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    Rarb retinoic acid receptor, beta [ Mus musculus (house mouse) ]

    Gene ID: 218772, updated on 9-Dec-2024

    Summary

    Official Symbol
    Rarbprovided by MGI
    Official Full Name
    retinoic acid receptor, betaprovided by MGI
    Primary source
    MGI:MGI:97857
    See related
    Ensembl:ENSMUSG00000017491 AllianceGenome:MGI:97857
    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
    Hap; Nr1b2; A830025K23
    Summary
    Enables DNA-binding transcription factor activity and sequence-specific DNA binding activity. Acts upstream of or within several processes, including embryonic morphogenesis; nervous system development; and regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Is expressed in several structures, including alimentary system; central nervous system; embryo mesenchyme; genitourinary system; and sensory organ. Human ortholog(s) of this gene implicated in asbestos-related lung carcinoma; lung adenocarcinoma; lung non-small cell carcinoma; lung small cell carcinoma; and syndromic microphthalmia 12. Orthologous to human RARB (retinoic acid receptor beta). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in CNS E18 (RPKM 5.2), limb E14.5 (RPKM 4.2) and 24 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Rarb in Genome Data Viewer
    Location:
    14 A1; 14 7.08 cM
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 14 NC_000080.7 (5387365..6038924)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (16430839..17082331, complement)

    Chromosome 14 - NC_000080.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_36033 Neighboring gene predicted gene, 32121 Neighboring gene STARR-seq mESC enhancer starr_36032 Neighboring gene POU domain, class 5, transcription factor 1, related sequence 6 Neighboring gene STARR-seq mESC enhancer starr_36031 Neighboring gene STARR-seq mESC enhancer starr_36030 Neighboring gene predicted gene, 18078 Neighboring gene triosephosphate isomerase related sequence 9 Neighboring gene STARR-seq mESC enhancer starr_36029 Neighboring gene STARR-seq mESC enhancer starr_36028 Neighboring gene ATP-binding cassette, sub-family E (OABP), member 1 pseudogene Neighboring gene STARR-seq mESC enhancer starr_36026 Neighboring gene predicted gene, 53820 Neighboring gene predicted gene, 46442 Neighboring gene STARR-seq mESC enhancer starr_36025 Neighboring gene STARR-positive B cell enhancer ABC_E1166 Neighboring gene STARR-seq mESC enhancer starr_36024 Neighboring gene topoisomerase (DNA) II beta Neighboring gene STARR-seq mESC enhancer starr_36023 Neighboring gene STARR-seq mESC enhancer starr_36022 Neighboring gene N-glycanase 1 Neighboring gene 3-oxoacyl-ACP synthase, mitochondrial

    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)

    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 transcription factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables heterocyclic compound binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables heterocyclic compound binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables nuclear receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables nuclear receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables nuclear retinoid X receptor binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables nuclear retinoid X 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 IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein-containing complex binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables sequence-specific DNA binding IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    enables sequence-specific double-stranded DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables sequence-specific double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of apoptotic process IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within bone development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of cell population proliferation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in embryonic digestive tract development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic digestive tract development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within embryonic eye morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within embryonic hindlimb morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within glandular epithelial cell development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within growth plate cartilage development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within multicellular organism growth IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of cartilage development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of chondrocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of stem cell proliferation IGI
    Inferred from Genetic Interaction
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in neural precursor cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neural precursor cell proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within neurogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of apoptotic process IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of programmed cell death IGI
    Inferred from Genetic Interaction
    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 
    acts_upstream_of programmed cell death IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in regulation of myelination IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of myelination ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in retinoic acid receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in retinoic acid receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of stem cell proliferation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within striatum development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within ureteric bud development IMP
    Inferred from Mutant Phenotype
    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
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    retinoic acid receptor beta
    Names
    RAR-beta
    nuclear receptor subfamily 1 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.

    mRNA and Protein(s)

    1. NM_001289760.1NP_001276689.1  retinoic acid receptor beta isoform beta3

      See identical proteins and their annotated locations for NP_001276689.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (beta3) encodes the longest isoform (beta3).
      Source sequence(s)
      AC137681, AC138667, AC167564, BC076597, X56574
      UniProtKB/Swiss-Prot
      P11417, P22604, P22605
      Conserved Domains (2) summary
      cd06937
      Location:213443
      NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
      cd06964
      Location:109193
      NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
    2. NM_001289761.1NP_001276690.1  retinoic acid receptor beta isoform beta1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (beta1) lacks an in-frame exon in the 5' coding region, compared to variant beta3. The resulting isoform (beta1) lacks an internal segment, compared to isoform beta3.
      Source sequence(s)
      AC138667, AC167564, BC076597, X56569
      UniProtKB/Swiss-Prot
      P22605
      UniProtKB/TrEMBL
      Q6DFX0
      Conserved Domains (2) summary
      cd06937
      Location:186416
      NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
      cd06964
      Location:82166
      NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
    3. NM_001289762.1NP_001276691.1  retinoic acid receptor beta isoform beta4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (beta4) has an alternate 5' UTR and 5' coding region which is initiated by a non-AUG (CUG) codon, compared to variant beta3. The resulting isoform (beta4) is shorter and has a distinct N-terminus, compared to isoform beta3.
      Source sequence(s)
      BC076597, S92180, X56573
      UniProtKB/TrEMBL
      A0A286YCH1
      Conserved Domains (2) summary
      cd06937
      Location:130360
      NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
      cd06964
      Location:26110
      NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
    4. NM_011243.2NP_035373.1  retinoic acid receptor beta isoform beta2

      See identical proteins and their annotated locations for NP_035373.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (beta2, also known as beta0) has an alternate 5' UTR and 5' coding region, compared to variant beta3. The resulting isoform (beta2) is shorter and has a distinct N-terminus, compared to isoform beta3.
      Source sequence(s)
      BC076597, S56660, X56573
      Consensus CDS
      CCDS26834.1
      UniProtKB/TrEMBL
      A0A286YCH1, Q6DFX0
      Related
      ENSMUSP00000067694.7, ENSMUST00000063750.8
      Conserved Domains (2) summary
      cd06937
      Location:179409
      NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
      cd06964
      Location:75159
      NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers

    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_000080.7 Reference GRCm39 C57BL/6J

      Range
      5387365..6038924
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)