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Aliases for CD1D Gene

Aliases for CD1D Gene

  • CD1d Molecule 2 3 5
  • 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. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]

GeneCards Summary for CD1D Gene

CD1D (CD1d Molecule) is a Protein Coding gene. Diseases associated with CD1D include Mycobacterium Malmoense. Among its related pathways are Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell and Innate Immune System. GO annotations related to this gene include receptor activity and cell adhesion molecule binding. An important paralog of this gene is CD1E.

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 CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CD1D Gene

Genomics for CD1D Gene

Regulatory Elements for CD1D Gene

Enhancers for CD1D Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01G158144 1.5 FANTOM5 Ensembl ENCODE 11.3 -30.2 -30168 6.2 ATF1 PKNOX1 CREB3L1 YY1 ETS1 TCF12 GLIS2 ELK1 ZNF143 FOS ELL2P1 CD1D KIRREL OR10R2 OR10X1 LINC01704
GH01G158208 0.8 dbSUPER 15.8 +31.0 31036 1.7 ZBTB40 YY1 FOSL1 POLR2A EED ETV6 IKZF2 CREM EZH2 MAZ ENSG00000176320 CD1D ELL2P1 CD1B GC01P158217
GH01G158818 1.8 FANTOM5 Ensembl ENCODE dbSUPER 4.5 +641.4 641398 2.1 PKNOX1 ATF1 ARNT TCF12 ZNF766 ELK1 GATA2 FOS JUNB NCOA1 MNDA CD1D PYHIN1 IFI16 OR10AA1P
GH01G158154 0.7 Ensembl 11.4 -23.7 -23738 0.6 SCRT1 TEAD4 JUNB ZNF83 EED IKZF1 SCRT2 ETV6 ZNF24 IKZF2 CD1D ELL2P1 CD1A CD1C LINC01704
GH01G158188 0.4 dbSUPER 17.9 +11.2 11207 1.4 ZNF585B ATF2 CD1D GC01M158195 ELL2P1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CD1D on UCSC Golden Path with GeneCards custom track

Promoters for CD1D Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000014378 -237 800 MAZ SP3 PKNOX1 ZSCAN4 SP2 MAFG ZBTB40 YY1 JUND ATF3

Genomic Location for CD1D Gene

Chromosome:
1
Start:
158,178,038 bp from pter
End:
158,186,427 bp from pter
Size:
8,390 bases
Orientation:
Plus strand

Genomic View for CD1D Gene

Genes around CD1D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CD1D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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:
    P15813-CD1D_HUMAN
    Recommended name:
    Antigen-presenting glycoprotein CD1d
    Protein Accession:
    P15813
    Secondary Accessions:
    • D3DVD5
    • Q5W0J3
    • Q9UMM3
    • Q9Y5M4

    Protein attributes for CD1D Gene

    Size:
    335 amino acids
    Molecular mass:
    37717 Da
    Quaternary structure:
    • Heterodimer with B2M (beta-2-microglobulin). Interacts with MHC II.
    Miscellaneous:
    • 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

Post-translational modifications for CD1D Gene

  • Glycosylation at posLast=3838, posLast=6060, posLast=126126, and posLast=181181
  • Modification sites at PhosphoSitePlus

Other Protein References for CD1D Gene

Antibody Products

  • Abcam antibodies for CD1D

No data available for DME Specific Peptides for CD1D Gene

Domains & Families for CD1D Gene

Gene Families for CD1D Gene

Suggested Antigen Peptide Sequences for CD1D Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

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

No data available for UniProtKB/Swiss-Prot for CD1D Gene

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:0030881 beta-2-microglobulin binding TAS 14500461
GO:0030882 lipid antigen binding IDA 19124746
GO:0030883 endogenous lipid antigen binding IBA --
GO:0030884 exogenous lipid antigen binding IDA 10523605
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

