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    Rara retinoic acid receptor, alpha [ Mus musculus (house mouse) ]

    Gene ID: 19401, updated on 7-May-2017
    Official Symbol
    Raraprovided by MGI
    Official Full Name
    retinoic acid receptor, alphaprovided by MGI
    Primary source
    MGI:MGI:97856
    See related
    Ensembl:ENSMUSG00000037992 Vega:OTTMUSG00000006440
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    RAR; Nr1b1; RARalpha1
    Orthologs
    Location:
    11 D; 11 62.76 cM
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 11 NC_000077.6 (98927813..98974942)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 11 NC_000077.5 (98799010..98836256)

    Chromosome 11 - NC_000077.6Genomic Context describing neighboring genes Neighboring gene WAS/WASL interacting protein family, member 2 Neighboring gene cell division cycle 6 Neighboring gene predicted gene, 46294 Neighboring gene gap junction protein, delta 3 Neighboring gene topoisomerase (DNA) II alpha

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    RNA polymerase II regulatory region DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    RNA polymerase II regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    alpha-actinin binding ISO
    Inferred from Sequence Orthology
    more info
     
    chromatin DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    drug binding ISO
    Inferred from Sequence Orthology
    more info
     
    enzyme binding ISO
    Inferred from Sequence Orthology
    more info
     
    histone deacetylase binding ISO
    Inferred from Sequence Orthology
    more info
     
    mRNA 5'-UTR binding ISO
    Inferred from Sequence Orthology
    more info
     
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    phosphatidylinositol 3-kinase regulator activity ISO
    Inferred from Sequence Orthology
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein domain specific binding ISO
    Inferred from Sequence Orthology
    more info
     
    protein heterodimerization activity ISO
    Inferred from Sequence Orthology
    more info
     
    protein kinase A binding ISO
    Inferred from Sequence Orthology
    more info
     
    protein kinase B binding ISO
    Inferred from Sequence Orthology
    more info
     
    receptor binding ISO
    Inferred from Sequence Orthology
    more info
     
    regulatory region DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    retinoic acid binding ISO
    Inferred from Sequence Orthology
    more info
     
    retinoic acid receptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    retinoic acid receptor activity ISO
    Inferred from Sequence Orthology
    more info
     
    retinoic acid-responsive element binding ISO
    Inferred from Sequence Orthology
    more info
     
    sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    sequence-specific DNA binding IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    steroid hormone receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    transcription coactivator activity ISO
    Inferred from Sequence Orthology
    more info
     
    transcription corepressor activity ISO
    Inferred from Sequence Orthology
    more info
     
    transcription factor activity, sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription factor activity, sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
     
    transcription regulatory region DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    translation repressor activity, nucleic acid binding ISO
    Inferred from Sequence Orthology
    more info
     
    zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    Sertoli cell fate commitment IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    apoptotic cell clearance ISO
    Inferred from Sequence Orthology
    more info
     
    bone development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    cellular response to estrogen stimulus ISO
    Inferred from Sequence Orthology
    more info
     
    cellular response to lipopolysaccharide IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cellular response to retinoic acid ISO
    Inferred from Sequence Orthology
    more info
     
    chondroblast differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    embryonic camera-type eye development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    face development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    germ cell development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    glandular epithelial cell development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    growth plate cartilage development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    limb development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    male gonad development ISO
    Inferred from Sequence Orthology
    more info
     
    multicellular organism growth IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    negative regulation of apoptotic process IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    negative regulation of cartilage development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of cell proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    negative regulation of gene expression IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    negative regulation of granulocyte differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    negative regulation of interferon-gamma production ISO
    Inferred from Sequence Orthology
    more info
     
    negative regulation of transcription from RNA polymerase II promoter IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of transcription from RNA polymerase II promoter IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    negative regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
     
    negative regulation of translation ISO
    Inferred from Sequence Orthology
    more info
     
    negative regulation of translational initiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of tumor necrosis factor production ISO
    Inferred from Sequence Orthology
    more info
     
    neural tube closure IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    outflow tract septum morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of ERK1 and ERK2 cascade ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of T-helper 2 cell differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of binding ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of cell cycle ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of cell proliferation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of cell proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of interleukin-13 production ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of interleukin-4 production ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of interleukin-5 production ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of phosphatidylinositol 3-kinase signaling ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of protein kinase B signaling ISO
    Inferred from Sequence Orthology
    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 IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of transcription from RNA polymerase II promoter ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
     
    protein phosphorylation ISO
    Inferred from Sequence Orthology
    more info
     
    regulation of apoptotic process ISO
    Inferred from Sequence Orthology
    more info
     
    regulation of granulocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of myelination ISO
    Inferred from Sequence Orthology
    more info
     
    regulation of synaptic plasticity ISO
    Inferred from Sequence Orthology
    more info
     
    regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    response to ethanol ISO
    Inferred from Sequence Orthology
    more info
     
    response to retinoic acid IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    response to retinoic acid ISO
    Inferred from Sequence Orthology
    more info
     
    retinoic acid receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    signal transduction ISO
    Inferred from Sequence Orthology
    more info
     
    spermatogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    steroid hormone mediated signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    trachea cartilage development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    ureteric bud development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    ventricular cardiac muscle cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    actin cytoskeleton ISO
    Inferred from Sequence Orthology
    more info
     
