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Cd1d1 CD1d1 antigen [ Mus musculus (house mouse) ]

Gene ID: 12479, updated on 10-Oct-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, Apr 2022]
Expression
Biased expression in subcutaneous fat pad adult (RPKM 94.7), liver adult (RPKM 78.0) and 12 other tissues See more
Orthologs
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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 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 (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)

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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
  5. NM_001409615.1NP_001396544.1  antigen-presenting glycoprotein CD1d1 isoform 1 precursor

    Status: VALIDATED

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

    Status: VALIDATED

    Source sequence(s)
    AC132346
    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
    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
    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
  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
  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