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    Cd1d1 CD1d1 antigen [ Mus musculus (house mouse) ]

    Gene ID: 12479, updated on 7-May-2019

    Summary

    Official Symbol
    Cd1d1provided by MGI
    Official Full Name
    CD1d1 antigenprovided by MGI
    Primary source
    MGI:MGI:107674
    See related
    Ensembl:ENSMUSG00000028076
    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
    Cd1a; Cd1d; CD1.1; Ly-38; AI747460
    Expression
    Biased expression in subcutaneous fat pad adult (RPKM 94.7), liver adult (RPKM 78.0) and 12 other tissues See more
    Orthologs

    Genomic context

    See Cd1d1 in Genome Data Viewer
    Location:
    3 F1; 3 37.91 cM
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 3 NC_000069.6 (86995834..86999340, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 3 NC_000069.5 (86799756..86803262, complement)

    Chromosome 3 - NC_000069.6Genomic Context describing neighboring genes Neighboring gene doublecortin-like kinase 2 Neighboring gene predicted gene, 46810 Neighboring gene CD1d2 antigen Neighboring gene aminoacyl tRNA synthetase complex-interacting multifunctional protein 1 pseudogene Neighboring gene C-terminal binding protein 2 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 FunctionsWhat's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from BioSystems

    • Amoebiasis, organism-specific biosystem (from KEGG)
      Amoebiasis, organism-specific biosystemEntamoeba histolytica, an extracellular protozoan parasite is a human pathogen that invades the intestinal epithelium. Infection occurs on ingestion of contaminated water and food. The pathogenesis o...
    • Amoebiasis, conserved biosystem (from KEGG)
      Amoebiasis, conserved biosystemEntamoeba histolytica, an extracellular protozoan parasite is a human pathogen that invades the intestinal epithelium. Infection occurs on ingestion of contaminated water and food. The pathogenesis o...
    • Hematopoietic cell lineage, organism-specific biosystem (from KEGG)
      Hematopoietic cell lineage, organism-specific biosystemBlood-cell development progresses from a hematopoietic stem cell (HSC), which can undergo either self-renewal or differentiation into a multilineage committed progenitor cell: a common lymphoid proge...
    • Hematopoietic cell lineage, conserved biosystem (from KEGG)
      Hematopoietic cell lineage, conserved biosystemBlood-cell development progresses from a hematopoietic stem cell (HSC), which can undergo either self-renewal or differentiation into a multilineage committed progenitor cell: a common lymphoid proge...
    • Tight junction, organism-specific biosystem (from KEGG)
      Tight junction, organism-specific biosystemTight junctions (TJs) are essential for establishing a selectively permeable barrier to diffusion through the paracellular space between neighboring cells. TJs are composed of at least three types of...
    • Tight junction, conserved biosystem (from KEGG)
      Tight junction, conserved biosystemTight junctions (TJs) are essential for establishing a selectively permeable barrier to diffusion through the paracellular space between neighboring cells. TJs are composed of at least three types of...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    T cell receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cell adhesion molecule binding ISO
    Inferred from Sequence Orthology
    more info
     
    endogenous lipid antigen binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    endogenous lipid antigen binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    exogenous lipid antigen binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    exogenous lipid antigen binding ISO
    Inferred from Sequence Orthology
    more info
     
    histone binding ISO
    Inferred from Sequence Orthology
    more info
     
    lipid antigen binding ISO
    Inferred from Sequence Orthology
    more info
     
    lipopeptide binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    NK T cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    antigen processing and presentation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    antigen processing and presentation, endogenous lipid antigen via MHC class Ib IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    antigen processing and presentation, endogenous lipid antigen via MHC class Ib ISO
    Inferred from Sequence Orthology
    more info
     
    antigen processing and presentation, exogenous lipid antigen via MHC class Ib IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    antigen processing and presentation, exogenous lipid antigen via MHC class Ib IDA
    Inferred from Direct Assay
    more info
    PubMed 
    immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    immune system process IEA
    Inferred from Electronic Annotation
    more info
     
    innate immune response IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of NK T cell activation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of NK T cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of T cell mediated cytotoxicity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    positive regulation of T cell mediated cytotoxicity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of T cell proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of interferon-gamma biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of interleukin-2 biosynthetic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of interleukin-4 biosynthetic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of interleukin-4 biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of macrophage activation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive thymic T cell selection IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of immature T cell proliferation in thymus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of immune response IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    cell surface ISO
    Inferred from Sequence Orthology
    more info
     
    cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    early endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    endoplasmic reticulum ISO
    Inferred from Sequence Orthology
    more info
     
    endosome IEA
    Inferred from Electronic Annotation
    more info
     
    external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    external side of plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    late endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    lysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    membrane IEA
    Inferred from Electronic Annotation
    more info
     
    plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    antigen-presenting glycoprotein CD1d1
    Names
    T-cell surface glycoprotein CD1d1

    NCBI Reference Sequences (RefSeq)

    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_007639.3NP_031665.2  antigen-presenting glycoprotein CD1d1 precursor

      See identical proteins and their annotated locations for NP_031665.2

      Status: VALIDATED

      Source sequence(s)
      AI550455, AI553409, AK002582, M63695
      Consensus CDS
      CCDS17449.1
      UniProtKB/Swiss-Prot
      P11609
      UniProtKB/TrEMBL
      A0A0R4J090
      Related
      ENSMUSP00000029717.2, ENSMUST00000029717.3
      Conserved Domains (2) summary
      cd07698
      Location:205298
      IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
      pfam16497
      Location:19200
      MHC_I_3; MHC-I family domain

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

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

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000069.6 Reference GRCm38.p4 C57BL/6J

      Range
      86995834..86999340 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006500958.2XP_006501021.1  antigen-presenting glycoprotein CD1d1 isoform X1

      Conserved Domains (2) summary
      cd07698
      Location:235328
      IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
      pfam16497
      Location:51230
      MHC_I_3; MHC-I family domain
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