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CD1D CD1d molecule [ Homo sapiens (human) ]

Gene ID: 912, updated on 19-Jul-2014
Official Symbol
CD1Dprovided by HGNC
Official Full Name
CD1d moleculeprovided by HGNC
Primary source
HGNC:1637
See related
Ensembl:ENSG00000158473; HPRD:01780; MIM:188410; Vega:OTTHUMG00000022436
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
R3; CD1A
Summary
This gene encodes a divergent member of the CD1 family of transmembrane glycoproteins, which are structurally related to the major histocompatibility complex (MHC) proteins and form heterodimers with beta-2-microglobulin. The CD1 proteins mediate the presentation of primarily lipid and glycolipid antigens of self or microbial origin to T cells. The human genome contains five CD1 family genes organized in a cluster on chromosome 1. The CD1 family members are thought to differ in their cellular localization and specificity for particular lipid ligands. The protein encoded by this gene localizes to late endosomes and lysosomes via a tyrosine-based motif in the cytoplasmic tail. [provided by RefSeq, Jul 2008]
See CD1D in Epigenomics, MapViewer
Location:
1q23.1
Exon count:
7
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 1 NC_000001.11 (158179947..158186427)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (158147828..158156217)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene hCG1654703 Neighboring gene elongation factor, RNA polymerase II, 2 pseudogene 1 Neighboring gene ribosomal protein S10 pseudogene 8 Neighboring gene CD1a molecule

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env CD1d surface expression on human cell lines is downregulated after infection with M-tropic HIV, T-tropic HIV, or after exposure to HIV gp120 in vitro PubMed
Nef nef HIV-1 Vpu and Nef cooperatively inhibit CD1d-mediated lipid antigen presentation in HIV-1-infected DCs PubMed
nef Nef-induced downregulation of CD1d is observed when cells are co-expressing Nef and CD1d, and six amino acids (300-305) in the cytoplasmic tail of CD1d are required for the downregulation by Nef PubMed
nef HIV-1 Nef-mediated downregulation of CD1d requires a tyrosine-based motif in the CD1d cytoplasmic tail and four Nef amino acid motifs (EEEE65, PxxP75, DD165, and LL175), which are known to be involved in the downregulation of MHC-I and CD4 PubMed
nef HIV-1 Nef downregulates the expression of the non-classical MHC-I like CD1d molecule by increasing internalization of CD1d molecules from the cell surface and retaining CD1d in the trans-Golgi-network (TGN) PubMed
Vpu vpu HIV-1 Vpu proteins from Cameroonian group N viruses are largely unable to downregulate CD1D PubMed
vpu HIV-1 Vpu and Nef cooperatively inhibit CD1d-mediated lipid antigen presentation in HIV-1-infected DCs PubMed
vpu HIV-1 Vpu downregulates CD1d from the cell surface by inhibiting CD1d recycling from early endosomal compartments to the cell surface PubMed

Go to the HIV-1, Human Protein Interaction Database

  • 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...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • MGC34622

Gene Ontology Provided by GOA

Function Evidence Code Pubs
beta-2-microglobulin binding TAS
Traceable Author Statement
more info
PubMed 
cell adhesion molecule binding IPI
Inferred from Physical Interaction
more info
PubMed 
exogenous lipid antigen binding IDA
Inferred from Direct Assay
more info
PubMed 
histone binding IPI
Inferred from Physical Interaction
more info
 
lipid antigen binding IDA
Inferred from Direct Assay
more info
PubMed 
receptor activity IC
Inferred by Curator
more info
PubMed 
Process Evidence Code Pubs
T cell selection TAS
Traceable Author Statement
more info
PubMed 
antigen processing and presentation, endogenous lipid antigen via MHC class Ib IDA
Inferred from Direct Assay
more info
PubMed 
detection of bacterium TAS
Traceable Author Statement
more info
PubMed 
heterotypic cell-cell adhesion TAS
Traceable Author Statement
more info
PubMed 
innate immune response IEA
Inferred from Electronic Annotation
more info
 
positive regulation of T cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of innate immune response TAS
Traceable Author Statement
more info
PubMed 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cell surface IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
endosome membrane IEA
Inferred from Electronic Annotation
more info
 
integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
lysosomal membrane IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
antigen-presenting glycoprotein CD1d
Names
antigen-presenting glycoprotein CD1d
R3G1
thymocyte antigen CD1D
CD1D antigen, d polypeptide
T-cell surface glycoprotein CD1d
differentiation antigen CD1-alpha-3
HMC class I antigen-like glycoprotein CD1D

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_001766.3NP_001757.1  antigen-presenting glycoprotein CD1d precursor

    See proteins identical to NP_001757.1

    Status: REVIEWED

    Source sequence(s)
    AL138899, BC027926, BX106524
    Consensus CDS
    CCDS1173.1
    UniProtKB/Swiss-Prot
    P15813
    Conserved Domains (2) summary
    cd07698
    Location:203295
    Blast Score: 296
    IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    cl08246
    Location:114199
    Blast Score: 86
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000001.11 

    Range
    158179947..158186427
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006711620.1XP_006711683.1  

    Conserved Domains (1) summary
    cl08246
    Location:114199
    Blast Score: 87
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
  2. XM_005245583.1XP_005245640.1  

    See proteins identical to XP_005245640.1

    Conserved Domains (2) summary
    cd07698
    Location:99191
    Blast Score: 300
    IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    cl08246
    Location:1095
    Blast Score: 89
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
  3. XM_006711621.1XP_006711684.1  

    See proteins identical to XP_006711684.1

    Conserved Domains (2) summary
    cd07698
    Location:99191
    Blast Score: 300
    IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    cl08246
    Location:1095
    Blast Score: 89
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

Alternate HuRef

Genomic

  1. AC_000133.1 

    Range
    129508011..129514491
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018912.2 

    Range
    159546145..159552625
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)