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    Rara retinoic acid receptor, alpha [ Rattus norvegicus (Norway rat) ]

    Gene ID: 24705, updated on 3-Dec-2024

    Summary

    Official Symbol
    Raraprovided by RGD
    Official Full Name
    retinoic acid receptor, alphaprovided by RGD
    Primary source
    RGD:3534
    See related
    EnsemblRapid:ENSRNOG00000009972 AllianceGenome:RGD:3534
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Enables heterocyclic compound binding activity; histone deacetylase binding activity; and nucleic acid binding activity. Involved in several processes, including reproductive structure development; response to estradiol; and response to vitamin A. Located in dendrite and perinuclear region of cytoplasm. Biomarker of amyotrophic lateral sclerosis. Human ortholog(s) of this gene implicated in acute promyelocytic leukemia. Orthologous to human RARA (retinoic acid receptor alpha). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Lung (RPKM 102.3), Kidney (RPKM 75.0) and 9 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Rara in Genome Data Viewer
    Location:
    10q31
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (84379780..84424371)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (83883490..83928932)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (86838819..86884224)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene U6 spliceosomal RNA Neighboring gene WAS/WASL interacting protein family, member 2 Neighboring gene cell division cycle 6 Neighboring gene uncharacterized LOC134480867 Neighboring gene uncharacterized LOC120095181 Neighboring gene gap junction protein, delta 3 Neighboring gene DNA topoisomerase II alpha

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA-binding transcription repressor activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables alpha-actinin binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables chromatin DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables enzyme binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables heterocyclic compound binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone deacetylase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables mRNA 5'-UTR binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables mRNA regulatory element binding translation repressor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables nuclear receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables nuclear receptor activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables nuclear receptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables protein domain specific binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein kinase A binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein kinase B binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables retinoic acid binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables retinoic acid-responsive element binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables sequence-specific double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables signaling receptor binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables transcription cis-regulatory region binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables transcription coactivator binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in Sertoli cell fate commitment ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in apoptotic cell clearance ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within bone development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cellular response to estrogen stimulus ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cellular response to lipopolysaccharide ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cellular response to retinoic acid ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within chondroblast differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within embryonic camera-type eye development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within face development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in female pregnancy IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in germ cell development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within glandular epithelial cell development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within growth plate cartilage development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in hippocampus development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    acts_upstream_of_or_within limb development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in liver development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in mRNA transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in male gonad development IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within multicellular organism growth ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within negative regulation of cartilage development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within negative regulation of cell differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of cell population proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of granulocyte differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of miRNA transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of translation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of tumor necrosis factor production ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of type II interferon production ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within neural tube closure ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in outflow tract septum morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of T-helper 2 cell differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of cell cycle ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within positive regulation of cell population proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of cell population proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of interleukin-13 production ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of interleukin-4 production ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of interleukin-5 production ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of neuron differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in prostate gland development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in protein phosphorylation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within regulation of granulocyte differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within regulation of hematopoietic progenitor cell differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of myelination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of synaptic plasticity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to cytokine IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to estradiol IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to ethanol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within response to retinoic acid ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in response to retinoic acid ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in response to vitamin A IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in retinoic acid receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in retinoic acid receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in spermatogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within trachea cartilage development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within ureteric bud development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within ventricular cardiac muscle cell differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    part_of RNA polymerase II transcription regulator complex ISO
    Inferred from Sequence Orthology
    more info
     
    located_in actin cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
     
    located_in actin cytoskeleton ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in chromatin ISO
    Inferred from Sequence Orthology
    more info
     
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    located_in dendrite IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
     
    part_of protein-containing complex ISO
    Inferred from Sequence Orthology
    more info
     
    part_of transcription regulator complex ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    retinoic acid receptor alpha

    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.

    mRNA and Protein(s)

    1. NM_001429976.1NP_001416905.1  retinoic acid receptor alpha isoform a

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010
      UniProtKB/TrEMBL
      A0A0G2JW78, A6HIV8, Q9QWJ1
    2. NM_001429977.1NP_001416906.1  retinoic acid receptor alpha isoform a

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010
      UniProtKB/TrEMBL
      A0A0G2JW78, A6HIV8, Q9QWJ1
    3. NM_001429978.1NP_001416907.1  retinoic acid receptor alpha isoform a

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010
      UniProtKB/TrEMBL
      A0A0G2JW78, A6HIV8, Q9QWJ1
    4. NM_031528.3NP_113716.2  retinoic acid receptor alpha isoform b

      See identical proteins and their annotated locations for NP_113716.2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010
      UniProtKB/TrEMBL
      A6HIV9, F7EXR0, Q499N1, Q9QWJ1
      Related
      ENSRNOP00000008659.4, ENSRNOT00000008659.6
      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

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086028.1 Reference GRCr8

      Range
      84379780..84424371
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063268421.1XP_063124491.1  retinoic acid receptor alpha isoform X1

      UniProtKB/TrEMBL
      A0A0G2JW78, A6HIV8, Q9QWJ1
    2. XM_017597011.3XP_017452500.1  retinoic acid receptor alpha isoform X1

      Related
      ENSRNOP00000069776.1, ENSRNOT00000084644.3
      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_063268422.1XP_063124492.1  retinoic acid receptor alpha isoform X1

      UniProtKB/TrEMBL
      A0A0G2JW78, A6HIV8, Q9QWJ1
    4. XM_063268423.1XP_063124493.1  retinoic acid receptor alpha isoform X1

      UniProtKB/TrEMBL
      A0A0G2JW78, A6HIV8, Q9QWJ1
    5. XM_039085214.2XP_038941142.1  retinoic acid receptor alpha isoform X1

      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
    6. XM_063268424.1XP_063124494.1  retinoic acid receptor alpha isoform X1

      UniProtKB/TrEMBL
      A0A0G2JW78, A6HIV8, Q9QWJ1
    7. XM_039085219.2XP_038941147.1  retinoic acid receptor alpha isoform X1

      UniProtKB/TrEMBL
      A0A0G2JW78, A6HIV8, Q9QWJ1
      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