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Aliases for CD3D Gene

Aliases for CD3D Gene

  • CD3d Molecule, Delta (CD3-TCR Complex) 2 3
  • T3D 3 4 6
  • CD3d Antigen, Delta Polypeptide (TiT3 Complex) 2 3
  • T-Cell Receptor T3 Delta Chain 3 4
  • IMD19 3 6
  • T-Cell Surface Glycoprotein CD3 Delta Chain 3
  • CD3 Antigen, Delta Subunit 3
  • OKT3, Delta Chain 3
  • CD3d Antigen 4
  • CD3 Delta 3
  • CD3-DELTA 3

External Ids for CD3D Gene

Previous HGNC Symbols for CD3D Gene

  • T3D

Previous GeneCards Identifiers for CD3D Gene

  • GC11M120566
  • GC11M119721
  • GC11M118239
  • GC11M117747
  • GC11M117714
  • GC11M118212
  • GC11M114143

Summaries for CD3D Gene

Entrez Gene Summary for CD3D Gene

  • The protein encoded by this gene is part of the T-cell receptor/CD3 complex (TCR/CD3 complex) and is involved in T-cell development and signal transduction. The encoded membrane protein represents the delta subunit of the CD3 complex, and along with four other CD3 subunits, binds either TCR alpha/beta or TCR gamma/delta to form the TCR/CD3 complex on the surface of T-cells. Defects in this gene are a cause of severe combined immunodeficiency autosomal recessive T-cell-negative/B-cell-positive/NK-cell-positive (SCIDBNK). Two transcript variants encoding different isoforms have been found for this gene. Other variants may also exist, but the full-length natures of their transcripts has yet to be defined. [provided by RefSeq, Feb 2009]

GeneCards Summary for CD3D Gene

CD3D (CD3d Molecule, Delta (CD3-TCR Complex)) is a Protein Coding gene. Diseases associated with CD3D include immunodeficiency 19 and severe combined immune deficiency, autosomal recessive, t cell-negative, b cell-positive, nk cell-positive, cd3d-related. Among its related pathways are Class I MHC mediated antigen processing and presentation and Akt Signaling. GO annotations related to this gene include protein heterodimerization activity and transmembrane signaling receptor activity. An important paralog of this gene is CD3G.

UniProtKB/Swiss-Prot for CD3D Gene

  • The CD3 complex mediates signal transduction

Gene Wiki entry for CD3D Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CD3D Gene

Genomics for CD3D Gene

Regulatory Elements for CD3D Gene

Genomic Location for CD3D Gene

118,338,954 bp from pter
118,342,744 bp from pter
3,791 bases
Minus strand

Genomic View for CD3D Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for CD3D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CD3D Gene

Proteins for CD3D Gene

  • Protein details for CD3D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    T-cell surface glycoprotein CD3 delta chain
    Protein Accession:
    Secondary Accessions:
    • A8MVP6

    Protein attributes for CD3D Gene

    171 amino acids
    Molecular mass:
    18930 Da
    Quaternary structure:
    • The TCR/CD3 complex of T-lymphocytes consists of either a TCR alpha/beta or TCR gamma/delta heterodimer coexpressed at the cell surface with the invariant subunits of CD3 labeled gamma, delta, epsilon, zeta, and eta.

    Three dimensional structures from OCA and Proteopedia for CD3D Gene

    Alternative splice isoforms for CD3D Gene


neXtProt entry for CD3D Gene

Proteomics data for CD3D Gene at MOPED

Post-translational modifications for CD3D Gene

  • Ubiquitination at Lys62, Lys80, and Lys82
  • Glycosylation at Asn38 and Asn74
  • Modification sites at PhosphoSitePlus

Other Protein References for CD3D Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

Antibody Products

  • R&D Systems Antibodies for CD3D (TCR gamma/delta)

No data available for DME Specific Peptides for CD3D Gene

Domains for CD3D Gene

Gene Families for CD3D Gene

Suggested Antigen Peptide Sequences for CD3D Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 ITAM domain.
  • Contains 1 ITAM domain.
genes like me logo Genes that share domains with CD3D: view