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for CD1D

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets 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. Basolateral cell membrane; Single-pass type I membrane protein. Endosome membrane; Single-pass type I membrane protein. Lysosome membrane; Single-pass type I membrane protein. Endoplasmic reticulum membrane; Single-pass type I membrane protein. Note=Subject to intracellular trafficking between the cell membrane, endosomes and lysosomes. {ECO:0000269 PubMed:9973405}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CD1D gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 5
lysosome 4
endosome 4
extracellular 2
cytosol 2
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 IEA --
GO:0005765 lysosomal membrane IEA --
GO:0005768 endosome IEA --
GO:0005783 endoplasmic reticulum IDA --
genes like me logo Genes that share ontologies with CD1D: view

Pathways & Interactions for CD1D Gene

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

Interacting Proteins for CD1D Gene

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000357153%0d%0a9606.ENSP00000452780%0d%0a9606.ENSP00000431445%0d%0a9606.ENSP00000300692%0d%0a9606.ENSP00000354566%0d%0a9606.ENSP00000431254%0d%0a
Selected Interacting proteins: ENSP00000357153 P15813-CD1D_HUMAN for CD1D Gene via STRING IID

Symbol External ID(s) Details
HLA-B
HLA-A
HLA-C
HLA-DRB1
B2M

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

No data available for SIGNOR curated interactions for CD1D Gene

Drugs & Compounds for CD1D Gene

(6) Drugs for CD1D Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Cis-tetracosenoyl sulfatide Experimental Pharma Target 0
Sphingosine Experimental Pharma 0
sphinganine Pharma 0
sphingosine 1-phosphate Pharma Full agonist, Agonist 0

(467) Additional Compounds for CD1D Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
3-Dehydrosphinganine
  • (2S)-2-amino-1-hydroxyoctadecan-3-one
  • 1-Hydroxy-2-amino-3-oxo-octadecane
  • 2-Amino-1-hydroxy-3-Octadecanone
  • 3-Dehydro-D-sphinganine
  • 3-Dehydrosphinganine
16105-69-4
3-O-Sulfogalactosylceramide (d18:1/12:0)
  • 3'-O-Sulphogalactosylceramide
  • 3-O-Sulfo-beta-D-galactosylceramide
  • 3-O-Sulfo-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
852100-88-0
3-O-Sulfogalactosylceramide (d18:1/14:0)
  • 3'-O-Sulphogalactosylceramide
  • 3-O-Sulfo-beta-D-galactosylceramide
  • 3-O-Sulfo-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
3-O-Sulfogalactosylceramide (d18:1/16:0)
  • 3'-O-Sulphogalactosylceramide
  • 3-O-Sulfo-beta-D-galactosylceramide
  • 3-O-Sulfo-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
862509-48-6
3-O-Sulfogalactosylceramide (d18:1/18:0)
  • 3'-O-Sulphogalactosylceramide
  • 3-O-Sulfo-beta-D-galactosylceramide
  • 3-O-Sulfo-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
244215-65-4
genes like me logo Genes that share compounds with CD1D: view

Transcripts for CD1D Gene

mRNA/cDNA for CD1D Gene

Unigene Clusters for CD1D Gene

CD1d molecule:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for CD1D

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: - - -
SP6:
SP7: - -

Relevant External Links for CD1D Gene

GeneLoc Exon Structure for
CD1D
ECgene alternative splicing isoforms for
CD1D

Expression for CD1D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE 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 (x9.9), Spleen (x8.6), Small Intestine - Terminal Ileum (x5.5), and Liver (x4.9).

Protein differential expression in normal tissues from HIPED for CD1D Gene

This gene is overexpressed in Lung (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CD1D Gene



Protein tissue co-expression partners for CD1D Gene

NURSA nuclear receptor signaling pathways regulating expression of CD1D Gene:

CD1D

SOURCE GeneReport for Unigene cluster for CD1D Gene:

Hs.1799

mRNA Expression by UniProt/SwissProt for CD1D Gene:

P15813-CD1D_HUMAN
Tissue specificity: Expressed on cortical thymocytes, on certain T-cell leukemias, and in various other tissues.

