Free for academic non-profit institutions. Other users need a Commercial license

Aliases for CD1D Gene

Aliases for CD1D Gene

  • CD1d Molecule 2 3
  • CD1D Antigen, D Polypeptide 2 3
  • CD1d Antigen 2 4
  • R3G1 3 4
  • HMC Class I Antigen-Like Glycoprotein CD1D 3
  • Antigen-Presenting Glycoprotein CD1d 3
  • Differentiation Antigen CD1-Alpha-3 3
  • T-Cell Surface Glycoprotein CD1d 3
  • Thymocyte Antigen CD1D 3
  • CD1A 3
  • R3 3

External Ids for CD1D Gene

Previous GeneCards Identifiers for CD1D Gene

  • GC01P155941
  • GC01P153882
  • GC01P154927
  • GC01P155366
  • GC01P154962
  • GC01P156416
  • GC01P129508

Summaries for CD1D Gene

Entrez Gene Summary for CD1D Gene

  • 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]

GeneCards Summary for CD1D Gene

CD1D (CD1d Molecule) is a Protein Coding gene. Diseases associated with CD1D include mycobacterium malmoense and relapsing polychondritis. Among its related pathways are Amoebiasis and TNF Signaling. GO annotations related to this gene include receptor activity and cell adhesion molecule binding. An important paralog of this gene is CD1C.

UniProtKB/Swiss-Prot for CD1D Gene

  • Antigen-presenting protein that binds self and non-self glycolipids and presents them to T-cell receptors on natural killer T-cells.

Gene Wiki entry for CD1D Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CD1D Gene

Genomics for CD1D Gene

Regulatory Elements for CD1D Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for CD1D Gene

158,179,947 bp from pter
158,186,427 bp from pter
6,481 bases
Plus strand

Genomic View for CD1D Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for CD1D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CD1D Gene

Proteins for CD1D Gene

  • Protein details for CD1D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Antigen-presenting glycoprotein CD1d
    Protein Accession:
    Secondary Accessions:
    • D3DVD5
    • Q5W0J3
    • Q9UMM3
    • Q9Y5M4

    Protein attributes for CD1D Gene

    335 amino acids
    Molecular mass:
    37717 Da
    Quaternary structure:
    • Heterodimer with B2M (beta-2-microglobulin). Interacts with MHC II.
    • During protein synthesis and maturation, CD1 family members bind endogenous lipids that are replaced by lipid or glycolipid antigens when the proteins are internalized and pass through endosomes, before trafficking back to the cell surface.

    Three dimensional structures from OCA and Proteopedia for CD1D Gene

neXtProt entry for CD1D Gene

Proteomics data for CD1D Gene at MOPED

Post-translational modifications for CD1D Gene

  • Glycosylation at Asn38, Asn60, Asn126, and Asn181
  • Modification sites at PhosphoSitePlus

Other Protein References for CD1D Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

No data available for DME Specific Peptides for CD1D Gene

Domains for CD1D Gene

Gene Families for CD1D Gene

  • C1SET :Immunoglobulin superfamily / C1-set domain containing
  • CD :CD molecules

Suggested Antigen Peptide Sequences for CD1D Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • P15813
  • Contains 1 Ig-like (immunoglobulin-like) domain.
genes like me logo Genes that share domains with CD1D: view

Function for CD1D Gene

Molecular function for CD1D Gene

GENATLAS Biochemistry:
cell differentiation antigen CD1D,49kDa,cell surface molecule,B2M associated,identified by monoclonal antibody NOR3.2 expressed on a cortical thymocyte cell line (see CD1@)
UniProtKB/Swiss-Prot Function:
Antigen-presenting protein that binds self and non-self glycolipids and presents them to T-cell receptors on natural killer T-cells.