Function for CD3D Gene

Molecular function for CD3D Gene

GENATLAS Biochemistry:
cell differentiation antigen CD3D (gp20),20kDa,delta polypeptide (see CD3@)
UniProtKB/Swiss-Prot Function:
The CD3 complex mediates signal transduction

Gene Ontology (GO) - Molecular Function for CD3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003713 transcription coactivator activity IDA 2017177
GO:0004888 transmembrane signaling receptor activity IC 9485181
GO:0005515 protein binding --
GO:0046982 protein heterodimerization activity IPI 9485181
genes like me logo Genes that share ontologies with CD3D: view

Phenotypes for CD3D Gene

genes like me logo Genes that share phenotypes with CD3D: view

Animal Models for CD3D Gene

MGI Knock Outs for CD3D:

Animal Model Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CD3D

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for CD3D Gene

Localization for CD3D Gene

Subcellular locations from UniProtKB/Swiss-Prot for CD3D Gene

Membrane; Single-pass type I membrane protein.

Subcellular locations from

Jensen Localization Image for CD3D Gene COMPARTMENTS Subcellular localization image for CD3D gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 2
cytosol 1
golgi apparatus 1
nucleus 1

Gene Ontology (GO) - Cellular Components for CD3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm NAS 1831653
GO:0005886 plasma membrane TAS --
GO:0016020 membrane --
GO:0016021 integral component of membrane IEA --
GO:0042101 T cell receptor complex NAS 9485181
genes like me logo Genes that share ontologies with CD3D: view

Pathways for CD3D Gene

genes like me logo Genes that share pathways with CD3D: view

PCR Array Products

Gene Ontology (GO) - Biological Process for CD3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007166 cell surface receptor signaling pathway IC 9485181
GO:0030217 T cell differentiation IDA 2017177
GO:0031295 T cell costimulation TAS --
GO:0045059 positive thymic T cell selection ISS --
GO:0045944 positive regulation of transcription from RNA polymerase II promoter IDA 2017177
genes like me logo Genes that share ontologies with CD3D: view

Drugs for CD3D Gene

(2) Drugbank Compounds for CD3D Gene

Compound Status Synonyms Cas Number PubChem ID Type Actions PubMed IDs
  • Anti-CD3
140608-64-6 Target approved, investigational
853426-35-4 Target activator approved
genes like me logo Genes that share compounds with CD3D: view

Transcripts for CD3D Gene

Unigene Clusters for CD3D Gene

CD3d molecule, delta (CD3-TCR complex):
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CD3D

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CD3D Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b
SP2: -
SP3: -
SP4: - -

Relevant External Links for CD3D Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CD3D Gene

mRNA expression in normal human tissues for CD3D Gene

mRNA differential expression in normal tissues according to GTEx for CD3D Gene

This gene is overexpressed in Whole Blood (21.3), Spleen (8.4), and Small Intestine - Terminal Ileum (6.6).

Protein differential expression in normal tissues for CD3D Gene

This gene is overexpressed in Tlymphocyte (43.3) and CD8 Tcells (7.3).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for CD3D Gene

SOURCE GeneReport for Unigene cluster for CD3D Gene Hs.504048

genes like me logo Genes that share expressions with CD3D: view

Expression partners for CD3D Gene

* - Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt for CD3D Gene

Orthologs for CD3D Gene

This gene was present in the common ancestor of chordates.

Orthologs for CD3D Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia CD3D 35
  • 77.31 (n)
  • 66.27 (a)
CD3D 36
  • 64 (a)
(Canis familiaris)
Mammalia CD3D 35
  • 80.51 (n)
  • 69.59 (a)
CD3D 36
  • 70 (a)
(Mus musculus)
Mammalia Cd3d 35
  • 75.24 (n)
  • 64.33 (a)
Cd3d 16
Cd3d 36
  • 64 (a)
(Pan troglodytes)
Mammalia CD3D 35
  • 99.03 (n)
  • 97.66 (a)
CD3D 36
  • 98 (a)
(Rattus norvegicus)
Mammalia Cd3d 35
  • 76.22 (n)
  • 69.01 (a)
(Monodelphis domestica)
Mammalia CD3D 36
  • 43 (a)
(Ornithorhynchus anatinus)
Mammalia CD3D 36
  • 38 (a)
(Gallus gallus)
Aves CD3D 35
  • 55.94 (n)
  • 45.89 (a)
CD3D 36
  • 38 (a)
(Anolis carolinensis)
Reptilia -- 36
  • 28 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cd3g 35
  • 53.17 (n)
  • 42.06 (a)
Species with no ortholog for CD3D:
  • 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)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for CD3D Gene

