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Rxra retinoid X receptor alpha [ Rattus norvegicus (Norway rat) ]

Gene ID: 25271, updated on 27-Nov-2024

Summary

Official Symbol
Rxraprovided by RGD
Official Full Name
retinoid X receptor alphaprovided by RGD
Primary source
RGD:3610
See related
EnsemblRapid:ENSRNOG00000009446 AllianceGenome:RGD:3610
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 nuclear retinoic acid receptor binding activity; nuclear thyroid hormone receptor binding activity; and protein domain specific binding activity. Contributes to double-stranded DNA binding activity. Involved in several processes, including cellular response to insulin stimulus; response to vitamin A; and response to vitamin D. Located in axon. Biomarker of alcoholic cardiomyopathy and prostate carcinoma in situ. Human ortholog(s) of this gene implicated in pancreatic cancer. Orthologous to human RXRA (retinoid X receptor alpha). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Liver (RPKM 297.8), Muscle (RPKM 203.4) and 9 other tissues See more
Orthologs
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Genomic context

See Rxra in Genome Data Viewer
Location:
3p12
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (31387892..31474415)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (10989832..11076366)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (6272560..6295354)

Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene U6atac minor spliceosomal RNA Neighboring gene uncharacterized LOC134486350 Neighboring gene collagen type V alpha 1 chain Neighboring gene ficolin B

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 domain binding IEA
Inferred from Electronic Annotation
more info
 
enables DNA binding domain binding ISO
Inferred from Sequence Orthology
more info
 
enables DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
enables LBD domain binding IEA
Inferred from Electronic Annotation
more info
 
enables LBD domain binding ISO
Inferred from Sequence Orthology
more info
 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables RNA polymerase II intronic transcription 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 chromatin DNA binding ISO
Inferred from Sequence Orthology
more info
 
contributes_to double-stranded DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables enzyme binding IEA
Inferred from Electronic Annotation
more info
 
enables enzyme binding ISO
Inferred from Sequence Orthology
more info
 
enables identical protein binding IEA
Inferred from Electronic Annotation
more info
 
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
 
enables nuclear receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
 
contributes_to nuclear receptor activity ISO
Inferred from Sequence Orthology
more info
 
enables nuclear receptor activity ISO
Inferred from Sequence Orthology
more info
 
enables nuclear retinoic acid receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables nuclear steroid receptor activity IEA
Inferred from Electronic Annotation
more info
 
enables nuclear steroid receptor activity TAS
Traceable Author Statement
more info
PubMed 
enables nuclear thyroid hormone receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables nuclear vitamin D receptor binding IEA
Inferred from Electronic Annotation
more info
 
enables nuclear vitamin D receptor binding ISO
Inferred from Sequence Orthology
more info
 
enables peptide binding IEA
Inferred from Electronic Annotation
more info
 
enables peptide binding ISO
Inferred from Sequence Orthology
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein domain specific binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein-containing complex binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables retinoic acid binding IEA
Inferred from Electronic Annotation
more info
 
enables retinoic acid binding ISO
Inferred from Sequence Orthology
more info
 
enables retinoic acid-responsive element binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables retinoic acid-responsive element binding IEA
Inferred from Electronic Annotation
more info
 
enables retinoic acid-responsive element binding ISO
Inferred from Sequence Orthology
more info
 
enables sequence-specific DNA binding IEA
Inferred from Electronic Annotation
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
 
contributes_to transcription cis-regulatory region 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 transcription coregulator binding IEA
Inferred from Electronic Annotation
more info
 
enables transcription coregulator binding ISO
Inferred from Sequence Orthology
more info
 
enables vitamin D response element binding IEA
Inferred from Electronic Annotation
more info
 
contributes_to vitamin D response element binding ISO
Inferred from Sequence Orthology
more info
 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
enables zinc ion binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
involved_in axon regeneration IEP
Inferred from Expression Pattern
more info
PubMed 
acts_upstream_of_or_within camera-type eye development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within cardiac muscle cell proliferation 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 insulin stimulus IEP
Inferred from Expression Pattern
more info
PubMed 
acts_upstream_of_or_within embryo implantation ISO
Inferred from Sequence Orthology
more info
 
involved_in female pregnancy IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in gene expression ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within heart development ISO
Inferred from Sequence Orthology
more info
 
involved_in hormone-mediated signaling pathway ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within in utero embryonic 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 IEA
Inferred from Electronic Annotation
more info
 
involved_in mRNA transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within maternal placenta development ISO
Inferred from Sequence Orthology
more info
 
involved_in midgut development IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in negative regulation of cell population proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
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 transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in nervous system development IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in peroxisome proliferator activated receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in peroxisome proliferator activated receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in placenta development IEP
Inferred from Expression Pattern
more info
PubMed 
acts_upstream_of_or_within placenta development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within positive regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of thyroid hormone receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
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
 
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
 
acts_upstream_of_or_within positive regulation of translational initiation by iron ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of vitamin D receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of vitamin D receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within regulation of branching involved in prostate gland morphogenesis ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of myelination IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in response to ethanol IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to glucocorticoid IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to glucocorticoid IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in response to nutrient IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to organic cyclic compound IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to retinoic acid IEA
Inferred from Electronic Annotation
more info
 
involved_in response to retinoic acid IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to retinoic acid ISO
Inferred from Sequence Orthology
more info
 
involved_in response to selenium ion IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to vitamin A IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to vitamin D 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 IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within retinoic acid receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in retinoic acid receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development ISO
Inferred from Sequence Orthology
more info
 
involved_in steroid hormone receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within ventricular cardiac muscle cell differentiation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within ventricular cardiac muscle tissue morphogenesis ISO
Inferred from Sequence Orthology
more info
 
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 IEA
Inferred from Electronic Annotation
more info
 
part_of RNA polymerase II transcription regulator complex ISO
Inferred from Sequence Orthology
more info
 
located_in axon IDA
Inferred from Direct Assay
more info
PubMed 
located_in chromatin IEA
Inferred from Electronic Annotation
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 mitochondrion IEA
Inferred from Electronic Annotation
more info
 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 
part_of receptor complex IEA
Inferred from Electronic Annotation
more info
 
part_of receptor 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 RXR-alpha
Names
nuclear receptor subfamily 2 group B 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_012805.3NP_036937.2  retinoic acid receptor RXR-alpha

    See identical proteins and their annotated locations for NP_036937.2

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000003
    UniProtKB/TrEMBL
    A0A8I6GFA6, F6T454, Q0VJ96
    Conserved Domains (3) summary
    cd06943
    Location:234445
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:138214
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:18131
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1

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_086021.1 Reference GRCr8

    Range
    31387892..31474415
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039104342.2XP_038960270.1  retinoic acid receptor RXR-alpha isoform X2

    UniProtKB/TrEMBL
    A0A8I6AQ23, A0A8I6GFA6
    Related
    ENSRNOP00000091257.1, ENSRNOT00000100573.2
    Conserved Domains (3) summary
    cd06943
    Location:274485
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:178254
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:58171
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
  2. XM_063283140.1XP_063139210.1  retinoic acid receptor RXR-alpha isoform X1

    Related
    ENSRNOP00000012892.4, ENSRNOT00000012892.6