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

Gene ID: 6257, updated on 3-Jan-2019

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
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

Genomic context

See RXRB in Genome Data Viewer
Location:
6p21.32
Exon count:
11
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 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

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

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

HIV-1 interactions

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 BioSystems

  • Adipocytokine signaling pathway, organism-specific biosystem (from KEGG)
    Adipocytokine signaling pathway, organism-specific biosystemIncreased adipocyte volume and number are positively correlated with leptin production, and negatively correlated with production of adiponectin. Leptin is an important regulator of energy intake and...
  • Adipocytokine signaling pathway, conserved biosystem (from KEGG)
    Adipocytokine signaling pathway, conserved biosystemIncreased adipocyte volume and number are positively correlated with leptin production, and negatively correlated with production of adiponectin. Leptin is an important regulator of energy intake and...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Generic Transcription Pathway, organism-specific biosystem (from REACTOME)
    Generic Transcription Pathway, organism-specific biosystemOVERVIEW OF TRANSCRIPTION REGULATION: Detailed studies of gene transcription regulation in a wide variety of eukaryotic systems has revealed the general principles and mechanisms by which cell- or t...
  • Non-small cell lung cancer, organism-specific biosystem (from KEGG)
    Non-small cell lung cancer, organism-specific biosystemLung cancer is a leading cause of cancer death among men and women in industrialized countries. Non-small-cell lung cancer (NSCLC) accounts for approximately 85% of lung cancer and represents a heter...
  • Non-small cell lung cancer, conserved biosystem (from KEGG)
    Non-small cell lung cancer, conserved biosystemLung cancer is a leading cause of cancer death among men and women in industrialized countries. Non-small-cell lung cancer (NSCLC) accounts for approximately 85% of lung cancer and represents a heter...
  • Nuclear Receptor transcription pathway, organism-specific biosystem (from REACTOME)
    Nuclear Receptor transcription pathway, organism-specific biosystemA classic example of bifunctional transcription factors is the family of Nuclear Receptor (NR) proteins. These are DNA-binding transcription factors that bind certain hormones, vitamins, and other s...
  • Nuclear Receptors, organism-specific biosystem (from WikiPathways)
    Nuclear Receptors, organism-specific biosystemNuclear receptors are a class of proteins found within the interior of cells that are responsible for sensing the presence of steroid and thyroid hormones and certain other molecules. In response, th...
  • PPAR signaling pathway, organism-specific biosystem (from KEGG)
    PPAR signaling pathway, organism-specific biosystemPeroxisome proliferator-activated receptors (PPARs) are nuclear hormone receptors that are activated by fatty acids and their derivatives. PPAR has three subtypes (PPARalpha, beta/delta, and gamma) s...
  • PPAR signaling pathway, conserved biosystem (from KEGG)
    PPAR signaling pathway, conserved biosystemPeroxisome proliferator-activated receptors (PPARs) are nuclear hormone receptors that are activated by fatty acids and their derivatives. PPAR has three subtypes (PPARalpha, beta/delta, and gamma) s...
  • Pathways in cancer, organism-specific biosystem (from KEGG)
    Pathways in cancer, organism-specific biosystem
    Pathways in cancer
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by Retinoic Acid, organism-specific biosystem (from REACTOME)
    Signaling by Retinoic Acid, organism-specific biosystemVitamin A (retinol) can be metabolised into active retinoid metabolites that function either as a chromophore in vision or in regulating gene expression transcriptionally and post-transcriptionally. ...
  • Small cell lung cancer, organism-specific biosystem (from KEGG)
    Small cell lung cancer, organism-specific biosystemLung cancer is a leading cause of cancer death among men and women in industrialized countries. Small cell lung carcinoma (SCLC) is a highly aggressive neoplasm, which accounts for approximately 25% ...
  • Small cell lung cancer, conserved biosystem (from KEGG)
    Small cell lung cancer, conserved biosystemLung cancer is a leading cause of cancer death among men and women in industrialized countries. Small cell lung carcinoma (SCLC) is a highly aggressive neoplasm, which accounts for approximately 25% ...
  • Th17 cell differentiation, organism-specific biosystem (from KEGG)
    Th17 cell differentiation, organism-specific biosystemInterleukin (IL)-17-producing helper T (Th17) cells serve as a subset of CD4+ T cells involved in epithelial cell- and neutrophil mediated immune responses against extracellular microbes and in the p...
