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Protein

Retinoic acid receptor alpha

Gene

RARA

Organism
Gallus gallus (Chicken)
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 and appears to be required for skin development.By similarity1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi88 – 15366Nuclear receptorPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri88 – 10821NR C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri124 – 14825NR C4-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • hindbrain morphogenesis Source: UniProtKB
  • 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

Names & Taxonomyi

Protein namesi
Recommended name:
Retinoic acid receptor alpha
Short name:
RAR-alpha
Alternative name(s):
Nuclear receptor subfamily 1 group B member 1
Gene namesi
Name:RARA
Synonyms:NR1B1
OrganismiGallus gallus (Chicken)
Taxonomic identifieri9031 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiArchelosauriaArchosauriaDinosauriaSaurischiaTheropodaCoelurosauriaAvesNeognathaeGalloanseraeGalliformesPhasianidaePhasianinaeGallus
Proteomesi
  • UP000000539 Componenti: Unplaced

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

  • cell Source: AgBase
  • nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 460460Retinoic acid receptor alphaPRO_0000053463Add
BLAST

Expressioni

Tissue specificityi

Ubiquitous.1 Publication

Developmental stagei

Expressed from day 7-8.5 during feather morphogenesis in dermal and epidermal cells. Also expressed in heart from day 8.5-14.5. At later stages, when the feather follicle forms, expression still abundant in the epidermis, especially in the feather barb ridges.1 Publication

Interactioni

Subunit structurei

Heterodimer; with an RXR molecule. Binds DNA preferentially as a RAR/RXR heterodimer.By similarity

Structurei

3D structure databases

ProteinModelPortaliQ90966.
SMRiQ90966. Positions 87-161, 182-416.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 8787ModulatingAdd
BLAST
Regioni154 – 19946HingeAdd
BLAST
Regioni200 – 419220Ligand-bindingAdd
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 fingeri88 – 10821NR C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri124 – 14825NR C4-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

HOVERGENiHBG005606.
InParanoidiQ90966.
KOiK08527.
PhylomeDBiQ90966.

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]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform Alpha-1 (identifier: Q90966-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MASNSSSCPT PGGGHLNGYP VTPYAFFFPH MLGGLSPPSS LPGIQHQLPV
60 70 80 90 100
SGYSTPSPAT VETQSTSSEE IVPSPPSPPP LPRIYKPCFV CQDKSSGYHY
110 120 130 140 150
GVSACEGCKG FFRRSIQKNM VYTCHRDKNC IINKVTRNRC QYCRLQKCFE
160 170 180 190 200
VGMSKESVRN DRNKKKKDVP KTECSESYIV TPEVEELIEK VRKAHQETFP
210 220 230 240 250
ALCQLGKYTT NNSSEQRVSL DIDLWDKFSE LSTKCIIKTV EFAKQLPGFT
260 270 280 290 300
TLTIADQITL LKAACLDILI LRICTRYTPE QDTMTFSDGL TLNRTQMHNA
310 320 330 340 350
GFGPLTDLVF AFANQLLPLE MDDAETGLLS AICLICGDRQ DLEQPDKVDK
360 370 380 390 400
LQEPLLEALK IYVRKRRPNK PHMFPKMLMK ITDLRSISAK GAERVITLKM
410 420 430 440 450
EIPGSMPPLI QEMLENSEGM DTLGGQPGGP RTGGLGPPPG SCSPSLSPSS
460
TRSSPATHSP
Length:460
Mass (Da):50,728
Last modified:November 1, 1996 - v1
Checksum:i99711F415E811CA2
GO
Isoform Alpha-2 (identifier: Q90966-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-60: MASNSSSCPT...SGYSTPSPAT → MFEGAEVAGL...APHWGASGRS

Show »
Length:453
Mass (Da):50,131
Checksum:i1360EE9559E33448
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 6060MASNS…PSPAT → MFEGAEVAGLPPPGPLPRMD CCGPGRGCLLPQCPPPPRTA PRRAPHWGASGRS in isoform Alpha-2. 1 PublicationVSP_003631Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X73972 mRNA. Translation: CAA52152.1.
X78335 mRNA. Translation: CAA55134.1.
PIRiI50674.
RefSeqiNP_989867.1. NM_204536.1. [Q90966-1]
UniGeneiGga.112.

Genome annotation databases

GeneIDi395213.
KEGGigga:395213.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X73972 mRNA. Translation: CAA52152.1.
X78335 mRNA. Translation: CAA55134.1.
PIRiI50674.
RefSeqiNP_989867.1. NM_204536.1. [Q90966-1]
UniGeneiGga.112.

3D structure databases

ProteinModelPortaliQ90966.
SMRiQ90966. Positions 87-161, 182-416.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi395213.
KEGGigga:395213.

Organism-specific databases

CTDi5914.

Phylogenomic databases

HOVERGENiHBG005606.
InParanoidiQ90966.
KOiK08527.
PhylomeDBiQ90966.

Miscellaneous databases

PROiQ90966.

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...

Publicationsi

  1. "Characterization of cDNAs encoding two chick retinoic acid receptor alpha isoforms and distribution of retinoic acid receptor alpha, beta and gamma transcripts during chick skin development."
    Michaille J.J., Kanzler B., Blanchet S., Garnier J.-M., Dhouailly D.
    Int. J. Dev. Biol. 39:587-596(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS ALPHA-1 AND ALPHA-2), TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
  2. "Hindbrain patterning involves graded responses to retinoic acid signalling."
    Dupe V., Lumsden A.
    Development 128:2199-2208(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiRARA_CHICK
AccessioniPrimary (citable) accession number: Q90966
Secondary accession number(s): Q90967
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 16, 2001
Last sequence update: November 1, 1996
Last modified: June 8, 2016
This is version 112 of the entry and version 1 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.