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Thra thyroid hormone receptor alpha [ Rattus norvegicus (Norway rat) ]

Gene ID: 81812, updated on 12-Jan-2022

Summary

Official Symbol
Thraprovided by RGD
Official Full Name
thyroid hormone receptor alphaprovided by RGD
Primary source
RGD:3857
See related
Ensembl:ENSRNOG00000009066
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
Also known as
ERBA1; Thra1; c-erbA-1
Summary
Enables DNA-binding transcription factor activity, RNA polymerase II-specific; nucleic acid binding activity; and protein homodimerization activity. Involved in several processes, including animal organ development; digestive tract development; and regulation of transcription, DNA-templated. Located in cytosol; mitochondrion; and nucleus. Human ortholog(s) of this gene implicated in congenital nongoitrous hypothyroidism 6 and renal cell carcinoma. Orthologous to human THRA (thyroid hormone receptor alpha). [provided by Alliance of Genome Resources, Nov 2021]
Expression
Biased expression in Brain (RPKM 397.8), Lung (RPKM 206.0) and 9 other tissues See more
Orthologs
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Genomic context

See Thra in Genome Data Viewer
Location:
10q31
Exon count:
10
Annotation release Status Assembly Chr Location
108 current mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (83701885..83729408)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (86657285..86684935)

Chromosome 10 - NC_051345.1Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORD124 Neighboring gene colony stimulating factor 3 Neighboring gene mediator complex subunit 24 Neighboring gene nuclear receptor subfamily 1, group D, member 1 Neighboring gene uncharacterized LOC108352130 Neighboring gene MSL complex subunit 1

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

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
NOT 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 factor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
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 IEA
Inferred from Electronic Annotation
more info
 
enables TBP-class protein binding ISO
Inferred from Sequence Orthology
more info
 
enables chromatin DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables chromatin DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables general transcription initiation factor binding ISO
Inferred from Sequence Orthology
more info
 
enables intronic transcription regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables nuclear receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables nuclear receptor activity IEA
Inferred from Electronic Annotation
more info
 
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 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 IDA
Inferred from Direct Assay
more info
PubMed 
enables protein-containing complex binding IDA
Inferred from Direct Assay
more info
PubMed 
enables protein-containing complex binding IEA
Inferred from Electronic Annotation
more info
 
enables protein-containing complex binding ISO
Inferred from Sequence Orthology
more info
 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables single-stranded RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables single-stranded RNA binding ISO
Inferred from Sequence Orthology
more info
 
enables steroid receptor RNA activator RNA binding ISO
Inferred from Sequence Orthology
more info
 
enables thyroid hormone binding IEA
Inferred from Electronic Annotation
more info
 
enables thyroid hormone binding ISO
Inferred from Sequence Orthology
more info
 
enables thyroid hormone binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables transcription cis-regulatory region binding IEA
Inferred from Electronic Annotation
more info
 
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
involved_in adrenal gland development IEP
Inferred from Expression Pattern
more info
PubMed 
acts_upstream_of_or_within animal organ morphogenesis ISO
Inferred from Sequence Orthology
more info
 
involved_in brain development IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in cartilage condensation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within cartilage condensation ISO
Inferred from Sequence Orthology
more info
 
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within cytoplasmic sequestering of transcription factor ISO
Inferred from Sequence Orthology
more info
 
involved_in digestive tract development IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in embryonic organ development IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in erythrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within erythrocyte differentiation ISO
Inferred from Sequence Orthology
more info
 
involved_in female courtship behavior IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within female courtship behavior ISO
Inferred from Sequence Orthology
more info
 
involved_in hormone-mediated signaling pathway IBA
Inferred from Biological aspect of Ancestor
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
 
involved_in kidney development IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in learning or memory IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within learning or memory ISO
Inferred from Sequence Orthology
more info
 
involved_in liver development IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in lung 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 negative regulation of DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
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
PubMed 
acts_upstream_of_or_within negative regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
involved_in ossification IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within ossification ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of cold-induced thermogenesis ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of cold-induced thermogenesis ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in positive regulation of female receptivity IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within positive regulation of female receptivity ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within positive regulation of myotube differentiation ISO
Inferred from Sequence Orthology
more info
 
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 
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 IEA
Inferred from Electronic Annotation
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 regulation of heart contraction IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within regulation of heart contraction ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of lipid catabolic process IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within regulation of lipid catabolic process ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of myeloid cell apoptotic process IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within regulation of myeloid cell apoptotic process ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of thyroid hormone mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within regulation of thyroid hormone mediated signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in response to cold IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within response to cold ISO
Inferred from Sequence Orthology
more info
 
involved_in response to nutrient levels IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to xenobiotic stimulus IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in thyroid gland development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within thyroid gland development ISO
Inferred from Sequence Orthology
more info
 
involved_in thyroid hormone mediated signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
 
involved_in type I pneumocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within type I pneumocyte 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 cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in cytosol IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol IEA
Inferred from Electronic Annotation
more info
 
located_in cytosol ISO
Inferred from Sequence Orthology
more info
 
located_in mitochondrion IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
thyroid hormone receptor alpha; c-erbAalpha2
Names
C-erbA-alpha
avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 1
c-erb-A thyroid hormone receptor
c-erbA-alpha2
nuclear receptor subfamily 1 group A member 1
thyroid hormone receptor alpha 1 (avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 1 formerly ERBA1)

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_001017960.2NP_001017960.1  thyroid hormone receptor alpha isoform TRalpha1

    See identical proteins and their annotated locations for NP_001017960.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (TRalpha1) differs in the 3' UTR and coding region compared to TRalpha2, resulting in a shorter isoform (TRalpha1) with a distinct C-terminus. The TRalpha1 isoform, also known as c-erbAalpha1, functions as a thyroid hormone-dependent transcription factor.
    Source sequence(s)
    JACYVU010000220
    UniProtKB/Swiss-Prot
    P63059
    Related
    ENSRNOP00000072739.1, ENSRNOT00000087346.2
    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
  2. NM_031134.2NP_112396.2  c-erbAalpha2 isoform TRalpha2

    See identical proteins and their annotated locations for NP_112396.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (TRalpha2) contains an alternate 3' terminal exon compared to variant TRalpha1. The resulting protein (c-erbAalpha2, also known as TRalpha 2) has a distinct C-terminus compared to isoform TRalpha1, and fails to bind thyroid hormones or to trans-activate thyroid hormone responsive genes.
    Source sequence(s)
    AI764185, CB580585, M31174
    UniProtKB/Swiss-Prot
    P63059
    UniProtKB/TrEMBL
    G3V764
    Related
    ENSRNOP00000012340.3, ENSRNOT00000012340.4
    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

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 108 details...Open this link in a new tab

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

Reference mRatBN7.2 Primary Assembly

Genomic

  1. NC_051345.1 Reference mRatBN7.2 Primary Assembly

    Range
    83701885..83729408
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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