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    Thra thyroid hormone receptor alpha [ Mus musculus (house mouse) ]

    Gene ID: 21833, updated on 3-Dec-2024

    Summary

    Official Symbol
    Thraprovided by MGI
    Official Full Name
    thyroid hormone receptor alphaprovided by MGI
    Primary source
    MGI:MGI:98742
    See related
    Ensembl:ENSMUSG00000058756 AllianceGenome:MGI:98742
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Rvr; Erba; Nr1a1; Thra1; Thra2; T3R[a]; T3Ralpha; c-erbA-1; c-erbAalpha; c-erbA-alpha; 6430529J03Rik
    Summary
    The protein encoded by this gene is one of several nuclear hormone receptors that bind thyroid hormones such as triiodothyronine and thyroxine with high affinity. The encoded protein is a transcription factor that can activate or repress transcription. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Sep 2015]
    Expression
    Broad expression in CNS E18 (RPKM 201.0), frontal lobe adult (RPKM 126.0) and 20 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Thra in Genome Data Viewer
    Location:
    11 D; 11 62.58 cM
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (98631539..98659832)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (98740776..98769006)

    Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene mediator complex subunit 24 Neighboring gene predicted gene, 22059 Neighboring gene predicted gene, 31252 Neighboring gene STARR-positive B cell enhancer ABC_E3017 Neighboring gene STARR-positive B cell enhancer ABC_E3018 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:98636882-98637065 Neighboring gene nuclear receptor subfamily 1, group D, member 1 Neighboring gene predicted gene, 31862 Neighboring gene STARR-positive B cell enhancer ABC_E468 Neighboring gene male specific lethal 1 Neighboring gene predicted gene 12359

    Genomic regions, transcripts, and products

    Expression

    • 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

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    NOT enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA-binding transcription factor activity, RNA polymerase II-specific 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 TBP-class protein binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables TBP-class protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables chromatin DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables general transcription initiation factor binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables intronic transcription regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    more info
     
    enables nuclear receptor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables nuclear receptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein domain specific binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein domain specific binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein homodimerization activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein-containing complex binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein-containing complex binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables single-stranded RNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables thyroid hormone binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    enables thyroid hormone binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables transcription cis-regulatory region binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription cis-regulatory region binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of_or_within animal organ morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within cartilage condensation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within erythrocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within female courtship behavior IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in hormone-mediated signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in hormone-mediated signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in intracellular receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within learning or memory IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in mRNA transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in mRNA transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of DNA-templated transcription initiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of RNA polymerase II transcription preinitiation complex assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of RNA polymerase II transcription preinitiation complex assembly 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 ossification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of canonical Wnt signaling pathway IC
    Inferred by Curator
    more info
    PubMed 
    involved_in positive regulation of cold-induced thermogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of female receptivity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of thyroid hormone receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of thyroid hormone receptor signaling pathway ISO
    Inferred from Sequence Orthology
    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 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 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 by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within regulation of heart contraction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within regulation of lipid catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within regulation of myeloid cell apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within regulation of thyroid hormone receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within response to cold IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in retinoic acid receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within thyroid gland development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in thyroid hormone receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within type I pneumocyte differentiation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of RNA polymerase II transcription regulator complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of RNA polymerase II transcription regulator complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of RNA polymerase II transcription regulator complex 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
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    thyroid hormone receptor alpha
    Names
    TR alpha 1
    TR alpha 2
    nuclear receptor subfamily 1 group A member 1

    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_001313983.1NP_001300912.1  thyroid hormone receptor alpha isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL590963, BC046795, CJ117879
      Consensus CDS
      CCDS83893.1
      UniProtKB/Swiss-Prot
      A3KFN4, P63058, Q542U8, Q80Y90
      UniProtKB/TrEMBL
      A0A0R4J1R8
      Related
      ENSMUSP00000068281.6, ENSMUST00000064187.12
      Conserved Domains (2) summary
      cd06935
      Location:162370
      NR_LBD_TR; The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear receptors
      cd06961
      Location:52138
      NR_DBD_TR; DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers
    2. NM_178060.4NP_835161.1  thyroid hormone receptor alpha isoform 2

      See identical proteins and their annotated locations for NP_835161.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AK078233, BB357897, CJ117879
      Consensus CDS
      CCDS25362.1
      UniProtKB/TrEMBL
      A0A0R4J1R8
      Related
      ENSMUSP00000099428.5, ENSMUST00000103139.11
      Conserved Domains (2) summary
      cd06935
      Location:162404
      NR_LBD_TR; The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear receptors
      cd06961
      Location:52138
      NR_DBD_TR; DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000077.7 Reference GRCm39 C57BL/6J

      Range
      98631539..98659832
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030245916.2XP_030101776.1  thyroid hormone receptor alpha isoform X1

      UniProtKB/TrEMBL
      A0A0R4J1R8
      Conserved Domains (2) summary
      cd06935
      Location:162404
      NR_LBD_TR; The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear receptors
      cd06961
      Location:52138
      NR_DBD_TR; DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers