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Protein

Retinoic acid receptor alpha-A

Gene

raraa

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 (By similarity). Required for hindbrain patterning.By similarity1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi72 – 14776Nuclear receptorPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri75 – 9521NR C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri111 – 13020NR C4-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • hindbrain morphogenesis Source: UniProtKB
  • liver development Source: ZFIN
  • response to retinoic acid 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 alpha-A
Short name:
RAR-alpha-A
Alternative name(s):
Nuclear receptor subfamily 1 group B member 1-A
Retinoic acid receptor alpha
Short name:
zRAR alpha
Retinoic acid receptor alpha-2.A
Short name:
RAR-alpha-2.A
Gene namesi
Name:raraaImported
Synonyms:nr1b1a, rara2aImported
ORF Names:zgc:109797
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
Proteomesi
  • UP000000437 Componenti: Chromosome 12

Organism-specific databases

ZFINiZDB-GENE-980526-284. raraa.

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 – 444444Retinoic acid receptor alpha-APRO_0000262962Add
BLAST

Proteomic databases

PaxDbiQ90271.

Expressioni

Tissue specificityi

In the embryo, zygotic expression largely overlaps that of rarab, with high levels in hindbrain, lateral mesoderm and tail bud. In the adult, strong expression in brain and muscle, weaker expression in ovary, liver and digestive tract.2 Publications

Developmental stagei

Not expressed maternally. First detected at 8 hours post-fertilization (hpf) during gastrulation, with expression being restricted to the posterior epiblast. Expression then increases, reaching a peak at 24 hpf and decreasing from 30-48 hpf. At 9 hpf, expressed throughout the dorsal epiblast except at the dorsal midline, and ventrally in prospective tail and head regions. At 10-11 hpf, expressed in presumptive hindbrain, posterior neural plate, lateral mesoderm and tail bud. At 12 hpf, strongly expressed in the neural epithelium and tail bud and expressed at low levels elsewhere including the eye. At 24 hpf, restricted to the hindbrain with an anterior border at rhombomere 6-7, to anterior spinal cord and to head mesenchyme just posterior to the otic vesicle. At 48 hpf, hindbrain expression remains and there is diffuse expression in non-neural tissue in the pharyngeal region.3 Publications

Inductioni

By retinoic acid in embryos.2 Publications

Gene expression databases

BgeeiQ90271.
ExpressionAtlasiQ90271. differential.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

STRINGi7955.ENSDARP00000073792.

Structurei

3D structure databases

ProteinModelPortaliQ90271.
SMRiQ90271. Positions 69-147, 169-403.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 7171ModulatingSequence analysisAdd
BLAST
Regioni148 – 19346HingeSequence analysisAdd
BLAST
Regioni194 – 367174Ligand-bindingSequence analysisAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi60 – 6910Poly-Pro
Compositional biasi151 – 1544Poly-Lys

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. NR1 subfamily.Sequence analysis
Contains 1 nuclear receptor DNA-binding domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri75 – 9521NR C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri111 – 13020NR C4-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG3575. Eukaryota.
ENOG410XRZC. LUCA.
GeneTreeiENSGT00840000129681.
HOGENOMiHOG000010312.
HOVERGENiHBG005606.
InParanoidiQ90271.
KOiK08527.
OrthoDBiEOG738053.
PhylomeDBiQ90271.
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. 1 hit.
PROSITEiPS00031. NUCLEAR_REC_DBD_1. 1 hit.
PS51030. NUCLEAR_REC_DBD_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q90271-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MYESVDVNPF LMMDYYNQSR GCLIPDKMPH PFSSSIRHQH WSGSNHSIET
60 70 80 90 100
QSTSSEEIVP SPPSPPPPPR IYKPCFVCQD KSSGYHYGVS ACEGCKGFFR
110 120 130 140 150
RSIQKNMVYT CHREKNCIIN KVTRNRCQYC RLQKCLEVGM SKESVRNDRN
160 170 180 190 200
KKKKEEKKPE CTENYTLSPD TEQMIDRVRK AHQETFPSLC QLGKYTTSNS
210 220 230 240 250
SERRVALDVD LWDKFSELST KCIIKTVEFA KQLPGFTTLT IADQITLLKA
260 270 280 290 300
ACLDILILRI CTRYTPEQDT MTFSDGLTLN RTQMHNAGFG PLTDLVFAFA
310 320 330 340 350
NQLLPLEMDD AETGLLSAIC LLCGDRQDLE QADKVDVLQE PLLEALKIYV
360 370 380 390 400
RNRRPHKPHM FPKMLMKITD LRSISAKGAE RVITLKMEIP GSMPPLIQEM
410 420 430 440
LENSEGLESS SGAQGSRASA TTPGSCSPSL SPNSAQSSPP TQSP
Length:444
Mass (Da):49,924
Last modified:November 28, 2006 - v2
Checksum:i7B0DED7B660D5E7F
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti381 – 3822RV → LL in AAA50049 (Ref. 2) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S74155 mRNA. Translation: AAB32276.1.
L03398 mRNA. Translation: AAA50049.1.
BC092692 mRNA. Translation: AAH92692.1.
PIRiI51256.
RefSeqiNP_571481.2. NM_131406.2.
UniGeneiDr.193.