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    dendrite IDA
    Inferred from Direct Assay
    more info
    PubMed 
    dendrite ISO
    Inferred from Sequence Orthology
    more info
     
    neuron projection ISO
    Inferred from Sequence Orthology
    more info
     
    neuronal cell body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nuclear chromatin ISO
    Inferred from Sequence Orthology
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    perinuclear region of cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    Preferred Names
    retinoic acid receptor alpha
    Names
    RAR alpha 1
    RAR-alpha
    nuclear receptor subfamily 1 group B member 1

    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_001176528.1NP_001169999.1  retinoic acid receptor alpha isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) has an alternate 5' sequence including the 5' CDS, as compared to variant 1. The resulting isoform (2) has a shorter and different N-terminus, as compared to isoform 1.
      Source sequence(s)
      AL591067
      Consensus CDS
      CCDS48905.1
      UniProtKB/Swiss-Prot
      P11416
      Related
      ENSMUSP00000103097.2, OTTMUSP00000006837, ENSMUST00000107473.2, OTTMUST00000014709
      Conserved Domains (2) summary
      cd06937
      Location:183413
      NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
      cd06964
      Location:79163
      NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
    2. NM_001177302.1NP_001170773.1  retinoic acid receptor alpha isoform 1

      See identical proteins and their annotated locations for NP_001170773.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has an additional exon in the 5' UTR, as compared to variant 1. Variants 1-3 encode the same isoform 1.
      Source sequence(s)
      AL591067
      Consensus CDS
      CCDS36304.1
      UniProtKB/Swiss-Prot
      P11416
      UniProtKB/TrEMBL
      Q3U3R3
      Related
      ENSMUSP00000069744.3, OTTMUSP00000006834, ENSMUST00000068133.9, OTTMUST00000014706
      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. NM_001177303.1NP_001170774.1  retinoic acid receptor alpha isoform 1

      See identical proteins and their annotated locations for NP_001170774.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) has an alternate 5' UTR exon, as compared to variant 1. Variants 1-3 encode the same isoform 1.
      Source sequence(s)
      AK042163, AL591067
      Consensus CDS
      CCDS36304.1
      UniProtKB/Swiss-Prot
      P11416
      UniProtKB/TrEMBL
      Q3U3R3
      Related
      ENSMUSP00000129791.1, ENSMUST00000164748.7
      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_009024.2NP_033050.2  retinoic acid receptor alpha isoform 1

      See identical proteins and their annotated locations for NP_033050.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AK042163, AL591067
      Consensus CDS
      CCDS36304.1
      UniProtKB/Swiss-Prot
      P11416
      UniProtKB/TrEMBL
      Q3U3R3
      Related
      ENSMUSP00000103099.2, OTTMUSP00000006835, ENSMUST00000107475.8, OTTMUST00000014707
      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

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106 details...Open this link in a new tab

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

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000077.6 Reference GRCm38.p4 C57BL/6J

      Range
      98927813..98974942
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006532592.3XP_006532655.1  retinoic acid receptor alpha isoform X1

      See identical proteins and their annotated locations for XP_006532655.1

      UniProtKB/Swiss-Prot
      P11416
      UniProtKB/TrEMBL
      Q3U3R3
      Related
      ENSMUSP00000103098.1, OTTMUSP00000006836, ENSMUST00000107474.7, OTTMUST00000014708
      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_006532593.2XP_006532656.1  retinoic acid receptor alpha isoform X1

      See identical proteins and their annotated locations for XP_006532656.1

      UniProtKB/Swiss-Prot
      P11416
      UniProtKB/TrEMBL
      Q3U3R3
      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_017314353.1XP_017169842.1  retinoic acid receptor alpha isoform X1

      UniProtKB/Swiss-Prot
      P11416
      UniProtKB/TrEMBL
      Q3U3R3
      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_006532597.2XP_006532660.1  retinoic acid receptor alpha isoform X2

      See identical proteins and their annotated locations for XP_006532660.1

      UniProtKB/TrEMBL
      Q3U5E7
      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
    5. XM_006532596.2XP_006532659.1  retinoic acid receptor alpha isoform X2

      See identical proteins and their annotated locations for XP_006532659.1

      UniProtKB/TrEMBL
      Q3U5E7
      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
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