Gene Tree for CD3D (if available)
Gene Tree for CD3D (if available)

Paralogs for CD3D Gene

Paralogs for CD3D Gene

(1) SIMAP similar genes for CD3D Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with CD3D: view

Variants for CD3D Gene

Sequence variations from dbSNP and Humsavar for CD3D Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type MAF
rs45510201 - 118,339,461(+) AGACC(C/T)GGTCA reference, missense
rs730880296 Pathogenic 118,340,370(-) AGTAC(A/G)TGCTT intron-variant
rs578129773 -- 118,338,929(+) GTGGC(A/G)AGAGA downstream-variant-500B
rs574464150 -- 118,341,859(+) TGCTA(A/G)GACAT intron-variant
rs574305362 -- 118,342,051(+) CCCAC(A/G)TGCAC intron-variant

Relevant External Links for CD3D Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)
Locus Specific Mutation Databases (LSDB)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for CD3D Gene

Disorders for CD3D Gene

(1) OMIM Diseases for CD3D Gene (186790)


  • Severe combined immunodeficiency autosomal recessive T-cell-negative/B-cell-positive/NK-cell-positive (T(-)B(+)NK(+) SCID) [MIM:608971]: A form of severe combined immunodeficiency (SCID), a genetically and clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and cell-mediated immunity, leukopenia, and low or absent antibody levels. Patients present in infancy recurrent, persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of T-cell-mediated cellular immunity due to a defect in T-cell development. {ECO:0000269 PubMed:14602880}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Immunodeficiency 19 (IMD19) [MIM:615617]: An autosomal recessive form of severe combined immunodeficiency characterized by onset in early infancy of recurrent bacterial, viral, and fungal infections. Patients usually have chronic diarrhea, recurrent respiratory infections, and failure to thrive. Immunologic work-up shows a T-cell negative, B-cell positive, NK-cell positive phenotype. {ECO:0000269 PubMed:15546002, ECO:0000269 PubMed:21883749}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(2) University of Copenhagen DISEASES for CD3D Gene

(3) Novoseek inferred disease relationships for CD3D Gene

Disease -log(P) Hits PubMed IDs
severe combined immunodeficiency 65 5
diabetes mellitus insulin-dependent 18.4 1
necrosis 0 1

Relevant External Links for CD3D

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with CD3D: view

No data available for Genatlas for CD3D Gene

Publications for CD3D Gene

  1. Severe combined immunodeficiency caused by deficiency in either the delta or the epsilon subunit of CD3. (PMID: 15546002) de Saint Basile G. … Le Deist F. (J. Clin. Invest. 2004) 3 4 23
  2. Isolation of cDNA clones encoding the 20K T3 glycoprotein of human T- cell receptor complex. (PMID: 6095101) van den Elsen P. … Terhorst C. (Nature 1984) 3 4
  3. A haplotype in the inducible T-cell tyrosine kinase is a risk factor for seasonal allergic rhinitis. (PMID: 19222422) Benson M. … Cardell L.O. (Allergy 2009) 3 48
  4. Crystal structure of a human CD3-epsilon/delta dimer in complex with a UCHT1 single-chain antibody fragment. (PMID: 15534202) Arnett K.L. … Wiley D.C. (Proc. Natl. Acad. Sci. U.S.A. 2004) 3 4
  5. Evaluation of 6 candidate genes on chromosome 11q23 for coeliac disease susceptibility: a case control study. (PMID: 20478055) Brophy K. … McManus R. (BMC Med. Genet. 2010) 3 48

Products for CD3D Gene

Sources for CD3D Gene

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