Evidence on tissue expression from TISSUES for CD1D Gene

  • Pancreas(4.2)
  • Blood(3.4)
  • Lymph node(3.1)
  • Spleen(3.1)
  • Liver(2.3)
  • Intestine(2.1)
  • Lung(2.1)
genes like me logo Genes that share expression patterns with CD1D: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CD1D Gene

Orthologs for CD1D Gene

This gene was present in the common ancestor of chordates.

Orthologs for CD1D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CD1D 34 35
  • 98.91 (n)
cow
(Bos Taurus)
Mammalia LOC788175 34
  • 80.33 (n)
-- 35
  • 65 (a)
OneToMany
-- 35
  • 62 (a)
OneToMany
-- 35
  • 62 (a)
OneToMany
CD1D 35
  • 45 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Cd1d1 34 16 35
  • 75.47 (n)
Cd1d2 35
  • 61 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Cd1d1 34
  • 74.87 (n)
dog
(Canis familiaris)
Mammalia CD1D 35
  • 58 (a)
OneToOne
chicken
(Gallus gallus)
Aves CD1A1 35
  • 24 (a)
ManyToMany
CD1.2 35
  • 22 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 26 (a)
OneToMany
Species where no ortholog for CD1D was found in the sources mined by GeneCards:
  • 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

ENSEMBL:
Gene Tree for CD1D (if available)
TreeFam:
Gene Tree for CD1D (if available)

Paralogs for CD1D Gene

Paralogs for CD1D Gene

(4) 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
rs1000391164 -- 158,180,483(+) CCTGG(C/G)ATATG intron-variant, upstream-variant-2KB
rs1000407328 -- 158,180,298(+) AAAGT(G/T)AATGA intron-variant, upstream-variant-2KB
rs1000581465 -- 158,184,298(+) TGAGG(A/C)AGCTT nc-transcript-variant, utr-variant-3-prime
rs1000655043 -- 158,184,651(+) TTTTA(C/G)AAAAT nc-transcript-variant, utr-variant-3-prime
rs1001587959 -- 158,185,845(+) GCTCA(A/G)TAGTC utr-variant-3-prime

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

Variant ID Type Subtype PubMed ID
esv3578208 CNV loss 25503493
nsv999542 CNV loss 25217958

Variation tolerance for CD1D Gene

Residual Variation Intolerance Score: 83.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.67; 31.99% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CD1D Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CD1D

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

Disorders for CD1D Gene

MalaCards: The human disease database

(1) MalaCards diseases for CD1D Gene - From: GeneCards

Disorder Aliases PubMed IDs
mycobacterium malmoense
  • m. malmoense
- elite association - COSMIC cancer census association via MalaCards
Search CD1D in MalaCards View complete list of genes associated with diseases

Relevant External Links for CD1D

Genetic Association Database (GAD)
CD1D
Human Genome Epidemiology (HuGE) Navigator
CD1D
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CD1D
genes like me logo Genes that share disorders with CD1D: view

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

Publications for CD1D Gene

  1. CD1d-lipid-antigen recognition by the semi-invariant NKT T-cell receptor. (PMID: 17581592) Borg N.A. … Rossjohn J. (Nature 2007) 3 4 22 64
  2. Susceptibility to Guillain-BarrAc syndrome is associated to polymorphisms of CD1 genes. (PMID: 16820217) Caporale C.M. … Uncini A. (J. Neuroimmunol. 2006) 3 22 46 64
  3. 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 22 64
  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 64
  5. Uncoupling between CD1d upregulation induced by retinoic acid and conduritol-B-epoxide and iNKT cell responsiveness. (PMID: 19651460) Balreira A. … Arosa F.A. (Immunobiology 2010) 3 22 64

Products for CD1D Gene

Sources for CD1D Gene

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