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raraa retinoic acid receptor, alpha a [ Danio rerio (zebrafish) ]

Gene ID: 30680, updated on 9-Sep-2025
Official Symbol
raraaprovided by ZNC
Official Full Name
retinoic acid receptor, alpha aprovided by ZNC
Primary source
ZFIN:ZDB-GENE-980526-284
See related
Ensembl:ENSDARG00000056783 AllianceGenome:ZFIN:ZDB-GENE-980526-284
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
rara; zRAR; rara2a; zRAR-alpha; zgc:109797; etID309833.12
Summary
Enables nuclear receptor activity. Involved in hindbrain morphogenesis and response to retinoic acid. Acts upstream of or within liver development. Predicted to be active in nucleus. Is expressed in several structures, including endoderm; gonad; mesoderm; nervous system; and neural keel. Human ortholog(s) of this gene implicated in acute promyelocytic leukemia; lung carcinoma (multiple); and syndromic microphthalmia 12. Orthologous to several human genes including RARA (retinoic acid receptor alpha). [provided by Alliance of Genome Resources, Apr 2025]
Orthologs
human mouse all
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See raraa in Genome Data Viewer
Location:
chromosome: 12
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2025_04 current GRCz12tu (GCF_049306965.1) 12 NC_133187.1 (11386769..11711599)
RS_2024_08 previous assembly GRCz11 (GCF_000002035.6) 12 NC_007123.7 (10833072..11157569)

Chromosome 12 - NC_133187.1Genomic Context describing neighboring genes Neighboring gene sterile alpha motif domain containing 14 Neighboring gene DNA topoisomerase II alpha Neighboring gene uncharacterized LOC141376766 Neighboring gene uncharacterized LOC141376767 Neighboring gene transfer RNA threonine (anticodon CGU) Neighboring gene disintegrin and metalloproteinase domain-containing protein 9-like Neighboring gene VPS35 endosomal protein sorting factor like Neighboring gene si:ch73-30l9.1

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Related articles in PubMed

  1. Effects of retinoic acid on the expression of retinoic acid receptors during zebrafish embryogenesis. Joore J, et al. Mech Dev, 1994 May. PMID 7918098
  2. A zebrafish retinoic acid receptor expressed in the regenerating caudal fin. White JA, et al. Development, 1994 Jul. PMID 7924993
  3. Structure-dependent activities of polybrominated diphenyl ethers and hydroxylated metabolites on zebrafish retinoic acid receptor. Zhao J, et al. Environ Sci Pollut Res Int, 2015 Feb. PMID 25077655
  4. Identification and characterization of a functional zebrafish smrt corepressor (ncor2). Linney E, et al. Gene, 2011 Oct 15. PMID 21767619, Free PMC Article
  5. Evolution of nuclear retinoic acid receptor alpha (RARα) phosphorylation sites. Serine gain provides fine-tuned regulation. Samarut E, et al. Mol Biol Evol, 2011 Jul. PMID 21297158

See all (60) citations in PubMed

GeneRIFs: Gene References Into Functions

Markers

Homology

Clone Names

  • MGC109797

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables nuclear receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables nuclear receptor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables nuclear receptor activity IEA
Inferred from Electronic Annotation
more info
  
enables sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in hindbrain morphogenesis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in liver development IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within liver development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in response to retinoic acid IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in retinoic acid receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within retinoic acid receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of RNA polymerase II transcription regulator complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
Preferred Names
retinoic acid receptor alpha-A
Names
NR1B1-A
RAR-alpha-2.A
RAR-alpha-A
RARalpha-A
nr1b1a
nuclear receptor subfamily 1 group B member 1-A
retinoic acid receptor alpha a 201
retinoic acid receptor alpha-2.A
retinoic acid receptor, alpha 2a
zRAR alpha
zRAR-alpha-2.A

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_131406.2 → NP_571481.2  retinoic acid receptor alpha-A

    See identical proteins and their annotated locations for NP_571481.2

    Status: PROVISIONAL

    Source sequence(s)
    BC092692
    UniProtKB/Swiss-Prot
    Q90271, Q91391
    Related
    ENSDARP00000073792.4, ENSDART00000079336.5
    Conserved Domains (2) summary
    cd06937
    Location:174 → 403
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:69 → 153
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers

RefSeqs of Annotated Genomes: GCF_049306965.1-RS_2025_04

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCz12tu Primary Assembly

Genomic

  1. NC_133187.1 Reference GRCz12tu Primary Assembly

    Range
    11386769..11711599
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_073917403.1 → XP_073773504.1  retinoic acid receptor alpha-A isoform X1

    UniProtKB/TrEMBL
    A0A8M2B2P2, T2DKU4

  2. XM_073917404.1 → XP_073773505.1  retinoic acid receptor alpha-A isoform X1

    UniProtKB/TrEMBL
    A0A8M2B2P2, T2DKU4

  3. XM_005156052.6 → XP_005156109.1  retinoic acid receptor alpha-A isoform X1

    See identical proteins and their annotated locations for XP_005156109.1

    UniProtKB/TrEMBL
    A0A8M2B2P2, T2DKU4
    Related
    ENSDARP00000139532.1
    Conserved Domains (2) summary
    cd06937
    Location:177 → 406
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:72 → 156
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers

  4. XM_073917405.1 → XP_073773506.1  retinoic acid receptor alpha-A isoform X1

    UniProtKB/TrEMBL
    A0A8M2B2P2, T2DKU4
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q90271.2 GenPept UniProtKB/Swiss-Prot:Q90271

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