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    Cd1d2 CD1d2 antigen [ Mus musculus (house mouse) ]

    Gene ID: 12480, updated on 9-Dec-2024

    Summary

    Official Symbol
    Cd1d2provided by MGI
    Official Full Name
    CD1d2 antigenprovided by MGI
    Primary source
    MGI:MGI:107675
    See related
    Ensembl:ENSMUSG00000041750 AllianceGenome:MGI:107675
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Cd1b; CD1.2; Ly-38
    Summary
    This gene encodes a MHC class I-like molecule involved in the presentation of lipid antigens to T cells, and is involved in the activation of Natural Killer T (NKT) cells. The gene is highly similar to the CD1d1 antigen gene, which is located adjacent to this gene in a tail-to-tail fashion. This gene contains a frameshift and does not produce a functional product in the C57BL/6 strain. Alternatively splice transcript variants encoding different isoforms have been found in non-C57BL/6 strains. [provided by RefSeq, Jan 2014]
    Annotation information
    Note: Genetic polymorphisms result in both protein coding and non-coding alleles of this gene.
    Expression
    Biased expression in liver adult (RPKM 33.3), subcutaneous fat pad adult (RPKM 32.4) and 12 other tissues See more
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    Genomic context

    See Cd1d2 in Genome Data Viewer
    Location:
    3 F1; 3 37.88 cM
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (86893875..86896843)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (86986586..86989533)

    Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene doublecortin-like kinase 2 Neighboring gene STARR-seq mESC enhancer starr_08132 Neighboring gene predicted gene, 46810 Neighboring gene STARR-positive B cell enhancer ABC_E6065 Neighboring gene STARR-seq mESC enhancer starr_08133 Neighboring gene STARR-seq mESC enhancer starr_08138 Neighboring gene predicted gene, 23376 Neighboring gene STARR-seq mESC enhancer starr_08141 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:86790904-86791087 Neighboring gene STARR-positive B cell enhancer ABC_E4550 Neighboring gene STARR-positive B cell enhancer mm9_chr3:86821685-86821986 Neighboring gene CD1d1 antigen Neighboring gene aminoacyl tRNA synthetase complex-interacting multifunctional protein 1 pseudogene

    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 (7) 
    • Targeted (1) 

    General gene information

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables cell adhesion molecule binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables endogenous lipid antigen binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables exogenous lipid antigen binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables exogenous lipid antigen binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables histone binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables lipid antigen binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables lipopeptide binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in cell surface ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in endoplasmic reticulum ISO
    Inferred from Sequence Orthology
    more info
     
    located_in endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in external side of plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in lysosomal membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in lysosome ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    antigen-presenting glycoprotein CD1d2
    Names
    T-cell surface glycoprotein CD1d2

    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_001289449.1NP_001276378.1  antigen-presenting glycoprotein CD1d2 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001276378.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has an alternate splice site, compared to variant 1. The reading frame is not affected and the resulting isoform (2) lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      BC057149
      UniProtKB/Swiss-Prot
      P11610
      UniProtKB/TrEMBL
      Q6PG97
      Conserved Domains (2) summary
      cd07698
      Location:167260
      IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
      cl08246
      Location:19162
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    2. NM_007640.2NP_031666.2  antigen-presenting glycoprotein CD1d2 isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes a functional protein in 129, NMRI, AKR/J, and other strains, but not in C57BL/6.
      Source sequence(s)
      M63697, X15036
      UniProtKB/Swiss-Prot
      P11610
      Conserved Domains (2) summary
      cd07698
      Location:205298
      IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
      cl08246
      Location:19200
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

    RNA

    1. NR_038188.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks a single internal nt, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC132346
      Related
      ENSMUST00000194208.6
    2. NR_172885.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has an alternate splice site, and lacks a single internal nt, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC132346
      Related
      ENSMUST00000192481.2

    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_000069.7 Reference GRCm39 C57BL/6J

      Range
      86893875..86896843
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)