  • Th17 cell differentiation, conserved biosystem (from KEGG)
    Th17 cell differentiation, conserved biosystemInterleukin (IL)-17-producing helper T (Th17) cells serve as a subset of CD4+ T cells involved in epithelial cell- and neutrophil mediated immune responses against extracellular microbes and in the p...
  • Thyroid cancer, organism-specific biosystem (from KEGG)
    Thyroid cancer, organism-specific biosystemThyroid cancer is the most common endocrine malignancy and accounts for the majority of endocrine cancer- related deaths each year. More than 95% of thyroid carcinomas are derived from follicular cel...
  • Thyroid cancer, conserved biosystem (from KEGG)
    Thyroid cancer, conserved biosystemThyroid cancer is the most common endocrine malignancy and accounts for the majority of endocrine cancer- related deaths each year. More than 95% of thyroid carcinomas are derived from follicular cel...
  • Thyroid hormone signaling pathway, organism-specific biosystem (from KEGG)
    Thyroid hormone signaling pathway, organism-specific biosystemThe thyroid hormones (THs) are important regulators of growth, development and metabolism. The action of TH is mainly mediated by T3 (3,5,3'-triiodo-L-thyronine). Thyroid hormones, L-thyroxine (T4) a...
  • Transcriptional misregulation in cancer, organism-specific biosystem (from KEGG)
    Transcriptional misregulation in cancer, organism-specific biosystem
    Transcriptional misregulation in cancer
  • Transcriptional misregulation in cancer, conserved biosystem (from KEGG)
    Transcriptional misregulation in cancer, conserved biosystem
    Transcriptional misregulation in cancer
  • Vitamin A and Carotenoid Metabolism, organism-specific biosystem (from WikiPathways)
    Vitamin A and Carotenoid Metabolism, organism-specific biosystemThis pathway is about carotenoid and vitamin A metabolism. The initial version was created by the NuGO focusteam on Carotenoid metabolism. It was used to test a text mining workflow which added some ...
  • Vitamin D Metabolism, organism-specific biosystem (from WikiPathways)
    Vitamin D Metabolism, organism-specific biosystemPhotochemical synthesis of vitamin D3 (cholecalciferol, D3) occurs cutaneously where pro-vitamin D3 (7-dehydrocholesterol) is converted to pre-vitamin D3 (pre-D3) in response to ultraviolet B (sunlig...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC1831

Gene Ontology Provided by GOA

Process Evidence Code Pubs
intracellular receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
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
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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)

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
    4960..12071
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001270401.1NP_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:298515
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:204279
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
  2. NM_001291989.1NP_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:108325
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:1489
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
  3. NM_021976.4NP_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 (2) summary
    cd06943
    Location:298511
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:204279
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p12 Primary Assembly

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

mRNA and Protein(s)

  1. XM_011514796.3XP_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:181398
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:87162
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
  2. XM_005249278.3XP_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:202419
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:108183
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
  3. XM_017011176.1XP_016866665.1  retinoic acid receptor RXR-beta isoform X3

    Conserved Domains (3) summary
    cd06943
    Location:175392
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:81156
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:1266
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1

Reference GRCh38.p12 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p12 ALT_REF_LOCI_2

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

Reference GRCh38.p12 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p12 ALT_REF_LOCI_3

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

Reference GRCh38.p12 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p12 ALT_REF_LOCI_4

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

Reference GRCh38.p12 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p12 ALT_REF_LOCI_5

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

Reference GRCh38.p12 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p12 ALT_REF_LOCI_6

    Range
    4387988..4395257 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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