Gene Ontology (GO) - Molecular Function for CD1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004872 receptor activity IC 11315191
GO:0005515 protein binding --
GO:0030881 beta-2-microglobulin binding TAS 14500461
GO:0030882 lipid antigen binding IDA 19124746
GO:0030883 endogenous lipid antigen binding IBA --
genes like me logo Genes that share ontologies with CD1D: view
genes like me logo Genes that share phenotypes with CD1D: view

Animal Models for CD1D Gene

MGI Knock Outs for CD1D:

Animal Model Products

CRISPR Products

miRNA for CD1D Gene

miRTarBase miRNAs that target CD1D

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CD1D

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for CD1D Gene

Localization for CD1D Gene

Subcellular locations from UniProtKB/Swiss-Prot for CD1D Gene

Cell membrane; Single-pass type I membrane protein. Endosome membrane. Lysosome membrane. Note=Subject to intracellular trafficking between the cell membrane, endosomes and lysosomes.

Subcellular locations from

Jensen Localization Image for CD1D Gene COMPARTMENTS Subcellular localization image for CD1D gene
Compartment Confidence
endosome 5
lysosome 5
plasma membrane 5
vacuole 5
endoplasmic reticulum 2
extracellular 1
nucleus 1

Gene Ontology (GO) - Cellular Components for CD1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA 19124746
GO:0005764 lysosome --
GO:0005765 lysosomal membrane IEA --
GO:0005768 endosome --
GO:0005887 integral component of plasma membrane TAS 11315191
genes like me logo Genes that share ontologies with CD1D: view

Pathways for CD1D Gene

genes like me logo Genes that share pathways with CD1D: view

Pathways by source for CD1D Gene

1 Sino Biological pathway for CD1D Gene
2 KEGG pathways for CD1D Gene

PCR Array Products

Gene Ontology (GO) - Biological Process for CD1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016032 viral process IEA --
GO:0016045 detection of bacterium TAS 14500461
GO:0034113 heterotypic cell-cell adhesion TAS 19124746
GO:0042102 positive regulation of T cell proliferation IDA 19124746
GO:0045058 T cell selection TAS 14500461
genes like me logo Genes that share ontologies with CD1D: view

Compounds for CD1D Gene

(519) HMDB Compounds for CD1D Gene

Compound Synonyms Cas Number PubMed IDs
  • 1-Hydroxy-2-amino-3-oxo-octadecane
3-O-Sulfogalactosylceramide (d18:1/12:0)
  • Sulfatide (d18:1/12:0)
3-O-Sulfogalactosylceramide (d18:1/14:0)
  • Sulfatide (d18:1/14:0)
Not Available
3-O-Sulfogalactosylceramide (d18:1/16:0)
  • Sulfatide (d18:1/16:0)
3-O-Sulfogalactosylceramide (d18:1/18:0)
  • Sulfatide (d18:1/18:0)

(1) Drugbank Compounds for CD1D Gene

Compound Synonyms Cas Number Type Actions PubMed IDs
Cis-tetracosenoyl sulfatide

(7) Novoseek inferred chemical compound relationships for CD1D Gene

Compound -log(P) Hits PubMed IDs
alpha-galactosylceramide 90 13
glycolipid 80.5 19
lipid 44.3 20
retinoid 19 2
ceramide 18.1 3
genes like me logo Genes that share compounds with CD1D: view

Transcripts for CD1D Gene

Unigene Clusters for CD1D Gene

CD1d molecule:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CD1D

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CD1D Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c · 2d ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b · 5c · 5d ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b
SP1: - -
SP2: - -
SP3: - -
SP4: - -
SP5: - - -
SP7: - -

Relevant External Links for CD1D Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CD1D Gene

mRNA expression in normal human tissues for CD1D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CD1D Gene

This gene is overexpressed in Whole Blood (9.9), Spleen (8.6), Small Intestine - Terminal Ileum (5.5), and Liver (4.9).

Protein differential expression in normal tissues for CD1D Gene

This gene is overexpressed in Lung (69.0).

Integrated Proteomics: protein expression from ProteomicsDB, MOPED, and MaxQB for CD1D Gene

SOURCE GeneReport for Unigene cluster for CD1D Gene Hs.1799

mRNA Expression by UniProt/SwissProt for CD1D Gene

Tissue specificity: Expressed on cortical thymocytes, on certain T-cell leukemias, and in various other tissues
genes like me logo Genes that share expressions with CD1D: view

Expression partners for CD1D Gene

In Situ Assay Products

Orthologs for CD1D Gene

This gene was present in the common ancestor of chordates.

