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

Gene ID: 6257, updated on 1-Jun-2020

Summary

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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
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; H-2RIIBP
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

Genomic context

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See RXRB in Genome Data Viewer
Location:
6p21.32
Exon count:
11
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (33193585..33200991, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (33161362..33168630, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375021 Neighboring gene HLA complex group 24 Neighboring gene collagen type XI alpha 2 chain Neighboring gene RNY4 pseudogene 10 Neighboring gene solute carrier family 39 member 7 Neighboring gene hydroxysteroid 17-beta dehydrogenase 8 Neighboring gene microRNA 219a-1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Retinoid X receptor beta polymorphisms do not explain functional differences in vitamins D and A response in Antineutrophil cytoplasmic antibody associated vasculitis patients. Kälsch AI, et al. Autoimmunity, 2009 Aug. PMID 19811264
  2. 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. Brtko J, et al. Mech Ageing Dev, 2007 Nov-Dec. PMID 17916375
  3. The structural basis for the specificity of retinoid-X receptor-selective agonists: new insights into the role of helix H12. Love JD, et al. J Biol Chem, 2002 Mar 29. PMID 11782480
  4. Mapping of RXRB to human chromosome 6p21.3. Fitzgibbon J, et al. Ann Hum Genet, 1993 Jul. PMID 8257090
  5. The human cDNA sequence homologous to the mouse MHC class I promoter-binding protein gene contains four additional codons in lymphocytes. Epplen C, et al. Mamm Genome, 1992. PMID 1514958

See all (92) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. RXR interaction is necessary for NPM-RAR-mediated myeloid maturation arrest.
    Title: Interaction with RXR is necessary for NPM-RAR-induced myeloid differentiation blockade.
  3. 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.
  4. 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.
  5. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
    Title: Genetic variability of RXRB, PPARA, and PPARG in Wegener's granulomatosis.
  6. 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.
  7. Observational study of gene-disease association. (HuGE Navigator)
    Title: Examination of genetic polymorphisms in newborns for signatures of sex-specific prenatal selection.
  8. 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.
  9. 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.
  10. Family studies revealed significant linkage disequilibrium between the RXRB alleles and a number of HLA-DPB1 alleles.
    Title: Linkage disequilibrium between HLA-DPB1 alleles and retinoid X receptor beta haplotypes.
Submit: New GeneRIF Correction See all GeneRIFs (16)

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

NHGRI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC1831

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription activator activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
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 
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 
nuclear receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
nuclear receptor activity IDA
Inferred from Direct Assay
more info
 PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
retinoic acid-responsive element binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
steroid hormone receptor activity IEA
Inferred from Electronic Annotation
more info
  
transcription coactivator activity TAS
Traceable Author Statement
more info
 PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
anatomical structure development IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
cell differentiation IBA
Inferred from Biological aspect of Ancestor
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 
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 
retinoic acid receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
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
  
Component Evidence Code Pubs
RNA polymerase II transcription factor complex IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
cytoplasm IEA
Inferred from Electronic Annotation
more info
  
host cell nucleus IEA
Inferred from Electronic Annotation
more info
  
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
  
nucleoplasm IDA
Inferred from Direct Assay
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 

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

  1. NG_023374.1 RefSeqGene

    Range
    4991..12068
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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/Swiss-Prot
    P28702
    UniProtKB/TrEMBL
    A0A0S2Z570
    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

  2. NM_001291989.1 → 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

  3. 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
    UniProtKB/TrEMBL
    Q5STP9
    Related
    ENSP00000363812.3, ENST00000374680.3
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    33193585..33200991 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011514796.3 → XP_011513098.1  retinoic acid receptor RXR-beta isoform X2

    See identical proteins and their annotated locations for XP_011513098.1

    Conserved Domains (2) summary
    cd06943
    Location:181 → 398
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:87 → 162
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers

  2. XM_005249278.3 → 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

  3. XM_017011176.1 → XP_016866665.1  retinoic acid receptor RXR-beta isoform X3

    Conserved Domains (3) summary
    cd06943
    Location:175 → 392
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:81 → 156
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:12 → 66
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1

Reference GRCh38.p13 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p13 ALT_REF_LOCI_2

    Range
    4605092..4612358 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p13 ALT_REF_LOCI_3

    Range
    4437084..4444352 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p13 ALT_REF_LOCI_4

    Range
    4613057..4620326 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p13 ALT_REF_LOCI_5

    Range
    4629541..4636806 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p13 ALT_REF_LOCI_6

    Range
    4387988..4395257 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P28702.2 GenPept UniProtKB/Swiss-Prot:P28702

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