RXRG retinoid X receptor gamma [Homo sapiens (human)] - Gene

Summary

Official Symbol: RXRGprovided by HGNC
Official Full Name: retinoid X receptor gammaprovided by HGNC
Primary source: HGNC:HGNC:10479
See related: Ensembl:ENSG00000143171 MIM:180247; AllianceGenome:HGNC:10479
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: RXRC; NR2B3; RXRgamma; RXR-gamma
Summary: This gene encodes a member of the retinoid X receptor (RXR) family of nuclear receptors which are involved in mediating the antiproliferative effects of retinoic acid (RA). This receptor forms dimers with the retinoic acid, thyroid hormone, and vitamin D receptors, increasing both DNA binding and transcriptional function on their respective response elements. This gene is expressed at significantly lower levels in non-small cell lung cancer cells. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jun 2010]
Expression: Broad expression in heart (RPKM 1.5), adrenal (RPKM 1.5) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q23.3

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (165400922..165445126, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (164747271..164791474, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (165370159..165414363, complement)

Chromosome 1 - NC_000001.11 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: 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Association between functional genetic variants in retinoid X receptor-alpha/gamma and the risk of gestational diabetes mellitus in a southern Chinese population.
Title: Association between functional genetic variants in retinoid X receptor-α/γ and the risk of gestational diabetes mellitus in a southern Chinese population.
Association between Single-nucleotide Polymorphisms of RXRG and Genetic Susceptibility to Type 2 Diabetes in South China.
Title: Association between Single-nucleotide Polymorphisms of RXRG and Genetic Susceptibility to Type 2 Diabetes in South China.
Using a progression model of epithelial ovarian cancer (EOC), a proteomics-based approach identified a specific loss of RXR-gamma driving the progression of EOC.
Title: Proteomics to Predict Loss of RXR-γ During Progression of Epithelial Ovarian Cancer.
Findings indicate that Gc globulin (GC) rs16847024, retinoid X receptor gamma (RXRG) rs17429130 and retinoid X receptor alpha (RXRA) rs4917356 were candidate susceptibility markers for gestational diabetes mellitus (GDM) in Chinese females.
Title: Genetic variants in vitamin D signaling pathways and risk of gestational diabetes mellitus.
genetic association studies in a population in Brazil: Data suggest that SNPs in RXRG (rs2134095) and GC (rs7041) are associated with low-density lipoprotein cholesterol levels and hypercholesterolemia in the population studied; there was no apparent association with an SNP in VDR (rs2228570). (RXRG = retinoid X receptor gamma; GC = vitamin D-binding protein; VDR = vitamin D receptor)
Title: A vitamin D pathway gene-gene interaction affects low-density lipoprotein cholesterol levels.
Germline mutations in the RXRG gene are linked to Familial isolated pituitary adenoma in a Brazilian Family.
Title: Whole-exome identifies RXRG and TH germline variants in familial isolated prolactinoma.
Data show that pregnane X receptor/retinoid X receptor PXR/RXR-[alpha], RXR-[beta], or RXR-[gamma] expression was noted in 9 (16.4%), 9 (16.4%), and 10 (18.2%) pancreatic adenocarcinoma cases, respectively.
Title: Pregnane X Receptor Expression in Human Pancreatic Adenocarcinoma: Associations With Clinicopathologic Parameters, Tumor Proliferative Capacity, Patients' Survival, and Retinoid X Receptor Expression.
Data show that some rexinoids display selective coactivator (CoA) recruitment by the retinoid X receptors (RXRs) homodimer and by the heterodimers nuclear receptor Nur77/RXR and Nurr1/RXR.
Title: Selective ligand activity at Nur/retinoid X receptor complexes revealed by dimer-specific bioluminescence resonance energy transfer-based sensors.
Differences in RAR and RXR subtype mRNA expression patterns in various PTCs may contribute to the immunochemistry data available, and may thus find exploitation in clinical oncology, particularly in the differential diagnosis of thyroid neoplasms.
Title: mRNA expression pattern of retinoic acid and retinoid X nuclear receptor subtypes in human thyroid papillary carcinoma.
loss of RXR-gamma levels appears to provide mechanistic benefits to transformed cells towards the acquisition of resistance to apoptosis hallmark of cancer
Title: Expression proteomics predicts loss of RXR-γ during progression of epithelial ovarian cancer.

