U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 6256, updated on 18-Sep-2024

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; AllianceGenome:HGNC:10477
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; RXRalpha; RXR-alpha
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See RXRA in Genome Data Viewer
Location:
9q34.2
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (134326455..134440585)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (146541633..146657063)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (137218301..137332431)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902299 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137159240-137159872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137165779-137166534 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137186973-137187694 Neighboring gene long intergenic non-protein coding RNA 2247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137210088-137210946 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137210947-137211805 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20478 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20479 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20480 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137219587-137220516 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137220517-137221446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137225116-137225782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137225783-137226449 Neighboring gene NFE2L2 motif-containing MPRA enhancer 298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137237611-137238182 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137241753-137242539 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137242540-137243325 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137243326-137244112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137244113-137244897 Neighboring gene RXRA intron CAGE-defined high expression enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137269547-137270338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137270339-137271130 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137271131-137271922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29276 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20481 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137276487-137276988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29277 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29279 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29280 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29281 Neighboring gene Sharpr-MPRA regulatory region 14205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29282 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29283 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137288759-137289667 Neighboring gene microRNA 4669 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137292875-137293376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137293377-137293876 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137298902-137299714 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137299715-137300527 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137300528-137301339 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137312909-137313409 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137325655-137326156 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137326157-137326656 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137328808-137329376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137335184-137335762 Neighboring gene uncharacterized LOC105376311 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:137338907-137339314 Neighboring gene Sharpr-MPRA regulatory region 11314 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137346195-137347030 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137347374-137348311 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137348312-137349248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137353764-137354264 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:137367387-137367888 Neighboring gene uncharacterized LOC100506532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137385020-137385642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137410305-137410805 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137414037-137414741 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137430547-137431179 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137437101-137437866

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues 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

EBI GWAS Catalog

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

Clone Names

  • FLJ00280, FLJ00318, FLJ16020, FLJ16733, MGC102720

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding domain binding IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
enables LBD domain binding IDA
Inferred from Direct Assay
more info
PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables double-stranded DNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
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 steroid receptor activity IEA
Inferred from Electronic Annotation
more info
 
enables nuclear vitamin D receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables peptide binding IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables retinoic acid binding IDA
Inferred from Direct Assay
more info
PubMed 
enables retinoic acid-responsive element binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables retinoic acid-responsive element binding IDA
Inferred from Direct Assay
more info
PubMed 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables transcription cis-regulatory region binding IDA
Inferred from Direct Assay
more info
PubMed 
enables transcription coregulator binding IPI
Inferred from Physical Interaction
more info
PubMed 
contributes_to vitamin D response element binding IDA
Inferred from Direct Assay
more info
PubMed 
enables zinc ion binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in hormone-mediated signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in hormone-mediated signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in mRNA transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in mRNA transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in mRNA transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in nervous system development IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in peroxisome proliferator activated receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of bone mineralization NAS
Non-traceable Author Statement
more info
PubMed 
acts_upstream_of positive regulation of cholesterol efflux TAS
Traceable Author Statement
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 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 ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
PubMed 
involved_in positive regulation of transporter activity TAS
Traceable Author Statement
more info
PubMed 
involved_in positive regulation of vitamin D receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in response to retinoic acid IMP
Inferred from Mutant Phenotype
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 IDA
Inferred from Direct Assay
more info
PubMed 
involved_in retinoic acid receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in steroid hormone receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
part_of RNA polymerase II transcription regulator complex EXP
Inferred from Experiment
more info
PubMed 
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 IPI
Inferred from Physical Interaction
more info
PubMed 
part_of RNA polymerase II transcription regulator complex ISS
Inferred from Sequence or Structural Similarity
more info
 
part_of RNA polymerase II transcription regulator complex NAS
Non-traceable Author Statement
more info
PubMed 
located_in chromatin IDA
Inferred from Direct Assay
more info
PubMed 
located_in chromatin ISA
Inferred from Sequence Alignment
more info
 
located_in cytosol TAS
Traceable Author Statement
more info
 
located_in mitochondrion IEA
Inferred from Electronic Annotation
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
part_of receptor complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of transcription regulator complex IPI
Inferred from Physical Interaction
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)

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_001291920.2NP_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
    Consensus CDS
    CCDS94525.1
    UniProtKB/TrEMBL
    A0A5F9ZHH6, 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
    B3KY83, P19793, Q2NL52, Q2V504
    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: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    134326455..134440585
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    146541633..146657063
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)