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RXRA retinoid X receptor alpha [ Homo sapiens (human) ]

Gene ID: 6256, updated on 9-Feb-2020

Summary

Official Symbol
RXRAprovided by HGNC
Official Full Name
retinoid X receptor alphaprovided by HGNC
Primary source
HGNC:HGNC:10477
See related
Ensembl:ENSG00000186350 MIM:180245
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NR2B1
Summary
Retinoid X receptors (RXRs) and retinoic acid receptors (RARs) are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors function as transcription factors by binding as homodimers or heterodimers to specific sequences in the promoters of target genes. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2014]
Expression
Ubiquitous expression in skin (RPKM 34.2), fat (RPKM 23.2) and 25 other tissues See more
Orthologs

Genomic context

See RXRA in Genome Data Viewer
Location:
9q34.2
Exon count:
12
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (134326455..134440586)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (137218316..137332431)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107987039 Neighboring gene long intergenic non-protein coding RNA 2247 Neighboring gene NFE2L2 motif-containing MPRA enhancer 298 Neighboring gene RXRA intron CAGE-defined high expression enhancer Neighboring gene microRNA 4669 Neighboring gene Sharpr-MPRA regulatory region 11314 Neighboring gene uncharacterized LOC105376311

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide association study of central corneal thickness in Latinos.
NHGRI GWA Catalog
Gene-age interactions in blood pressure regulation: a large-scale investigation with the CHARGE, Global BPgen, and ICBP Consortia.
NHGRI GWA Catalog
Genome-wide association analyses identify multiple loci associated with central corneal thickness and keratoconus.
NHGRI GWA Catalog
Genome-wide association study of chemotherapeutic agent-induced severe neutropenia/leucopenia for patients in Biobank Japan.
NHGRI GWA Catalog
Genome-wide association study of intelligence: additive effects of novel brain expressed genes.
NHGRI GWA Catalog
Multidimensional prognostic risk assessment identifies association between IL12B variation and surgery in Crohn's disease.
NHGRI GWA Catalog
Population-based meta-analysis in Caucasians confirms association with COL5A1 and ZNF469 but not COL8A2 with central corneal thickness.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120 upregulates the expression of retinoid X receptor-alpha (RXRA) in human B cells PubMed
Nef nef HIV-1 Nef induces loss of F-actin assembly and inhibits retinoid receptor-mediated transcription PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ00280, FLJ00318, FLJ16020, FLJ16733, MGC102720

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DBD domain binding IDA
Inferred from Direct Assay
more info
PubMed 
DNA binding TAS
Traceable Author Statement
more info
PubMed 
DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
contributes_to DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific NAS
Non-traceable Author Statement
more info
PubMed 
LBD domain binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA polymerase II regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
chromatin DNA binding IEA
Inferred from Electronic Annotation
more info
 
double-stranded DNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
nuclear receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
nuclear receptor activity TAS
Traceable Author Statement
more info
PubMed 
nuclear receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
peptide binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
retinoic acid binding IDA
Inferred from Direct Assay
more info
PubMed 
retinoic acid-responsive element binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
retinoic acid-responsive element binding IDA
Inferred from Direct Assay
more info
PubMed 
sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
signaling receptor activity TAS
Traceable Author Statement
more info
PubMed 
steroid hormone receptor activity IEA
Inferred from Electronic Annotation
more info
 
transcription coactivator activity TAS
Traceable Author Statement
more info
PubMed 
contributes_to transcription regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
vitamin D receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
contributes_to vitamin D response element binding IDA
Inferred from Direct Assay
more info
PubMed 
zinc ion binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
anatomical structure development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
bile acid and bile salt transport TAS
Traceable Author Statement
more info
 
camera-type eye development IEA
Inferred from Electronic Annotation
more info
 
cardiac muscle cell proliferation IEA
Inferred from Electronic Annotation
more info
 
cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cholesterol metabolic process TAS
Traceable Author Statement
more info
PubMed 
embryo implantation IEA
Inferred from Electronic Annotation
more info
 
in utero embryonic development IEA
Inferred from Electronic Annotation
more info
 
maternal placenta development IEA
Inferred from Electronic Annotation
more info
 
modulation by virus of host morphology or physiology IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
peroxisome proliferator activated receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of translational initiation by iron IEA
Inferred from Electronic Annotation
more info
 
regulation of branching involved in prostate gland morphogenesis IEA
Inferred from Electronic Annotation
more info
 
regulation of lipid metabolic process TAS
Traceable Author Statement
more info
 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
response to retinoic acid IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
response to retinoic acid IMP
Inferred from Mutant Phenotype
more info
PubMed 
retinoic acid receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
retinoic acid receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development IEA
Inferred from Electronic Annotation
more info
 
steroid hormone mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
transcription initiation from RNA polymerase II promoter TAS
Traceable Author Statement
more info
 
ventricular cardiac muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
ventricular cardiac muscle tissue morphogenesis IEA
Inferred from Electronic Annotation
more info
 
vitamin metabolic process TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
RNA polymerase II transcription factor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA polymerase II transcription factor complex IDA
Inferred from Direct Assay
more info
PubMed 
mitochondrion IEA
Inferred from Electronic Annotation
more info
 
nuclear chromatin IDA
Inferred from Direct Assay
more info
PubMed 
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 
receptor complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
retinoic acid receptor RXR-alpha
Names
nuclear receptor subfamily 2 group B member 1
retinoid X nuclear receptor alpha

NCBI Reference Sequences (RefSeq)

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_001291920.1NP_001278849.1  retinoic acid receptor RXR-alpha isoform b

    See identical proteins and their annotated locations for NP_001278849.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' terminal exon, and it thus differs in its 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AC156789, AF052092, AK131513, BC063827, BM563384, BP422254, BQ637722, CN391132
    UniProtKB/TrEMBL
    Q6P3U7
    Related
    ENSP00000500402.1, ENST00000672570.1
    Conserved Domains (3) summary
    cd06943
    Location:202413
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:106182
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:199
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
  2. NM_001291921.2NP_001278850.1  retinoic acid receptor RXR-alpha isoform c

    See identical proteins and their annotated locations for NP_001278850.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate 5' terminal exon, and it thus differs in its 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AF052092, AK131192, AL669970, BC063827, BM563384, BP422254, BQ637722, CN391132
    UniProtKB/Swiss-Prot
    P19793
    UniProtKB/TrEMBL
    Q6P3U7
    Conserved Domains (3) summary
    cd06943
    Location:132343
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:36112
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:129
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
  3. NM_002957.6NP_002948.1  retinoic acid receptor RXR-alpha isoform a

    See identical proteins and their annotated locations for NP_002948.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AF052092, AL354796, BC063827, BC110998, BM563384, BP422254, BQ220698, BQ637722, CN391132
    Consensus CDS
    CCDS35172.1
    UniProtKB/Swiss-Prot
    P19793
    UniProtKB/TrEMBL
    F1D8Q5, Q6P3U7
    Related
    ENSP00000419692.1, ENST00000481739.2
    Conserved Domains (3) summary
    cd06943
    Location:229440
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:133209
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:17126
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    134326455..134440586
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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