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Rxrb retinoid X receptor beta [ Mus musculus (house mouse) ]

Gene ID: 20182, updated on 12-May-2024

Summary

Official Symbol
Rxrbprovided by MGI
Official Full Name
retinoid X receptor betaprovided by MGI
Primary source
MGI:MGI:98215
See related
Ensembl:ENSMUSG00000039656 AllianceGenome:MGI:98215
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Rub; Nr2b2; RCoR-1; H-2RIIBP
Summary
Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; identical protein binding activity; and nuclear receptor activity. Involved in cellular response to retinoic acid. Acts upstream of or within several processes, including cardiac muscle tissue development; maternal placenta development; and retinoic acid receptor signaling pathway. Predicted to be located in nucleoplasm. Predicted to be part of RNA polymerase II transcription regulator complex. Is expressed in several structures, including alimentary system; branchial arch; central nervous system; genitourinary system; and sensory organ. Orthologous to human RXRB (retinoid X receptor beta). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in adrenal adult (RPKM 47.1), thymus adult (RPKM 33.9) and 28 other tissues See more
Orthologs
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Genomic context

See Rxrb in Genome Data Viewer
Location:
17 B1; 17 17.98 cM
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (34250786..34257377)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (34031812..34038403)

Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E5594 Neighboring gene hydroxysteroid 17-beta dehydrogenase 8 Neighboring gene STARR-positive B cell enhancer ABC_E5595 Neighboring gene solute carrier family 39 (zinc transporter), member 7 Neighboring gene collagen, type XI, alpha 2 Neighboring gene histocompatibility 2, P region beta locus

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (2) 
  • Targeted (4)  1 citation

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
 
enables DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables chromatin DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables nuclear receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables nuclear receptor activity ISO
Inferred from Sequence Orthology
more info
 
enables nuclear receptor coactivator activity ISO
Inferred from Sequence Orthology
more info
 
enables nuclear retinoic acid receptor binding ISO
Inferred from Sequence Orthology
more info
 
enables nuclear steroid receptor activity IEA
Inferred from Electronic Annotation
more info
 
enables nuclear thyroid hormone receptor binding ISO
Inferred from Sequence Orthology
more info
 
enables nuclear vitamin D receptor binding ISO
Inferred from Sequence Orthology
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein-containing complex binding ISO
Inferred from Sequence Orthology
more info
 
enables retinoic acid-responsive element binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables sequence-specific DNA binding IGI
Inferred from Genetic Interaction
more info
PubMed 
enables sequence-specific double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables transcription cis-regulatory region 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 anatomical structure development IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within cardiac muscle cell proliferation IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in cellular response to retinoic acid IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within in utero embryonic development IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within maternal placenta development IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in positive regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
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
 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of myelination ISO
Inferred from Sequence Orthology
more info
 
involved_in response to retinoic acid IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in retinoic acid receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within ventricular cardiac muscle cell differentiation IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within ventricular cardiac muscle cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 ISO
Inferred from Sequence Orthology
more info
 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
 
located_in cytosol ISO
Inferred from Sequence Orthology
more info
 
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
retinoic acid receptor RXR-beta
Names
MHC class I regulatory element-binding protein H-2RIIBP
nuclear receptor subfamily 2 group B member 2
putative retinoid X receptor beta

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.

mRNA and Protein(s)

  1. NM_001205214.1NP_001192143.1  retinoic acid receptor RXR-beta isoform 1

    See identical proteins and their annotated locations for NP_001192143.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    CR974462
    Consensus CDS
    CCDS57066.1
    UniProtKB/TrEMBL
    A0A068BGT5, Q3TWJ1
    Related
    ENSMUSP00000036585.9, ENSMUST00000044858.16
    Conserved Domains (3) summary
    cd06943
    Location:285502
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:191266
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:122176
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
  2. NM_001205215.1NP_001192144.1  retinoic acid receptor RXR-beta isoform 3

    See identical proteins and their annotated locations for NP_001192144.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    CR974462
    Consensus CDS
    CCDS57067.1
    UniProtKB/TrEMBL
    A0A068BES4, Q8VCR0
    Related
    ENSMUSP00000133661.2, ENSMUST00000173354.9
    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
  3. NM_001205216.1NP_001192145.1  retinoic acid receptor RXR-beta isoform 4

    See identical proteins and their annotated locations for NP_001192145.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) has multiple differences, compared to variant 1. These differences result in a distinct 5' UTR and cause translation initiation at a downstream start codon, compared to variant 1. The encoded protein (isoform 4) is shorter than isoform 1.
    Source sequence(s)
    CR974462
    Consensus CDS
    CCDS57068.1
    UniProtKB/TrEMBL
    A0A068BES4
    Related
    ENSMUSP00000112311.3, ENSMUST00000116612.3
    Conserved Domains (3) summary
    cd06943
    Location:175388
    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
  4. NM_011306.4NP_035436.1  retinoic acid receptor RXR-beta isoform 2

    See identical proteins and their annotated locations for NP_035436.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    CR974462
    Consensus CDS
    CCDS89073.1
    UniProtKB/Swiss-Prot
    P28704, P33243
    UniProtKB/TrEMBL
    A0A068BGV8
    Related
    ENSMUSP00000133775.4, ENSMUST00000174299.9
    Conserved Domains (3) summary
    cd06943
    Location:285498
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:191266
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:122176
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000083.7 Reference GRCm39 C57BL/6J

    Range
    34250786..34257377
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)