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

    Gene ID: 5914, updated on 22-Sep-2016
    Official Symbol
    RARAprovided by HGNC
    Official Full Name
    retinoic acid receptor alphaprovided by HGNC
    Primary source
    HGNC:HGNC:9864
    See related
    Ensembl:ENSG00000131759 HPRD:06769; MIM:180240; Vega:OTTHUMG00000133328
    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]
    Orthologs
    Location:
    17q21
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 17 NC_000017.11 (40309171..40357643)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (38465423..38513895)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene WAS/WASL interacting protein family member 2 Neighboring gene RNA, Ro-associated Y4 pseudogene 8 Neighboring gene cell division cycle 6 Neighboring gene uncharacterized LOC105371934 Neighboring gene RARA antisense RNA 1 Neighboring gene peptidylprolyl isomerase A (cyclophilin A) pseudogene Neighboring gene gap junction protein delta 3

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    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

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    • Pathways in cancer, organism-specific biosystem (from KEGG)
      Pathways in cancer, organism-specific biosystem
      Pathways in cancer
    • Retinoic acid receptors-mediated signaling, organism-specific biosystem (from Pathway Interaction Database)
      Retinoic acid receptors-mediated signaling, organism-specific biosystem
      Retinoic acid receptors-mediated signaling
    • Signal Transduction, organism-specific biosystem (from REACTOME)
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    • Signaling by Retinoic Acid, organism-specific biosystem (from REACTOME)
      Signaling by Retinoic Acid, organism-specific biosystemVitamin A (retinol) can be metabolised into active retinoid metabolites that function either as a chromophore in vision or in regulating gene expression transcriptionally and post-transcriptionally. ...
    • Transcriptional misregulation in cancer, organism-specific biosystem (from KEGG)
      Transcriptional misregulation in cancer, organism-specific biosystem
      Transcriptional misregulation in cancer
    • Transcriptional misregulation in cancer, conserved biosystem (from KEGG)
      Transcriptional misregulation in cancer, conserved biosystem
      Transcriptional misregulation in cancer
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    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    RNA polymerase II regulatory region sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    alpha-actinin binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    chromatin DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    drug binding IEA
    Inferred from Electronic Annotation
    more info
     
    enzyme binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    histone deacetylase binding IEA
    Inferred from Electronic Annotation
    more info
     
    mRNA 5'-UTR binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein domain specific binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein heterodimerization activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein kinase A binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein kinase B binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    retinoic acid binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    retinoic acid receptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    retinoic acid-responsive element binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    steroid hormone receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    transcription coactivator activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription coactivator activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    transcription corepressor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription factor activity, sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    translation repressor activity, nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
     
    zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    Sertoli cell fate commitment IEA
    Inferred from Electronic Annotation
    more info
     
    apoptotic cell clearance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cellular response to estrogen stimulus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cellular response to lipopolysaccharide IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to retinoic acid IDA
    Inferred from Direct Assay
    more info
    PubMed 
    chondroblast differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    embryonic camera-type eye development IEA
    Inferred from Electronic Annotation
    more info
     
    face development IEA
    Inferred from Electronic Annotation
    more info
     
    female pregnancy IEA
    Inferred from Electronic Annotation
    more info
     
    germ cell development IEA
    Inferred from Electronic Annotation
    more info
     
    glandular epithelial cell development IEA
    Inferred from Electronic Annotation
    more info
     
    growth plate cartilage development IEA
    Inferred from Electronic Annotation
    more info
     
    hippocampus development IEA
    Inferred from Electronic Annotation
    more info
     
    limb development IEA
    Inferred from Electronic Annotation
    more info
     
    liver development IEA
    Inferred from Electronic Annotation
    more info
     
    multicellular organism growth IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of cartilage development IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of granulocyte differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of interferon-gamma production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of transcription from RNA polymerase II promoter IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of translational initiation IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of tumor necrosis factor production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    neural tube closure IEA
    Inferred from Electronic Annotation
    more info
     
    outflow tract septum morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of T-helper 2 cell differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of interleukin-13 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of interleukin-4 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of interleukin-5 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of transcription from RNA polymerase II promoter IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transcription from RNA polymerase II promoter IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transcription, DNA-templated IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    prostate gland development IEA
    Inferred from Electronic Annotation
    more info
     
    protein phosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of myelination IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of synaptic plasticity IEA
    Inferred from Electronic Annotation
    more info
     
    response to cytokine IEA
    Inferred from Electronic Annotation
    more info
     
    response to estradiol IEA
    Inferred from Electronic Annotation
    more info
     
    response to ethanol IEA
    Inferred from Electronic Annotation
    more info
     
    response to retinoic acid IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    response to vitamin A IEA
    Inferred from Electronic Annotation
    more info
     
    retinoic acid receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    signal transduction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    spermatogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    steroid hormone mediated signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    trachea cartilage development IEA
    Inferred from Electronic Annotation
    more info
     
    transcription initiation from RNA polymerase II promoter TAS
    Traceable Author Statement
    more info
     
    ureteric bud development IEA
    Inferred from Electronic Annotation
    more info
     
    ventricular cardiac muscle cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    actin cytoskeleton IDA
    Inferred from Direct Assay
    more info
     
    cell surface IC
    Inferred by Curator
    more info
    PubMed 
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    dendrite IEA
    Inferred from Electronic Annotation
    more info
     
    neuronal cell body IEA
    Inferred from Electronic Annotation
    more info
     
    nuclear chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    Preferred Names
    retinoic acid receptor alpha
    Names
    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

    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
      5001..53473
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000964.3NP_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, OTTHUMP00000164453, ENST00000254066, OTTHUMT00000257136
      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_001024809.3NP_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, CB105313
      Consensus CDS
      CCDS42317.1
      UniProtKB/Swiss-Prot
      P10276
      UniProtKB/TrEMBL
      F1D8N9
      Related
      ENSP00000377643, OTTHUMP00000164456, ENST00000394081, OTTHUMT00000257139
      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_001145301.2NP_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, OTTHUMP00000164454, ENST00000394089, OTTHUMT00000257137
      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_001145302.2NP_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, OTTHUMP00000262026, ENST00000425707, OTTHUMT00000447443
      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 Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p7 Primary Assembly

      Range
      40309171..40357643
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011525095.1XP_011523397.1  

      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  

      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  

      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  

      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_005257552.4XP_005257609.1  

      See identical proteins and their annotated locations for XP_005257609.1

      UniProtKB/TrEMBL
      A8MUP8
      Related
      ENSP00000377648, OTTHUMP00000164455, ENST00000394086, OTTHUMT00000257138
      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_017024920.1XP_016880409.1  

      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

    Alternate CHM1_1.1

    Genomic

    1. NC_018928.2 Alternate CHM1_1.1

      Range
      38700731..38749203
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    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.
    Support Center