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

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: human all
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Genomic context

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_000077.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Comparative Phenotyping of Mice Reveals Canonical and Noncanonical Physiological Functions of TRalpha and TRbeta.
Title: Comparative Phenotyping of Mice Reveals Canonical and Noncanonical Physiological Functions of TRα and TRβ.
Hypothalamic Thyroid Hormone Receptor alpha1 Signaling Controls Body Temperature.
Title: Hypothalamic Thyroid Hormone Receptor α1 Signaling Controls Body Temperature.
Canonical and Noncanonical Contribution of Thyroid Hormone Receptor Isoforms Alpha and Beta to Cardiac Hypertrophy and Heart Rate in Male Mice.
Title: Canonical and Noncanonical Contribution of Thyroid Hormone Receptor Isoforms Alpha and Beta to Cardiac Hypertrophy and Heart Rate in Male Mice.
Aberrant expression of thyroidal hormone receptor alpha exasperating mitochondrial dysfunction induced sarcopenia in aged mice.
Title: Aberrant expression of thyroidal hormone receptor α exasperating mitochondrial dysfunction induced sarcopenia in aged mice.
Thyroid hormone receptor Thra and Thrb knockout differentially affects osteoblast biology and thyroid hormone responsiveness in vitro.
Title: Thyroid hormone receptor Thra and Thrb knockout differentially affects osteoblast biology and thyroid hormone responsiveness in vitro.
Morphological and Functional Colonic Defects Caused by a Mutated Thyroid Hormone Receptor alpha.
Title: Morphological and Functional Colonic Defects Caused by a Mutated Thyroid Hormone Receptor α.
Regulation of the THRA gene, encoding the thyroid hormone nuclear receptor TRalpha1, in intestinal lesions.
Title: Regulation of the THRA gene, encoding the thyroid hormone nuclear receptor TRα1, in intestinal lesions.
Ontogeny of TRalpha1 expression in the mouse testis and epididymis during postnatal development.
Title: Ontogeny of TRα1 expression in the mouse testis and epididymis during postnatal development.
A disease-associated mutation in thyroid hormone receptor alpha1 causes hearing loss and sensory hair cell patterning defects in mice.
Title: A disease-associated mutation in thyroid hormone receptor α1 causes hearing loss and sensory hair cell patterning defects in mice.
Thyroid Hormone Receptor alpha1 Mutants Impair B Lymphocyte Development in a Mouse Model.
Title: Thyroid Hormone Receptor α1 Mutants Impair B Lymphocyte Development in a Mouse Model.

Submit: New GeneRIF Correction See all GeneRIFs (128)

Variation

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Alleles

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

Endonuclease-mediated (10) 1 citation
Targeted (16) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PMC64989P1 (e-PCR)
- UniSTS:273425

PMC64989P2 (e-PCR)
- UniSTS:273426

AW259572 (e-PCR)
- UniSTS:180310

Thra (e-PCR), detects polymorphism
- UniSTS:463227

Thra (e-PCR), detects polymorphism
- UniSTS:507277

MARC_26124-26125:1030369359:1 (e-PCR)
- UniSTS:268948

THRA (e-PCR), detects polymorphism
- UniSTS:279191

PMC87157P1 (e-PCR)
- UniSTS:273584

PMC87157P2 (e-PCR)
- UniSTS:273585

THRA_2263 (e-PCR)
- UniSTS:281056

D17S2189 (e-PCR)
- UniSTS:53986

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

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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)

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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)

NM_001313983.1 → NP_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:162 → 370

NR_LBD_TR; The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear receptors

cd06961
Location:52 → 138

NR_DBD_TR; DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers
NM_178060.4 → NP_835161.1 thyroid hormone receptor alpha isoform 2

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:162 → 404

NR_LBD_TR; The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear receptors

cd06961
Location:52 → 138

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

NC_000077.7 Reference GRCm39 C57BL/6J

Range

98631539..98659832

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A0R4J1R8

Conserved Domains (2) summary

cd06935
Location:162 → 404

NR_LBD_TR; The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear receptors

cd06961
Location:52 → 138

NR_DBD_TR; DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers