D structure databases

ProteinModelPortaliA2T929.
SMRiA2T929. Positions 97-179, 193-430.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000104454.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Organism-specific databases

ZFINiZDB-GENE-070314-2. rxraa.

Phylogenomic databases

eggNOGiNOG327099.
HOGENOMiHOG000260821.
HOVERGENiHBG005606.
InParanoidiA2T929.
PhylomeDBiA2T929.

Miscellaneous databases

PROiA2T929.

Family and domain databases

Gene3Di1.10.565.10. 1 hit.
3.30.50.10. 1 hit.
InterProiIPR021780. Nuc_recep-AF1.
IPR008946. Nucl_hormone_rcpt_ligand-bd.
IPR000536. Nucl_hrmn_rcpt_lig-bd_core.
IPR000003. Retinoid-X_rcpt/HNF4.
IPR001723. Str_hrmn_rcpt.
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

  1. "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: NUCLEOTIDE SEQUENCE [MRNA] OF 1-312, DEVELOPMENTAL STAGE.
  2. "Nuclear receptors expression during zebrafish development reveals an unsuspected link with nervous system and retina development."
    Bertrand S., Sachs L., Bardet P.-L., Bonnelye E., Dufraisse M., Escriva H., Haramis A.-P., Marchand O., Safi R., Vanacker J.-M., Zelus D., Thisse C., Thisse B., Laudet V.
    Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 66-430.
  3. "Unexpected novel relational links uncovered by extensive developmental profiling of nuclear receptor expression."
    Bertrand S., Thisse B., Tavares R., Sachs L., Chaumot A., Bardet P.-L., Escriva H., Duffraisse M., Marchand O., Safi R., Thisse C., Laudet V.
    PLoS Genet. 3:E188-E188(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: DEVELOPMENTAL STAGE.

Entry informationi

Entry nameiRXRAA_DANRE
AccessioniPrimary (citable) accession number: A2T929
Secondary accession number(s): Q1L677
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 15, 2007
Last sequence update: May 15, 2007
Last modified: June 24, 2015
This is version 57 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

External Data

Dasty 3

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 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.