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Rxra retinoid X receptor alpha [ Mus musculus (house mouse) ]

Gene ID: 20181, updated on 13-May-2024

Summary

Official Symbol
Rxraprovided by MGI
Official Full Name
retinoid X receptor alphaprovided by MGI
Primary source
MGI:MGI:98214
See related
Ensembl:ENSMUSG00000015846 AllianceGenome:MGI:98214
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
Nr2b1; RXRalpha1; 9530071D11Rik
Summary
Enables DNA binding activity and DNA-binding transcription factor activity. Contributes to nuclear receptor activity and transcription cis-regulatory region binding activity. Involved in positive regulation of transcription by RNA polymerase II. Acts upstream of or within several processes, including animal organ development; regulation of branching involved in prostate gland morphogenesis; and regulation of cellular macromolecule biosynthetic process. Located in nucleus. Part of RNA polymerase II transcription regulator complex. Is expressed in several structures, including alimentary system; central nervous system; genitourinary system; liver; and sensory organ. Used to study congenital heart disease; dilated cardiomyopathy; and systemic lupus erythematosus. Human ortholog(s) of this gene implicated in pancreatic cancer. Orthologous to human RXRA (retinoid X receptor alpha). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in liver adult (RPKM 80.9), mammary gland adult (RPKM 32.7) and 23 other tissues See more
Orthologs
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Genomic context

See Rxra in Genome Data Viewer
Location:
2 A3; 2 19.38 cM
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (27566457..27653331)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (27676445..27763319)

Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_04008 Neighboring gene STARR-seq mESC enhancer starr_04009 Neighboring gene STARR-seq mESC enhancer starr_04010 Neighboring gene predicted gene 13421 Neighboring gene predicted gene, 52506 Neighboring gene predicted gene, 39776 Neighboring gene STARR-seq mESC enhancer starr_04015 Neighboring gene STARR-seq mESC enhancer starr_04016 Neighboring gene STARR-seq mESC enhancer starr_04017 Neighboring gene predicted gene, 39777 Neighboring gene collagen, type V, alpha 1 Neighboring gene predicted gene 13372

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)
  • Chemically induced (ENU) (1)  1 citation
  • Endonuclease-mediated (2) 
  • Gene trapped (1) 
  • Targeted (11)  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 IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA binding domain binding ISO
Inferred from Sequence Orthology
more info
 
enables DNA-binding transcription factor activity IGI
Inferred from Genetic Interaction
more info
PubMed 
enables DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
enables LBD domain binding ISO
Inferred from Sequence Orthology
more info
 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables RNA polymerase II intronic transcription 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 ISO
Inferred from Sequence Orthology
more info
 
enables chromatin DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
contributes_to double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables enzyme binding ISO
Inferred from Sequence Orthology
more info
 
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
 
enables ion binding ISO
Inferred from Sequence Orthology
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables nuclear receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
 
contributes_to nuclear receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables nuclear receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables nuclear receptor activity ISO
Inferred from Sequence Orthology
more info
 
enables nuclear receptor binding 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 peptide binding ISO
Inferred from Sequence Orthology
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein domain specific binding ISO
Inferred from Sequence Orthology
more info
 
enables protein-containing complex binding ISO
Inferred from Sequence Orthology
more info
 
enables retinoic acid binding ISO
Inferred from Sequence Orthology
more info
 
enables retinoic acid-responsive element binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables retinoic acid-responsive element binding ISO
Inferred from Sequence Orthology
more info
 
enables sequence-specific DNA binding IGI
Inferred from Genetic Interaction
more info
PubMed 
enables sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables sequence-specific double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
 
contributes_to transcription cis-regulatory region binding IDA
Inferred from Direct Assay
more info
PubMed 
enables transcription cis-regulatory region binding ISO
Inferred from Sequence Orthology
more info
 
enables transcription coactivator binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables transcription coregulator binding ISO
Inferred from Sequence Orthology
more info
 
contributes_to vitamin D response element binding ISO
Inferred from Sequence Orthology
more info
 
enables zinc ion binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
involved_in anatomical structure development IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in angiogenesis involved in coronary vascular morphogenesis TAS
Traceable Author Statement
more info
PubMed 
acts_upstream_of_or_within camera-type eye development IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in cardiac muscle cell differentiation TAS
Traceable Author Statement
more info
PubMed 
acts_upstream_of_or_within cardiac muscle cell proliferation IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within cardiac muscle cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cardiac muscle cell proliferation TAS
Traceable Author Statement
more info
PubMed 
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within embryo implantation IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within heart development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in heart development TAS
Traceable Author Statement
more info
PubMed 
involved_in heart morphogenesis TAS
Traceable Author Statement
more info
PubMed 
involved_in hormone-mediated signaling pathway ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within in utero embryonic development IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in mRNA transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in mRNA transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in mRNA transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
PubMed 
acts_upstream_of_or_within maternal placenta development IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in mesenchyme development TAS
Traceable Author Statement
more info
PubMed 
involved_in negative regulation of cell population proliferation ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of gene expression TAS
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
 
