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CD1D CD1d molecule [ Homo sapiens (human) ]

Gene ID: 912, updated on 8-Dec-2018

Summary

Official Symbol
CD1Dprovided by HGNC
Official Full Name
CD1d moleculeprovided by HGNC
Primary source
HGNC:HGNC:1637
See related
Ensembl:ENSG00000158473 IMGT/GENE-DB:CD1D; MIM:188410
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; R3G1
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. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]
Expression
Broad expression in appendix (RPKM 5.0), spleen (RPKM 5.0) and 17 other tissues See more
Orthologs

Genomic context

See CD1D in Genome Data Viewer
Location:
1q23.1
Exon count:
8
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (158178038..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 long intergenic non-protein coding RNA 1704 Neighboring gene uncharacterized LOC105371460 Neighboring gene elongation factor for RNA polymerase II 2 pseudogene 1 Neighboring gene ribosomal protein S10 pseudogene 8 Neighboring gene CD1a molecule

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

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 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
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
Vpr vpr HIV-1 Vpr downregulates the expression of CD1D in human monocyte-derived dendritic cells PubMed
Vpu vpu The conserved APW motif in the alpha-helix II domain at the C-terminal region of HIV-1 Vpu is involved in CD1d downregulation PubMed
vpu HIV-1 Vpu proteins from group M, O, and P, and SIV Vpu proteins efficiently downregulate CD1d surface levels PubMed
vpu HIV-1 Vpu downregulates CD1d from the cell surface by inhibiting CD1d recycling from early endosomal compartments to the cell surface PubMed
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

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Adaptive Immune System, organism-specific biosystem (from REACTOME)
    Adaptive Immune System, organism-specific biosystemAdaptive immunity refers to antigen-specific immune response efficiently involved in clearing the pathogens. The adaptive immune system is comprised of B and T lymphocytes that express receptors with...
  • 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...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, organism-specific biosystem (from REACTOME)
    Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, organism-specific biosystemA number of receptors and cell adhesion molecules play a key role in modifying the response of cells of lymphoid origin (such as B-, T- and NK cells) to self and tumor antigens, as well as to pathoge...
  • 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

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 
endogenous lipid antigen binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
exogenous lipid antigen binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
exogenous lipid antigen binding IDA
Inferred from Direct Assay
more info
PubMed 
histone binding IPI
Inferred from Physical Interaction
more info
PubMed 
lipid antigen binding IDA
Inferred from Direct Assay
more info
PubMed 
lipopeptide binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
basolateral plasma membrane IEA
Inferred from Electronic Annotation
more info
 
cell surface IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 
endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
 
endosome membrane IEA
Inferred from Electronic Annotation
more info
 
external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
lysosomal membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
antigen-presenting glycoprotein CD1d
Names
CD1D antigen, d polypeptide
HMC class I antigen-like glycoprotein CD1D
T-cell surface glycoprotein CD1d
differentiation antigen CD1-alpha-3
thymocyte antigen CD1D

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_001319145.1NP_001306074.1  antigen-presenting glycoprotein CD1d isoform 2 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon and has a shorter 3' UTR compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AK225996, AL138899, BC027926
    UniProtKB/Swiss-Prot
    P15813
    Conserved Domains (1) summary
    pfam16497
    Location:20198
    MHC_I_3; MHC-I family domain
  2. NM_001766.3NP_001757.1  antigen-presenting glycoprotein CD1d isoform 1 precursor

    See identical proteins and their annotated locations for NP_001757.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AL138899, BC027926, BX106524
    Consensus CDS
    CCDS1173.1
    UniProtKB/Swiss-Prot
    P15813
    Related
    ENSP00000357153.3, ENST00000368171.3
    Conserved Domains (2) summary
    cd07698
    Location:203295
    IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    pfam16497
    Location:20198
    MHC_I_3; MHC-I family domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    158178038..158186427
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011510125.1XP_011508427.1  antigen-presenting glycoprotein CD1d isoform X1

    See identical proteins and their annotated locations for XP_011508427.1

    UniProtKB/Swiss-Prot
    P15813
    Conserved Domains (2) summary
    cd07698
    Location:203295
    IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    pfam16497
    Location:20198
    MHC_I_3; MHC-I family domain
  2. XM_011510127.1XP_011508429.1  antigen-presenting glycoprotein CD1d isoform X2

    See identical proteins and their annotated locations for XP_011508429.1

    Conserved Domains (2) summary
    cd07698
    Location:99191
    IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    cl08246
    Location:194
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
  3. XM_005245583.1XP_005245640.1  antigen-presenting glycoprotein CD1d isoform X2

    See identical proteins and their annotated locations for XP_005245640.1

    Conserved Domains (2) summary
    cd07698
    Location:99191
    IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    cl08246
    Location:194
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
  4. XM_006711621.1XP_006711684.1  antigen-presenting glycoprotein CD1d isoform X2

    See identical proteins and their annotated locations for XP_006711684.1

    Conserved Domains (2) summary
    cd07698
    Location:99191
    IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    cl08246
    Location:194
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

RNA

  1. XR_001737534.2 RNA Sequence

  2. XR_921995.3 RNA Sequence

  3. XR_921996.3 RNA Sequence

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