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

    Gene ID: 20181, updated on 9-Dec-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; DNA-binding transcription factor activity; and transcription coactivator binding activity. Contributes to nuclear receptor activity and transcription cis-regulatory region binding activity. Involved in several processes, including mRNA transcription by RNA polymerase II; positive regulation of thyroid hormone receptor signaling pathway; and retinoic acid receptor signaling pathway. Acts upstream of or within several processes, including cardiac muscle tissue development; regulation of branching involved in prostate gland morphogenesis; and regulation of gene expression. 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, Dec 2024]
    Expression
    Ubiquitous expression in liver adult (RPKM 80.9), mammary gland adult (RPKM 32.7) and 23 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:
    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
     
    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 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 IEA
    Inferred from Electronic Annotation
    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 IEA
    Inferred from Electronic Annotation
    more info
     
    enables zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    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
     
    involved_in hormone-mediated signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    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 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 
    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 
    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 nervous system development IBA
    Inferred from Biological aspect of Ancestor
    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 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 receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of thyroid hormone receptor 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 ISO
    Inferred from Sequence Orthology
    more info
     
    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 
    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 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 
    involved_in 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 
    involved_in steroid hormone receptor signaling pathway IEA
    Inferred from Electronic Annotation
    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 
    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 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 
    located_in axon ISO
    Inferred from Sequence Orthology
    more info
     
    located_in chromatin ISO
    Inferred from Sequence Orthology
    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 IEA
    Inferred from Electronic Annotation
    more info
     
    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