U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Cd1d2 CD1d2 antigen [ Mus musculus (house mouse) ]

Gene ID: 12480, updated on 8-Feb-2024

Summary

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. Identification of a new mouse Cd1d2 allele. Gozalbo-López B, et al. Eur J Immunogenet, 2004 Feb. PMID 15009173
  2. α-Galactosylceramide treatment before allergen sensitization promotes iNKT cell-mediated induction of Treg cells, preventing Th2 cell responses in murine asthma. Chen Q, et al. J Biol Chem, 2019 Apr 5. PMID 30745361, Free PMC Article
  3. Hepatic Natural Killer T-cell and CD8+ T-cell Signatures in Mice with Nonalcoholic Steatohepatitis. Bhattacharjee J, et al. Hepatol Commun, 2017 Jun. PMID 29152605, Free PMC Article
  4. CD1d-mediated activation of group 3 innate lymphoid cells drives IL-22 production. Saez de Guinoa J, et al. EMBO Rep, 2017 Jan. PMID 27799287, Free PMC Article
  5. Bacterial sphingophospholipids containing non-hydroxy fatty acid activate murine macrophages via Toll-like receptor 4 and stimulate bacterial clearance. Fujiwara N, et al. Biochim Biophys Acta, 2013 Jun. PMID 23545566

See all (153) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Intrinsic factors and CD1d1 but not CD1d2 expression levels control invariant natural killer T cell subset differentiation.
    Title: Intrinsic factors and CD1d1 but not CD1d2 expression levels control invariant natural killer T cell subset differentiation.
  2. These data demonstrate that both the developmental requirements and functions of Cd1b-autoreactive T cells resemble those of Invariant Natural Killer T-Cells cells and could in turn be manipulated for use in anti-microbial therapies.
    Title: Autoreactive CD1b-restricted T cells: a new innate-like T-cell population that contributes to immunity against infection.
  3. Crystal structures of mouse CD1d-iGb3 complex and its cognate Valpha14 T cell receptor.
    Title: Crystal structures of mouse CD1d-iGb3 complex and its cognate Valpha14 T cell receptor suggest a model for dual recognition of foreign and self glycolipids.
  4. a new allele for Cd1d2 is characterized by a point mutation, resulting in a replacement of alanine at position 176 by a valine
    Title: Identification of a new mouse Cd1d2 allele.
  5. CD1a and CD1b surface expression is independent from de novo synthesized glycosphingolipids.
    Title: CD1a and CD1b surface expression is independent from de novo synthesized glycosphingolipids.
Submit: New GeneRIF Correction

Variation

Go to the top of the page Help

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (1) 
  • Endonuclease-mediated (6) 

General gene information

Go to the top of the page Help

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
  
Process Evidence Code Pubs
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
  
involved_in immune response IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within positive regulation of NK T cell activation IDA
Inferred from Direct Assay
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 
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
  
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 lysosome ISO
Inferred from Sequence Orthology
more info
  

General protein information

Go to the top of the page Help
Preferred Names
antigen-presenting glycoprotein CD1d2
Names
T-cell surface glycoprotein CD1d2

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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_001289449.1 → NP_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:167 → 260
    IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    cl08246
    Location:19 → 162
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

  2. NM_007640.2 → NP_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:205 → 298
    IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    cl08246
    Location:19 → 200
    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)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P11610.2 GenPept UniProtKB/Swiss-Prot:P11610

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases
Research Materials
Tools
Miscellaneous