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

    Gene ID: 6256, updated on 1-Jul-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See RXRA in Genome Data Viewer
    Location:
    9q34.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (134326455..134440585)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (146541633..146657063)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (137218301..137332431)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902299 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137159240-137159872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137165779-137166534 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137186973-137187694 Neighboring gene long intergenic non-protein coding RNA 2247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137210088-137210946 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137210947-137211805 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20478 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20479 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20480 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137219587-137220516 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137220517-137221446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137225116-137225782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137225783-137226449 Neighboring gene NFE2L2 motif-containing MPRA enhancer 298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137237611-137238182 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137241753-137242539 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137242540-137243325 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137243326-137244112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137244113-137244897 Neighboring gene RXRA intron CAGE-defined high expression enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137269547-137270338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137270339-137271130 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137271131-137271922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29276 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20481 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137276487-137276988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29277 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29279 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29280 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29281 Neighboring gene Sharpr-MPRA regulatory region 14205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29282 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29283 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137288759-137289667 Neighboring gene microRNA 4669 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137292875-137293376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137293377-137293876 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137298902-137299714 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137299715-137300527 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137300528-137301339 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137312909-137313409 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137325655-137326156 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137326157-137326656 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137328808-137329376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137335184-137335762 Neighboring gene uncharacterized LOC105376311 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:137338907-137339314 Neighboring gene Sharpr-MPRA regulatory region 11314 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137346195-137347030 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137347374-137348311 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137348312-137349248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137353764-137354264 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:137367387-137367888 Neighboring gene uncharacterized LOC100506532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137385020-137385642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137410305-137410805 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137414037-137414741 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137430547-137431179 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137437101-137437866

    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 Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

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

    HIV-1 interactions

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 anatomical structure development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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 
    part_of chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of 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

    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)

    NEW Try the new Transcript table

    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)

    1. NM_001291920.2NP_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:202413
      NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
      cd06956
      Location:106182
      NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
      pfam11825
      Location:199
      Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
    2. NM_001291921.2NP_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:132343
      NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
      cd06956
      Location:36112
      NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
      pfam11825
      Location:129
      Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
    3. NM_002957.6NP_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:229440
      NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
      cd06956
      Location:133209
      NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
      pfam11825
      Location:17126
      Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      134326455..134440585
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      146541633..146657063
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)