Genome annotation databases

EnsembliENSDART00000079336; ENSDARP00000073792; ENSDARG00000056783.
GeneIDi30680.
KEGGidre:30680.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S74155 mRNA. Translation: AAB32276.1.
L03398 mRNA. Translation: AAA50049.1.
BC092692 mRNA. Translation: AAH92692.1.
PIRiI51256.
RefSeqiNP_571481.2. NM_131406.2.
UniGeneiDr.193.

3D structure databases

ProteinModelPortaliQ90271.
SMRiQ90271. Positions 69-147, 169-403.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000073792.

Proteomic databases

PaxDbiQ90271.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSDART00000079336; ENSDARP00000073792; ENSDARG00000056783.
GeneIDi30680.
KEGGidre:30680.

Organism-specific databases

CTDi30680.
ZFINiZDB-GENE-980526-284. raraa.

Phylogenomic databases

eggNOGiKOG3575. Eukaryota.
ENOG410XRZC. LUCA.
GeneTreeiENSGT00840000129681.
HOGENOMiHOG000010312.
HOVERGENiHBG005606.
InParanoidiQ90271.
KOiK08527.
OrthoDBiEOG738053.
PhylomeDBiQ90271.
TreeFamiTF328382.

Enzyme and pathway databases

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

Miscellaneous databases

NextBioi20807033.
PROiQ90271.

Gene expression databases

BgeeiQ90271.
ExpressionAtlasiQ90271. differential.

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. 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. "Effects of retinoic acid on the expression of retinoic acid receptors during zebrafish embryogenesis."
    Joore J., van der Lans G.B.L.J., Lanser P.H., Vervaart J.M.A., Zivkovic D., Speksnijder J.E., Kruijer W.
    Mech. Dev. 46:137-150(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, INDUCTION.
    Tissue: Embryo1 Publication.
  2. "The molecular characterization of three zebrafish retinoic acid receptor genes suggests the retinoic acid pathway functions in embryonic hindbrain development."
    Stachel S.E., Kushner P.
    Submitted (DEC-1992) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: GastrulaImported.
  3. NIH - Zebrafish Gene Collection (ZGC) project
    Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: BrainImported.
  4. "Characterization of the retinoic acid receptor genes raraa, rarab and rarg during zebrafish development."
    Hale L.A., Tallafuss A., Yan Y.-L., Dudley L., Eisen J.S., Postlethwait J.H.
    Gene Expr. Patterns 6:546-555(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: DEVELOPMENTAL STAGE, TISSUE SPECIFICITY.
  5. "Combinatorial roles for zebrafish retinoic acid receptors in the hindbrain, limbs and pharyngeal arches."
    Linville A., Radtke K., Waxman J.S., Yelon D., Schilling T.F.
    Dev. Biol. 325:60-70(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: DEVELOPMENTAL STAGE, INDUCTION, FUNCTION.

Entry informationi

Entry nameiRARAA_DANRE
AccessioniPrimary (citable) accession number: Q90271
Secondary accession number(s): Q91391
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 28, 2006
Last sequence update: November 28, 2006
Last modified: May 11, 2016
This is version 118 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.