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RARA retinoic acid receptor alpha [ Homo sapiens (human) ]

Gene ID: 5914, updated on 26-Nov-2021

Summary

Official Symbol
RARAprovided by HGNC
Official Full Name
retinoic acid receptor alphaprovided by HGNC
Primary source
HGNC:HGNC:9864
See related
Ensembl:ENSG00000131759 MIM:180240
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RAR; NR1B1
Summary
This gene represents a nuclear retinoic acid receptor. The encoded protein, retinoic acid receptor alpha, regulates transcription in a ligand-dependent manner. This gene has been implicated in regulation of development, differentiation, apoptosis, granulopoeisis, and transcription of clock genes. Translocations between this locus and several other loci have been associated with acute promyelocytic leukemia. Alternatively spliced transcript variants have been found for this locus.[provided by RefSeq, Sep 2010]
Expression
Ubiquitous expression in lung (RPKM 10.4), spleen (RPKM 8.4) and 25 other tissues See more
Orthologs
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Genomic context

See RARA in Genome Data Viewer
Location:
17q21.2
Exon count:
17
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (40309180..40357643)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (38465432..38513895)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene WAS/WASL interacting protein family member 2 Neighboring gene RNY4 pseudogene 8 Neighboring gene cell division cycle 6 Neighboring gene uncharacterized LOC105371934 Neighboring gene RARA antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 13940 Neighboring gene peptidylprolyl isomerase A pseudogene 54 Neighboring gene gap junction protein delta 3

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Nef nef HIV-1 Nef induces loss of F-actin assembly and inhibits retinoid receptor-mediated transcription PubMed
matrix gag HIV-1 MA upregulates RARA gene expression in HepG2 cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
enables DNA-binding transcription repressor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables alpha-actinin binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables chromatin DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
enables enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables histone deacetylase binding IEA
Inferred from Electronic Annotation
more info
 
enables mRNA 5'-UTR binding IEA
Inferred from Electronic Annotation
more info
 
enables nuclear receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables nuclear receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein domain specific binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein kinase A binding IDA
Inferred from Direct Assay
more info
PubMed 
enables protein kinase B binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables retinoic acid binding IDA
Inferred from Direct Assay
more info
PubMed 
enables retinoic acid-responsive element binding IDA
Inferred from Direct Assay
more info
PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables signaling receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
enables transcription coactivator binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables translation repressor activity, mRNA regulatory element 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 Sertoli cell fate commitment IEA
Inferred from Electronic Annotation
more info
 
involved_in apoptotic cell clearance IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cellular response to estrogen stimulus IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cellular response to lipopolysaccharide IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to retinoic acid IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in chondroblast differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in embryonic camera-type eye development IEA
Inferred from Electronic Annotation
more info
 
involved_in face development IEA
Inferred from Electronic Annotation
more info
 
involved_in female pregnancy IEA
Inferred from Electronic Annotation
more info
 
involved_in germ cell development IEA
Inferred from Electronic Annotation
more info
 
involved_in glandular epithelial cell development IEA
Inferred from Electronic Annotation
more info
 
involved_in growth plate cartilage development IEA
Inferred from Electronic Annotation
more info
 
involved_in hippocampus development IEA
Inferred from Electronic Annotation
more info
 
involved_in hormone-mediated signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in limb development IEA
Inferred from Electronic Annotation
more info
 
involved_in liver development IEA
Inferred from Electronic Annotation
more info
 
involved_in mRNA transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in multicellular organism growth IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of cartilage development IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of cell population proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of granulocyte differentiation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of interferon-gamma production IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of pri-miRNA transcription by RNA polymerase II 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
PubMed 
involved_in negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of translation IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of tumor necrosis factor production IDA
Inferred from Direct Assay
more info
PubMed 
involved_in neural tube closure IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of T-helper 2 cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of cell population proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of interleukin-13 production IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of interleukin-4 production IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of interleukin-5 production IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in prostate gland development IEA
Inferred from Electronic Annotation
more info
 
involved_in protein phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of apoptotic process IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of myelination IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of synaptic plasticity IEA
Inferred from Electronic Annotation
more info
 
involved_in response to cytokine IEA
Inferred from Electronic Annotation
more info
 
involved_in response to estradiol IEA
Inferred from Electronic Annotation
more info
 
involved_in response to ethanol IEA
Inferred from Electronic Annotation
more info
 
involved_in response to retinoic acid IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in response to vitamin A IEA
Inferred from Electronic Annotation
more info
 
involved_in retinoic acid receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in retinoic acid receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in retinoic acid receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in signal transduction IDA
Inferred from Direct Assay
more info
PubMed 
involved_in trachea cartilage development IEA
Inferred from Electronic Annotation
more info
 
involved_in ureteric bud development IEA
Inferred from Electronic Annotation
more info
 
involved_in ventricular cardiac muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
part_of RNA polymerase II transcription regulator complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in actin cytoskeleton IDA
Inferred from Direct Assay
more info
 
located_in cell surface IC
Inferred by Curator
more info
PubMed 
located_in chromatin IDA
Inferred from Direct Assay
more info
PubMed 
located_in chromatin ISA
Inferred from Sequence Alignment
more info
 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
located_in dendrite IEA
Inferred from Electronic Annotation
more info
 
located_in nucleolus IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
 
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of transcription regulator complex IPI
Inferred from Physical Interaction
more info
PubMed 

General protein information

Preferred Names
retinoic acid receptor alpha
Names
PML-DDX5-RARA fusion
PML-DDX5-RARA fusion protein
RAR-alpha
nuclear receptor subfamily 1 group B member 1
nucleophosmin-retinoic acid receptor alpha fusion protein NPM-RAR long form
retinoic acid nuclear receptor alpha variant 1
retinoic acid nuclear receptor alpha variant 2
retinoic acid receptor, alpha polypeptide

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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.

