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

Gene ID: 21833, updated on 21-Dec-2022

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
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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
109 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 nuclear receptor subfamily 1, group D, member 1 Neighboring gene predicted gene, 31862 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

Homology

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
PubMed 
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 metal ion 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 nuclear receptor activity ISO
Inferred from Sequence Orthology
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 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 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
PubMed 
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 ISO
Inferred from Sequence Orthology
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
 
involved_in negative regulation of DNA-binding transcription factor activity 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 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
PubMed 
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 mediated signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of thyroid hormone mediated 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
PubMed 
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
 
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
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 mediated 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
PubMed 
acts_upstream_of_or_within thyroid gland development IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in thyroid hormone mediated signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 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 cytoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in cytosol ISO
Inferred from Sequence Orthology
more info
 
located_in mitochondrion ISO
Inferred from Sequence Orthology
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
    P63058
    UniProtKB/TrEMBL
    A0A8C6I7L5
    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/Swiss-Prot
    P63058
    UniProtKB/TrEMBL
    A0A6P5QUJ1, A0A8C6I6M2
    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: Mus musculus Annotation Release 109 details...Open this link in a new tab

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
    A0A6P5QUJ1, A0A8C6I6M2
    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