Submit: New GeneRIF Correction See all GeneRIFs (26)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study of personality traits in bipolar patients. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genomewide association study of a rapid progression cohort identifies new susceptibility alleles for AIDS (ANRS Genomewide Association Study 03). EBI GWAS Catalog EBI GWAS CatalogPubMed
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. EBI GWAS Catalog EBI GWAS CatalogPubMed
Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies. 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
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

WI-15938 (e-PCR)
- UniSTS:18182

D1S2878 (e-PCR), detects polymorphism
- UniSTS:63648

Rxrg (e-PCR), detects polymorphism
- UniSTS:536548

SHGC-89236 (e-PCR)
- UniSTS:170476

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables molecular condensate scaffold activity	IDA Inferred from Direct Assay more info	PubMed
enables nuclear receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables nuclear steroid receptor activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables retinoic acid-responsive element binding	IBA Inferred from Biological aspect of Ancestor more info
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in nervous system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in retinoic acid receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
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	IBA Inferred from Biological aspect of Ancestor more info
located_in chromatin	ISA Inferred from Sequence Alignment more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	TAS Traceable Author Statement more info

General protein information

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Preferred Names: retinoic acid receptor RXR-gamma

Names: nuclear receptor subfamily 2 group B member 3

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.

Genomic

NG_029517.2 RefSeqGene

Range

5230..49434

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001256570.2 → NP_001243499.1 retinoic acid receptor RXR-gamma isoform c

See identical proteins and their annotated locations for NP_001243499.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) includes an additional exon in its 5' UTR, and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (c, also known as RXRgamma2) is shorter at the N-terminus, compared to isoform a. Both variants 3 and 4 encode isoform c.

Source sequence(s)

AB593016, AL160058, BE349162

Consensus CDS

CCDS72970.1

UniProtKB/TrEMBL

A0A087WZ88

Related

ENSP00000482458.1, ENST00000619224.1

Conserved Domains (2) summary

cd06943
Location:110 → 318

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

cd06956
Location:14 → 90

NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
NM_001256571.2 → NP_001243500.1 retinoic acid receptor RXR-gamma isoform c

See identical proteins and their annotated locations for NP_001243500.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses an alternate internal promoter, and it thus differs in the 5' UTR and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (c, also known as RXRgamma2) is shorter at the N-terminus, compared to isoform a. Both variants 3 and 4 encode isoform c.

Source sequence(s)

BC012063, BE349162, BI768747, DA893476

Consensus CDS

CCDS72970.1

UniProtKB/TrEMBL

A0A087WZ88

Conserved Domains (2) summary

cd06943
Location:110 → 318

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

cd06956
Location:14 → 90

NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
NM_006917.5 → NP_008848.1 retinoic acid receptor RXR-gamma isoform a

See identical proteins and their annotated locations for NP_008848.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (a, also known as RXRgamma1).

Source sequence(s)

BC012063, BE349162, DA251671

Consensus CDS

CCDS1248.1

UniProtKB/Swiss-Prot

A6NIP1, P48443, Q6IBU7

UniProtKB/TrEMBL

B2R7C0, B6ZGT6, F1D8Q7

Related

ENSP00000352900.5, ENST00000359842.10

Conserved Domains (3) summary

cd06943
Location:233 → 441

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

cd06956
Location:137 → 213

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

pfam11825
Location:25 → 133

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

RNA

NR_033824.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains the same 5' exon but lacks the remaining exons, and instead includes an alternate 3' exon, compared to variant 1. It is represented as non-coding because it lacks the majority of the coding region found in variant 1.

Source sequence(s)

BM684530, BX118484

Related

ENST00000465764.1