Genomic

  1. NG_027701.1 RefSeqGene

    Range
    5010..53473
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1070

mRNA and Protein(s)

  1. NM_000964.4NP_000955.1  retinoic acid receptor alpha isoform 1

    See identical proteins and their annotated locations for NP_000955.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest protein (isoform 1). Variants 1 and 3 encode the same isoform (1).
    Source sequence(s)
    BC008727, BM992549, DA061829, X06614
    Consensus CDS
    CCDS11366.1
    UniProtKB/Swiss-Prot
    P10276
    UniProtKB/TrEMBL
    Q6I9R7
    Related
    ENSP00000254066.5, ENST00000254066.10
    Conserved Domains (2) summary
    cd06937
    Location:186416
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:82166
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
  2. NM_001024809.4NP_001019980.1  retinoic acid receptor alpha isoform 2

    See identical proteins and their annotated locations for NP_001019980.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) reflects the use of an alternate promoter and has a distinct 5' exon, compared to transcript variant 1. Translation is predicted to initiate from this alternate exon, and the resulting protein (isoform 2) has a shorter and a distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AC080112, BC071733, BM838347, BM992549
    Consensus CDS
    CCDS42317.1
    UniProtKB/Swiss-Prot
    P10276
    UniProtKB/TrEMBL
    F1D8N9
    Related
    ENSP00000377643.3, ENST00000394081.7
    Conserved Domains (2) summary
    cd06937
    Location:181411
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:77161
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
  3. NM_001145301.3NP_001138773.1  retinoic acid receptor alpha isoform 1

    See identical proteins and their annotated locations for NP_001138773.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) reflects the use of an alternate promoter and contains a different 5' UTR segment, compared to variant 1. Variants 1 and 3 encode the same isoform (1).
    Source sequence(s)
    AK292205, BG394590, BM992549, X06614
    Consensus CDS
    CCDS11366.1
    UniProtKB/Swiss-Prot
    P10276
    UniProtKB/TrEMBL
    A8K840, Q6I9R7
    Related
    ENSP00000377649.2, ENST00000394089.6
    Conserved Domains (2) summary
    cd06937
    Location:186416
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:82166
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
  4. NM_001145302.3NP_001138774.1  retinoic acid receptor alpha isoform 4

    See identical proteins and their annotated locations for NP_001138774.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) reflects the use of an alternate promoter and contains a different 5' UTR segment. This variant also lacks two in-frame coding exons, compared to variant 1. The resulting protein (isoform 4) is shorter compared to isoform 1.
    Source sequence(s)
    AC080112, BG394590, BM992549, FJ487576
    Consensus CDS
    CCDS45671.1
    UniProtKB/Swiss-Prot
    P10276
    Related
    ENSP00000389993.3, ENST00000425707.7
    Conserved Domains (1) summary
    cd06937
    Location:89319
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

    Range
    40309180..40357643
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011525095.1XP_011523397.1  retinoic acid receptor alpha isoform X1

    See identical proteins and their annotated locations for XP_011523397.1

    UniProtKB/Swiss-Prot
    P10276
    UniProtKB/TrEMBL
    Q6I9R7
    Conserved Domains (2) summary
    cd06937
    Location:186416
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:82166
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
  2. XM_005257554.1XP_005257611.1  retinoic acid receptor alpha isoform X1

    See identical proteins and their annotated locations for XP_005257611.1

    UniProtKB/Swiss-Prot
    P10276
    UniProtKB/TrEMBL
    Q6I9R7
    Conserved Domains (2) summary
    cd06937
    Location:186416
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:82166
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
  3. XM_005257553.1XP_005257610.1  retinoic acid receptor alpha isoform X1

    See identical proteins and their annotated locations for XP_005257610.1

    UniProtKB/Swiss-Prot
    P10276
    UniProtKB/TrEMBL
    Q6I9R7
    Conserved Domains (2) summary
    cd06937
    Location:186416
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:82166
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
  4. XM_011525096.1XP_011523398.1  retinoic acid receptor alpha isoform X2

    Conserved Domains (2) summary
    cd06937
    Location:128358
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:24108
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
  5. XM_005257552.5XP_005257609.1  retinoic acid receptor alpha isoform X4

    See identical proteins and their annotated locations for XP_005257609.1

    UniProtKB/TrEMBL
    A8MUP8
    Related
    ENSP00000377648.3, ENST00000394086.7
    Conserved Domains (2) summary
    cd06937
    Location:202432
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:98182
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
  6. XM_017024920.2XP_016880409.1  retinoic acid receptor alpha isoform X3

    Conserved Domains (2) summary
    cd06937
    Location:67297
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cl02596
    Location:144
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001033603.1: Suppressed sequence

    Description
    NM_001033603.1: This RefSeq was permanently suppressed because the 3'UTR is not supported and the transcript is a nonsense-mediated mRNA decay (NMD) candidate.
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