Orthologs for CD1D Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia LOC788175 35
  • 80.33 (n)
  • 69.26 (a)
-- 36
  • 62 (a)
-- 36
  • 65 (a)
-- 36
  • 62 (a)
CD1D 36
  • 45 (a)
(Mus musculus)
Mammalia Cd1d1 35
  • 75.47 (n)
  • 62.58 (a)
Cd1d1 16
Cd1d1 36
  • 61 (a)
Cd1d2 36
  • 61 (a)
(Pan troglodytes)
Mammalia CD1D 35
  • 98.91 (n)
  • 98.21 (a)
CD1D 36
  • 98 (a)
(Rattus norvegicus)
Mammalia Cd1d1 35
  • 74.87 (n)
  • 65.11 (a)
(Canis familiaris)
Mammalia CD1D 36
  • 58 (a)
(Gallus gallus)
Aves CD1.2 36
  • 22 (a)
CD1A1 36
  • 24 (a)
(Anolis carolinensis)
Reptilia -- 36
  • 26 (a)
Species with no ortholog for CD1D:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for CD1D Gene

Gene Tree for CD1D (if available)
Gene Tree for CD1D (if available)

Paralogs for CD1D Gene

Paralogs for CD1D Gene

Selected SIMAP similar genes for CD1D Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with CD1D: view

Variants for CD1D Gene

Sequence variations from dbSNP and Humsavar for CD1D Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type MAF
rs11762 -- 158,184,604(+) TCTGG(A/T)TTTTC utr-variant-3-prime
rs422236 -- 158,185,303(-) CCAAC(A/C)GTTAA utr-variant-3-prime, downstream-variant-500B
rs426336 -- 158,184,206(-) GTCTT(A/G)GGAAC utr-variant-3-prime
rs692565 -- 158,183,736(-) CTTTG(A/G)CATTT intron-variant
rs703113 -- 158,185,707(-) ATTTA(A/G)AAGCT utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for CD1D Gene

Variant ID Type Subtype PubMed ID
dgv393n71 CNV Gain 21882294

Relevant External Links for CD1D Gene

HapMap Linkage Disequilibrium report

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CD1D Gene

Disorders for CD1D Gene

MalaCards: The human disease database

MalaCards: The human disease database.

Search for CD1D Gene in MalaCards »

(2) Diseases for CD1D Gene including...

(1) University of Copenhagen DISEASES for CD1D Gene

(7) Novoseek inferred disease relationships for CD1D Gene

Disease -log(P) Hits PubMed IDs
autoimmunity 40.5 1
autoimmune diseases 37.5 5
rheumatoid arthritis 6.37 2
multiple sclerosis 4.53 2
inflammation 1.59 3

Relevant External Links for CD1D

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with CD1D: view

No data available for OMIM , UniProtKB/Swiss-Prot and Genatlas for CD1D Gene

Publications for CD1D Gene

  1. Regulation of intracellular trafficking of human CD1d by association with MHC class II molecules. (PMID: 11927549) Kang S.-J. … Cresswell P. (EMBO J. 2002) 3 4 23
  2. Susceptibility to Guillain-BarrAc syndrome is associated to polymorphisms of CD1 genes. (PMID: 16820217) Caporale C.M. … Uncini A. (J. Neuroimmunol. 2006) 3 23 48
  3. CD1d-lipid-antigen recognition by the semi-invariant NKT T-cell receptor. (PMID: 17581592) Borg N.A. … Rossjohn J. (Nature 2007) 3 4 23
  4. Isolation and characterization of a cDNA and gene coding for a fourth CD1 molecule. (PMID: 2463622) Balk S.P. … Terhorst C. (Proc. Natl. Acad. Sci. U.S.A. 1989) 2 3 4
  5. Two classes of CD1 genes. (PMID: 2467814) Calabi F. … Milstein C. (Eur. J. Immunol. 1989) 3 4

Products for CD1D Gene

Sources for CD1D Gene

Back to Top