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

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: human mouse all
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Genomic context

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_086021.1 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: 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

RXRalpha Blocks Nerve Regeneration after Spinal Cord Injury by Targeting p66shc.
Title: RXRα Blocks Nerve Regeneration after Spinal Cord Injury by Targeting p66shc.
RXRalpha and MRTF-A have a synergistic effect in the retinoic acid-induced neural-like differentiation of adult bone marrow-derived mesenchymal stem cells.
Title: RXRα and MRTF-A have a synergistic effect in the retinoic acid-induced neural-like differentiation of adult bone marrow-derived mesenchymal stem cells.
A complex and coordinated time-dependent interplay between pro- and anti-inflammatory signaling pathways highlights a potential anti-inflammatory role of LXR/RXR, PPARalpha/RXRalpha and STAT3 signaling pathways in resolving inflammatory corneal angiogenesis.
Title: Time-dependent LXR/RXR pathway modulation characterizes capillary remodeling in inflammatory corneal neovascularization.
Data suggest cells of the adrenal gland that contain RXRalpha are primarily localized in zona fasciculata and adrenal medulla with RXRalpha almost exclusively localized in cell nucleus; cells that contain RXRbeta are primarily localized in zona fasciculata. RXR ligands, such as all-trans-retinoic acid and long-chain polyunsaturated fatty acids, are also present in the adrenal gland.
Title: Fundamental studies of adrenal retinoid-X-receptor: Protein isoform, tissue expression, subcellular distribution, and ligand availability.
The results suggest that an increase in the expression of PPARalpha/beta/gamma and RXRalpha as well as a decrease in AP-1 and importin-alpha3 expression/activity participates in the protective effect of 5,14-HEDGE against hypotension, tachycardia, and inflammation during endotoxemia and thus have a beneficial effect in septic shock treatment
Title: Contribution of PPARα/β/γ, AP-1, importin-α3, and RXRα to the protective effect of 5,14-HEDGE, a 20-HETE mimetic, against hypotension, tachycardia, and inflammation in a rat model of septic shock.
The results imply that activation of RXRa was required for DHA protection whereas Trk receptors were not involved in this protection.
Title: Retinoid X receptor activation is essential for docosahexaenoic acid protection of retina photoreceptors.
RXRalpha were hardly detected in female brain, but were detected more frequently in male rats.
Title: Expression of retinoic acid receptors and retinoid X receptors in normal and vitamin A deficient adult rat brain.
We showed that the embryo hearts from vitamin A insufficient groups exhibited ultrastructural changes and significantly lowe expression of GATA-4, RARalpha and gamma, and higher expression of RXRalpha and beta.
Title: Ectopic expression of retinoic acid receptors and change of myocardial structure in the offspring heart with vitamin A deficiency.
a potential role of CRBP1 in the regulation of beta-catenin turnover which can greatly affect the process of osteogenesis and adipogenesis of mesenchymal stem cells
Title: Cellular retinol-binding protein 1 (CRBP-1) regulates osteogenenesis and adipogenesis of mesenchymal stem cells through inhibiting RXRα-induced β-catenin degradation.
The impaired RAR/RXR signaling and oxidative stress/JNK pathway forms a vicious circle, which significantly contributes to hyperglycemia induced cardiomyocyte apoptosis.
Title: High glucose-induced repression of RAR/RXR in cardiomyocytes is mediated through oxidative stress/JNK signaling.

Submit: New GeneRIF Correction See all GeneRIFs (21)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AU047320 (e-PCR)
- UniSTS:110624

D3Arb4 (e-PCR)
- UniSTS:239928

Rxra (e-PCR), detects polymorphism
- UniSTS:186540

Rxra (e-PCR), detects polymorphism
- UniSTS:536547

Rxra (e-PCR), detects polymorphism
- UniSTS:465406

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

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Preferred Names: retinoic acid receptor RXR-alpha

Names: nuclear receptor subfamily 2 group B 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_012805.3 → NP_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:234 → 445

NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily

cd06956
Location:138 → 214

NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers

pfam11825
Location:18 → 131

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

NC_086021.1 Reference GRCr8

Range

31387892..31474415

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A8I6AQ23, A0A8I6GFA6

Related

ENSRNOP00000091257.1, ENSRNOT00000100573.2

Conserved Domains (3) summary

cd06943
Location:274 → 485

NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily

cd06956
Location:178 → 254

NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers

pfam11825
Location:58 → 171

Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
XM_063283140.1 → XP_063139210.1 retinoic acid receptor RXR-alpha isoform X1

Related

ENSRNOP00000012892.4, ENSRNOT00000012892.6