U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from OMIM

    • Showing Current items.

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

    Gene ID: 6257, updated on 10-Dec-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See RXRB in Genome Data Viewer
    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_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375021 Neighboring gene HLA complex group 24 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33131677-33132178 Neighboring gene collagen type XI alpha 2 chain Neighboring gene ReSE screen-validated silencer GRCh37_chr6:33165434-33165634 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:33168171-33168672 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33168673-33169174 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33169175-33169676 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33172262-33173144 Neighboring gene RNY4 pseudogene 10 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33173145-33174025 Neighboring gene solute carrier family 39 member 7 Neighboring gene hydroxysteroid 17-beta dehydrogenase 8

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC1831

    Gene Ontology Provided by GOA

    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

    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)

    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.

    Genomic

    1. NG_023374.1 RefSeqGene

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

    mRNA and Protein(s)

    1. NM_001270401.2NP_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: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_001291989.2NP_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_021976.5NP_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: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
      pfam11825
      Location:135189
      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

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      33193588..33200853 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047419238.1XP_047275194.1  retinoic acid receptor RXR-beta isoform X2

    2. XM_005249278.4XP_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_047419239.1XP_047275195.1  retinoic acid receptor RXR-beta isoform X3

      UniProtKB/TrEMBL
      Q06310, Q30190
      Conserved Domains (1) summary
      cd06943
      Location:29246
      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

    1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      4605095..4612358 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054329847.1XP_054185822.1  retinoic acid receptor RXR-beta isoform X2

    2. XM_054329846.1XP_054185821.1  retinoic acid receptor RXR-beta isoform X1

    3. XM_054329848.1XP_054185823.1  retinoic acid receptor RXR-beta isoform X3

      UniProtKB/TrEMBL
      Q06310, Q30190

    RNA

    1. XR_008485662.1 RNA Sequence

    Reference GRCh38.p14 ALT_REF_LOCI_3

    Genomic

    1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

      Range
      4437087..4444352 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330330.1XP_054186305.1  retinoic acid receptor RXR-beta isoform X2

    2. XM_054330329.1XP_054186304.1  retinoic acid receptor RXR-beta isoform X1

    3. XM_054330331.1XP_054186306.1  retinoic acid receptor RXR-beta isoform X3

      UniProtKB/TrEMBL
      Q06310, Q30190

    Reference GRCh38.p14 ALT_REF_LOCI_4

    Genomic

    1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

      Range
      4613060..4620326 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330621.1XP_054186596.1  retinoic acid receptor RXR-beta isoform X2

    2. XM_054330620.1XP_054186595.1  retinoic acid receptor RXR-beta isoform X1

    3. XM_054330622.1XP_054186597.1  retinoic acid receptor RXR-beta isoform X3

      UniProtKB/TrEMBL
      Q06310, Q30190

    Reference GRCh38.p14 ALT_REF_LOCI_5

    Genomic

    1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

      Range
      4629544..4636806 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330846.1XP_054186821.1  retinoic acid receptor RXR-beta isoform X2

    2. XM_054330845.1XP_054186820.1  retinoic acid receptor RXR-beta isoform X1

    3. XM_054330847.1XP_054186822.1  retinoic acid receptor RXR-beta isoform X3

      UniProtKB/TrEMBL
      Q06310, Q30190

    Reference GRCh38.p14 ALT_REF_LOCI_6

    Genomic

    1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

      Range
      4387991..4395257 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331108.1XP_054187083.1  retinoic acid receptor RXR-beta isoform X2

    2. XM_054331107.1XP_054187082.1  retinoic acid receptor RXR-beta isoform X1

    3. XM_054331109.1XP_054187084.1  retinoic acid receptor RXR-beta isoform X3

      UniProtKB/TrEMBL
      Q06310, Q30190

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      33014941..33022206 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356193.1XP_054212168.1  retinoic acid receptor RXR-beta isoform X2

    2. XM_054356192.1XP_054212167.1  retinoic acid receptor RXR-beta isoform X1

    3. XM_054356194.1XP_054212169.1  retinoic acid receptor RXR-beta isoform X3

      UniProtKB/TrEMBL
      Q06310, Q30190

    RNA

    1. XR_008487422.1 RNA Sequence