RXRB retinoid X receptor beta [Homo sapiens (human)] - Gene

Summary

Official Symbol: RXRBprovided by HGNC
Official Full Name: retinoid X receptor betaprovided by HGNC
Primary source: HGNC:HGNC:10478
See related: Ensembl:ENSG00000204231 MIM:180246; AllianceGenome:HGNC:10478
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: NR2B2; DAUDI6; RCoR-1; RXRbeta; H-2RIIBP; RXR-beta
Summary: This gene encodes a member of the retinoid X receptor (RXR) family of nuclear receptors which are involved in mediating the effects of retinoic acid (RA). The encoded protein forms homodimers with the retinoic acid, thyroid hormone, and vitamin D receptors, increasing both DNA binding and transcriptional function on their respective response elements. This gene lies within the major histocompatibility complex (MHC) class II region on chromosome 6. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]
Expression: Ubiquitous expression in thyroid (RPKM 13.3), spleen (RPKM 12.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p21.32

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (33193588..33200853, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (33014941..33022206, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (33161365..33168630, complement)

Chromosome 6 - NC_000006.12 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?

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.
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.
RXR interaction is necessary for NPM-RAR-mediated myeloid maturation arrest.
Title: Interaction with RXR is necessary for NPM-RAR-induced myeloid differentiation blockade.
A fatty acid-binding protein 7/RXRbeta pathway enhances survival and proliferation in triple-negative breast cancer.
Title: A fatty acid-binding protein 7/RXRβ pathway enhances survival and proliferation in triple-negative breast cancer.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
Title: Genetic variability of RXRB, PPARA, and PPARG in Wegener's granulomatosis.
Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Vitamin D-related genes, serum vitamin D concentrations and prostate cancer risk.
Observational study of gene-disease association. (HuGE Navigator)
Title: Examination of genetic polymorphisms in newborns for signatures of sex-specific prenatal selection.
In healthy elderly men reduction of RXRbeta expression in peripheral blood mononuclear cells might be a common feature of physiological senescence.
Title: Age-related change in the retinoid X receptor beta gene expression in peripheral blood mononuclear cells of healthy volunteers: effect of 13-cis retinoic acid supplementation.
PPARgamma/retinoid X receptor complex released from activated platelets in microparticles was internalized by a monocytic cell line.
Title: Peroxisome proliferator-activated receptor gamma and retinoid X receptor transcription factors are released from activated human platelets and shed in microparticles.

Submit: New GeneRIF Correction See all GeneRIFs (17)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Association of granulomatosis with polyangiitis (Wegener's) with HLA-DPB1*04 and SEMA6A gene variants: evidence from genome-wide analysis. 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

MARC_26740-26741:1037207926:1 (e-PCR)
- UniSTS:269065

MARC_5891-5892:991939781:1 (e-PCR)
- UniSTS:231181

MARC_5891-5892:997299401:1 (e-PCR)
- UniSTS:231181

MARC_6301-6302:997299518:1 (e-PCR)
- UniSTS:269632

ksks12 (e-PCR)
- UniSTS:514143

STS-X66424 (e-PCR)
- UniSTS:34427

RXRB_2036 (e-PCR)
- UniSTS:280976

SHGC-56505 (e-PCR)
- UniSTS:44179

G10518 (e-PCR)
- UniSTS:32168

RH46226 (e-PCR)
- UniSTS:12484

RH69971 (e-PCR)
- UniSTS:46538

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	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 RNA polymerase II transcription regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay 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 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 hormone-mediated signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in mRNA transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in nervous system development	IBA Inferred from Biological aspect of Ancestor more info
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
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	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 vitamin D receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity 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
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
located_in chromatin	ISA Inferred from Sequence Alignment more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: retinoic acid receptor RXR-beta

Names: MHC class I promoter binding protein; nuclear receptor subfamily 2 group B member 2

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_023374.1 RefSeqGene

Range

4991..12068

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001270401.2 → NP_001257330.1 retinoic acid receptor RXR-beta isoform 1

See identical proteins and their annotated locations for NP_001257330.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AK225842, AL645940, AW473828, DC425042

Consensus CDS

CCDS59007.1

UniProtKB/TrEMBL

A0A0S2Z570, J3JS71

Related

ENSP00000363817.4, ENST00000374685.8

Conserved Domains (2) summary

cd06943
Location:298 → 515

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

cd06956
Location:204 → 279

NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
NM_001291989.2 → NP_001278918.1 retinoic acid receptor RXR-beta isoform 3

See identical proteins and their annotated locations for NP_001278918.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) has a shorter and distinct N-terminus compared to isoform 1.

