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    Cd1d1 CD1d1 antigen [ Mus musculus (house mouse) ]

    Gene ID: 12479, updated on 3-Dec-2024

    Summary

    Official Symbol
    Cd1d1provided by MGI
    Official Full Name
    CD1d1 antigenprovided by MGI
    Primary source
    MGI:MGI:107674
    See related
    Ensembl:ENSMUSG00000028076 AllianceGenome:MGI:107674
    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
    Summary
    Enables T cell receptor binding activity and endogenous lipid antigen binding activity. Involved in NK T cell differentiation and regulation of immature T cell proliferation in thymus. Acts upstream of or within several processes, including antigen processing and presentation, exogenous lipid antigen via MHC class Ib; positive regulation of cytokine production; and positive regulation of leukocyte activation. Located in endosome; external side of plasma membrane; and lysosome. Is expressed in forebrain; intestine; jaw bone; and liver. Human ortholog(s) of this gene implicated in pulmonary tuberculosis. Orthologous to human CD1D (CD1d molecule). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in subcutaneous fat pad adult (RPKM 94.7), liver adult (RPKM 78.0) and 12 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See Cd1d1 in Genome Data Viewer
    Location:
    3 F1; 3 37.91 cM
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (86903141..86919665, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (86995834..87012358, complement)

    Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 23376 Neighboring gene STARR-seq mESC enhancer starr_08141 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:86790904-86791087 Neighboring gene CD1d2 antigen Neighboring gene STARR-positive B cell enhancer ABC_E4550 Neighboring gene STARR-positive B cell enhancer mm9_chr3:86821685-86821986 Neighboring gene aminoacyl tRNA synthetase complex-interacting multifunctional protein 1 pseudogene Neighboring gene STARR-seq mESC enhancer starr_08145 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 Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (8) 
    • 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 T cell receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 endogenous lipid antigen binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in NK T cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within antigen processing and presentation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in antigen processing and presentation, endogenous lipid antigen via MHC class Ib IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in antigen processing and presentation, endogenous lipid antigen via MHC class Ib ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in antigen processing and presentation, exogenous lipid antigen via MHC class Ib IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within antigen processing and presentation, exogenous lipid antigen via MHC class Ib IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in innate immune response IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within positive regulation of NK T cell activation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of NK T cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of T cell mediated cytotoxicity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within positive regulation of T cell mediated cytotoxicity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of T cell proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within positive regulation of interleukin-2 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of interleukin-4 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of interleukin-4 production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of macrophage activation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of type II interferon production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within positive thymic T cell selection IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of immature T cell proliferation in thymus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within regulation of immune response IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 early endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 late endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosomal membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosome ISO
    Inferred from Sequence Orthology
    more info
     
    located_in lysosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

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

    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_001379501.1NP_001366430.1  antigen-presenting glycoprotein CD1d1 isoform 2 precursor

      Status: VALIDATED

      Source sequence(s)
      AC132346
      UniProtKB/Swiss-Prot
      P11609, Q91XK9
      Conserved Domains (2) summary
      cd21029
      Location:167259
      IgC1_CD1; Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig superfamily (IgSF) domains
      cl08246
      Location:19162
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    2. NM_001379502.1NP_001366431.1  antigen-presenting glycoprotein CD1d1 isoform 3 precursor

      Status: VALIDATED

      Source sequence(s)
      AC132346
      UniProtKB/TrEMBL
      E9Q395, Q7TMK5
      Related
      ENSMUSP00000070616.6, ENSMUST00000063869.11
      Conserved Domains (2) summary
      cd21029
      Location:74166
      IgC1_CD1; Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig superfamily (IgSF) domains
      cl08246
      Location:1973
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    3. NM_001379503.1NP_001366432.1  antigen-presenting glycoprotein CD1d1 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC132346
      UniProtKB/Swiss-Prot
      P11609, Q91XK9
      Conserved Domains (2) summary
      cd21029
      Location:173265
      IgC1_CD1; Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig superfamily (IgSF) domains
      cl08246
      Location:1168
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    4. NM_001409614.1NP_001396543.1  antigen-presenting glycoprotein CD1d1 isoform 5 precursor

      Status: VALIDATED

      Source sequence(s)
      AC132346
      UniProtKB/Swiss-Prot
      P11609, Q91XK9
    5. NM_001409615.1NP_001396544.1  antigen-presenting glycoprotein CD1d1 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AC132346
      UniProtKB/Swiss-Prot
      P11609, Q91XK9
      UniProtKB/TrEMBL
      A0A0R4J090
    6. NM_001409616.1NP_001396545.1  antigen-presenting glycoprotein CD1d1 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC132346
      UniProtKB/Swiss-Prot
      P11609, Q91XK9
      Conserved Domains (2) summary
      cd21029
      Location:173265
      IgC1_CD1; Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig superfamily (IgSF) domains
      cl08246
      Location:1168
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    7. NM_001409617.1NP_001396546.1  antigen-presenting glycoprotein CD1d1 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC132346
      UniProtKB/Swiss-Prot
      P11609, Q91XK9
      Conserved Domains (2) summary
      cd21029
      Location:173265
      IgC1_CD1; Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig superfamily (IgSF) domains
      cl08246
      Location:1168
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    8. NM_001409618.1NP_001396547.1  antigen-presenting glycoprotein CD1d1 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC132346
      UniProtKB/Swiss-Prot
      P11609, Q91XK9
      Conserved Domains (2) summary
      cd21029
      Location:173265
      IgC1_CD1; Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig superfamily (IgSF) domains
      cl08246
      Location:1168
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    9. NM_001409619.1NP_001396548.1  antigen-presenting glycoprotein CD1d1 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC132346
      UniProtKB/TrEMBL
      B9VQY2
    10. NM_001409620.1NP_001396549.1  antigen-presenting glycoprotein CD1d1 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AC132346
    11. NM_001409621.1NP_001396550.1  antigen-presenting glycoprotein CD1d1 isoform 9 precursor

      Status: VALIDATED

      Source sequence(s)
      AC132346
    12. NM_001409622.1NP_001396551.1  antigen-presenting glycoprotein CD1d1 isoform 7 precursor

      Status: VALIDATED

      Source sequence(s)
      AC132346
      UniProtKB/Swiss-Prot
      P11609, Q91XK9
    13. NM_007639.4NP_031665.2  antigen-presenting glycoprotein CD1d1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_031665.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC132346
      Consensus CDS
      CCDS17449.1
      UniProtKB/Swiss-Prot
      P11609, Q91XK9
      UniProtKB/TrEMBL
      A0A0R4J090
      Related
      ENSMUSP00000029717.3, ENSMUST00000029717.4
      Conserved Domains (2) summary
      cd07698
      Location:205298
      IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
      pfam16497
      Location:1200
      MHC_I_3; MHC-I family domain

    RNA

    1. NR_166722.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC132346

    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
      86903141..86919665 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030252404.1XP_030108264.1  antigen-presenting glycoprotein CD1d1 isoform X1

      UniProtKB/Swiss-Prot
      P11609, Q91XK9
      UniProtKB/TrEMBL
      A0A0R4J090
      Conserved Domains (2) summary
      cd07698
      Location:205298
      IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
      pfam16497
      Location:1200
      MHC_I_3; MHC-I family domain