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

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: mouse all
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Genomic context

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_000009.12 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

ZNF148 inhibits HBV replication by downregulating RXRalpha transcription.
Title: ZNF148 inhibits HBV replication by downregulating RXRα transcription.
Linc-ROR inhibits NK cell-killing activity by promoting RXRA ubiquitination and reducing MICB expression in gastric cancer patients.
Title: Linc-ROR inhibits NK cell-killing activity by promoting RXRA ubiquitination and reducing MICB expression in gastric cancer patients.
Stationary-to-migratory transition in glioblastoma stem-like cells driven by a fatty acid-binding protein 7-RXRalpha neurogenic pathway.
Title: Stationary-to-migratory transition in glioblastoma stem-like cells driven by a fatty acid-binding protein 7-RXRα neurogenic pathway.
SNP rs11185644 in RXRA gene and SNP rs2235544 in DIO1 gene predict dosage requirements in a cross-sectional sample of hypothyroid patients.
Title: SNP rs11185644 in RXRA gene and SNP rs2235544 in DIO1 gene predict dosage requirements in a cross-sectional sample of hypothyroid patients.
lncRNA RMST suppresses the progression of colorectal cancer by competitively binding to miR-27a-3p/RXRalpha axis and inactivating Wnt signaling pathway.
Title: lncRNA RMST suppresses the progression of colorectal cancer by competitively binding to miR-27a-3p/RXRα axis and inactivating Wnt signaling pathway.
Computational refinement identifies functional destructive single nucleotide polymorphisms associated with human retinoid X receptor gene.
Title: Computational refinement identifies functional destructive single nucleotide polymorphisms associated with human retinoid X receptor gene.
Integrated analysis of mRNA-seq and miRNA-seq reveals the potential roles of Egr1, Rxra and Max in kidney stone disease.
Title: Integrated analysis of mRNA-seq and miRNA-seq reveals the potential roles of Egr1, Rxra and Max in kidney stone disease.
Cytoplasmic Colocalization of RXRalpha and PPARgamma as an Independent Negative Prognosticator for Breast Cancer Patients.
Title: Cytoplasmic Colocalization of RXRα and PPARγ as an Independent Negative Prognosticator for Breast Cancer Patients.
The role of resveratrol, Sirtuin1 and RXRalpha as prognostic markers in ovarian cancer.
Title: The role of resveratrol, Sirtuin1 and RXRα as prognostic markers in ovarian cancer.
Genetic variant of RXR involved in the vitamin D metabolic pathway was linked to HCV infection outcomes among a high-risk Chinese population.
Title: Genetic variant of RXR involved in the vitamin D metabolic pathway was linked to HCV infection outcomes among a high-risk Chinese population.

Submit: New GeneRIF Correction See all GeneRIFs (211)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH36155 (e-PCR)
- UniSTS:48129

NoName (e-PCR)
- UniSTS:483853

RH119378 (e-PCR)
- UniSTS:132918

WI-22534 (e-PCR)
- UniSTS:3144

RH71144 (e-PCR)
- UniSTS:39774

G67257 (e-PCR)
- UniSTS:186477

G67258 (e-PCR)
- UniSTS:186478

G67259 (e-PCR)
- UniSTS:186479

G67260 (e-PCR)
- UniSTS:186480

G67261 (e-PCR)
- UniSTS:186481

G67262 (e-PCR)
- UniSTS:186482

G67263 (e-PCR)
- UniSTS:186483

G67264 (e-PCR)
- UniSTS:186484

STS-AA004312 (e-PCR)
- UniSTS:68216

GDB:376726 (e-PCR)
- UniSTS:157063

RXRA_2235 (e-PCR)
- UniSTS:280975

STS-Z41140 (e-PCR)
- UniSTS:69782

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

RH70281 (e-PCR)
- UniSTS:65231

RH48538 (e-PCR)
- UniSTS:3321

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
is_active_in chromatin	IDA Inferred from Direct Assay 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

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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)

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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_001291920.2 → NP_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:202 → 413

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

cd06956
Location:106 → 182

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

pfam11825
Location:1 → 99

Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
NM_001291921.2 → NP_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:132 → 343

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

cd06956
Location:36 → 112

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

pfam11825
Location:1 → 29

Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
NM_002957.6 → NP_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:229 → 440

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

cd06956
Location:133 → 209

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

pfam11825
Location:17 → 126

Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1