Source sequence(s)

AK225842, AK302125, AL645940

UniProtKB/TrEMBL

A0A0G2JKR7, B7Z7J5

Conserved Domains (2) summary

cd06943
Location:108 → 325

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

cd06956
Location:14 → 89

NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
NM_021976.5 → NP_068811.1 retinoic acid receptor RXR-beta isoform 2

See identical proteins and their annotated locations for NP_068811.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AL645940, AW473828, BC001167, BE704198, DC425042

Consensus CDS

CCDS4768.1

UniProtKB/Swiss-Prot

P28702, P28703, Q59G65, Q5JP92, Q5STQ1

UniProtKB/TrEMBL

J3JS71, Q5STP9

Related

ENSP00000363812.3, ENST00000374680.4

Conserved Domains (3) summary

cd06943
Location:298 → 511

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

cd06956
Location:204 → 279

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

pfam11825
Location:135 → 189

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

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

33193588..33200853 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047419238.1 → XP_047275194.1 retinoic acid receptor RXR-beta isoform X2
XM_005249278.4 → XP_005249335.1 retinoic acid receptor RXR-beta isoform X1

See identical proteins and their annotated locations for XP_005249335.1

Conserved Domains (2) summary

cd06943
Location:202 → 419

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

cd06956
Location:108 → 183

NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
XM_047419239.1 → XP_047275195.1 retinoic acid receptor RXR-beta isoform X3

UniProtKB/TrEMBL

Q06310, Q30190

Conserved Domains (1) summary

cd06943
Location:29 → 246

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

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

Range

4605095..4612358 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054329847.1 → XP_054185822.1 retinoic acid receptor RXR-beta isoform X2
XM_054329846.1 → XP_054185821.1 retinoic acid receptor RXR-beta isoform X1
XM_054329848.1 → XP_054185823.1 retinoic acid receptor RXR-beta isoform X3

UniProtKB/TrEMBL

Q06310, Q30190

RNA

XR_008485662.1 RNA Sequence

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

Range

4437087..4444352 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054330330.1 → XP_054186305.1 retinoic acid receptor RXR-beta isoform X2
XM_054330329.1 → XP_054186304.1 retinoic acid receptor RXR-beta isoform X1
XM_054330331.1 → XP_054186306.1 retinoic acid receptor RXR-beta isoform X3

UniProtKB/TrEMBL

Q06310, Q30190

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

Range

4613060..4620326 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054330621.1 → XP_054186596.1 retinoic acid receptor RXR-beta isoform X2
XM_054330620.1 → XP_054186595.1 retinoic acid receptor RXR-beta isoform X1
XM_054330622.1 → XP_054186597.1 retinoic acid receptor RXR-beta isoform X3

UniProtKB/TrEMBL

Q06310, Q30190

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

Range

4629544..4636806 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054330846.1 → XP_054186821.1 retinoic acid receptor RXR-beta isoform X2
XM_054330845.1 → XP_054186820.1 retinoic acid receptor RXR-beta isoform X1
XM_054330847.1 → XP_054186822.1 retinoic acid receptor RXR-beta isoform X3

UniProtKB/TrEMBL

Q06310, Q30190

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

Range

4387991..4395257 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054331108.1 → XP_054187083.1 retinoic acid receptor RXR-beta isoform X2
XM_054331107.1 → XP_054187082.1 retinoic acid receptor RXR-beta isoform X1
XM_054331109.1 → XP_054187084.1 retinoic acid receptor RXR-beta isoform X3

UniProtKB/TrEMBL

Q06310, Q30190

Alternate T2T-CHM13v2.0

Genomic

NC_060930.1 Alternate T2T-CHM13v2.0

Range

33014941..33022206 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054356193.1 → XP_054212168.1 retinoic acid receptor RXR-beta isoform X2
XM_054356192.1 → XP_054212167.1 retinoic acid receptor RXR-beta isoform X1
XM_054356194.1 → XP_054212169.1 retinoic acid receptor RXR-beta isoform X3

UniProtKB/TrEMBL

Q06310, Q30190