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in peroxisome proliferator activated receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within placenta development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within positive regulation of DNA-templated transcription 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 DNA-templated transcription TAS
Traceable Author Statement
more info
PubMed 
involved_in positive regulation of apoptotic process 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 thyroid hormone mediated signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of thyroid hormone mediated signaling pathway ISO
Inferred from Sequence Orthology
more info
 
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 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
PubMed 
acts_upstream_of_or_within positive regulation of translational initiation by iron IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in positive regulation of vitamin D receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within regulation of branching involved in prostate gland morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of myelination ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in response to glucocorticoid ISO
Inferred from Sequence Orthology
more info
 
involved_in response to retinoic acid IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in response to retinoic acid ISO
Inferred from Sequence Orthology
more info
 
involved_in retinoic acid receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within retinoic acid receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within retinoic acid receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in retinoic acid receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 
acts_upstream_of_or_within ventricular cardiac muscle tissue morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in visceral serous pericardium development TAS
Traceable Author Statement
more info
PubMed 
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 ISO
Inferred from Sequence Orthology
more info
 
part_of RNA polymerase II transcription regulator complex NAS
Non-traceable Author Statement
more info
PubMed 
located_in axon ISO
Inferred from Sequence Orthology
more info
 
part_of chromatin ISO
Inferred from Sequence Orthology
more info
 
located_in cytoplasm IEA
Inferred from Electronic Annotation
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 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 
part_of receptor complex ISO
Inferred from Sequence Orthology
more info
 
part_of transcription regulator complex EXP
Inferred from Experiment
more info
PubMed 
part_of transcription regulator complex IPI
Inferred from Physical Interaction
more info
PubMed 
part_of transcription regulator complex ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
retinoic acid receptor RXR-alpha
Names
RXR alpha 1
nuclear receptor subfamily 2 group B member 1

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_001290481.1NP_001277410.1  retinoic acid receptor RXR-alpha isoform 2

    See identical proteins and their annotated locations for NP_001277410.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' terminal exon and it thus differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (2) is shorter at the N-terminus, compared to isoform 1. Both variants 2 and 3 encode isoform 2.
    Source sequence(s)
    AI647710, AK029121, BC138800
    Consensus CDS
    CCDS71011.1
    UniProtKB/TrEMBL
    Q3UMU4, Q6LC96
    Related
    ENSMUSP00000097822.3, ENSMUST00000100251.9
    Conserved Domains (3) summary
    cd06943
    Location:206417
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:110186
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:1103
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
  2. NM_001290482.1NP_001277411.1  retinoic acid receptor RXR-alpha isoform 2

    See identical proteins and their annotated locations for NP_001277411.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains an alternate 5' terminal exon and it thus differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (2) is shorter at the N-terminus, compared to isoform 1. Both variants 2 and 3 encode isoform 2.
    Source sequence(s)
    AK029121, AL772166, BC138800
    Consensus CDS
    CCDS71011.1
    UniProtKB/TrEMBL
    Q3UMU4, Q6LC96
    Related
    ENSMUSP00000109567.2, ENSMUST00000113934.2
    Conserved Domains (3) summary
    cd06943
    Location:206417
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:110186
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:1103
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
  3. NM_011305.3NP_035435.1  retinoic acid receptor RXR-alpha isoform 1

    See identical proteins and their annotated locations for NP_035435.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK029121, AK144675, X66223
    Consensus CDS
    CCDS15830.1
    UniProtKB/Swiss-Prot
    P28700
    UniProtKB/TrEMBL
    A2AJP1, Q3UMU4
    Related
    ENSMUSP00000076491.6, ENSMUST00000077257.12
    Conserved Domains (3) summary
    cd06943
    Location:234445
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:138214
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:18131
    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_000068.8 Reference GRCm39 C57BL/6J

    Range
    27566457..27653331
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006497805.2XP_006497868.1  retinoic acid receptor RXR-alpha isoform X1

    See identical proteins and their annotated locations for XP_006497868.1

    UniProtKB/TrEMBL
    Q3UMU4, Q6LC96
    Related
    ENSMUSP00000159198.2, ENSMUST00000238913.2
    Conserved Domains (3) summary
    cd06943
    Location:206417
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:110186
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:1103
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
  2. XM_030248867.2XP_030104727.1  retinoic acid receptor RXR-alpha isoform X1

    UniProtKB/TrEMBL
    Q3UMU4, Q6LC96
    Conserved Domains (3) summary
    cd06943
    Location:206417
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:110186
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:1103
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1