Atlas of Genetics and Cytogenetics in Oncology and Haematology

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CD3D (CD3d molecule)

Identity

Alias_namesT3D
CD3d antigen, delta polypeptide (TiT3 complex)
CD3d molecule, delta (CD3-TCR complex)
Other aliasCD3-DELTA
IMD19
HGNC (Hugo) CD3D
LocusID (NCBI) 915
Atlas_Id 52453
Location 11q23.3  [Link to chromosome band 11q23]
Location_base_pair Starts at 118339074 and ends at 118342744 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
CAT (11p13) / CD3D (11q23.3)CD3D (11q23.3) / KIAA0100 (17q11.2)CD3D (11q23.3) / MRPS5 (2q11.1)
SIK3 (11q23.3) / CD3D (11q23.3)CAT 11p13 / CD3D 11q23.3SIK3 11q23.3 / CD3D 11q23.3

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 2 ]
  t(11;11)(p13;q23) CAT/CD3D
SIK3/CD3D (11q23)

External links

Nomenclature
HGNC (Hugo)CD3D   1673
LRG (Locus Reference Genomic)LRG_37
Cards
Entrez_Gene (NCBI)CD3D  915  CD3d molecule
AliasesCD3-DELTA; IMD19; T3D
GeneCards (Weizmann)CD3D
Ensembl hg19 (Hinxton)ENSG00000167286 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000167286 [Gene_View]  ENSG00000167286 [Sequence]  chr11:118339074-118342744 [Contig_View]  CD3D [Vega]
ICGC DataPortalENSG00000167286
TCGA cBioPortalCD3D
AceView (NCBI)CD3D
Genatlas (Paris)CD3D
WikiGenes915
SOURCE (Princeton)CD3D
Genetics Home Reference (NIH)CD3D
Genomic and cartography
GoldenPath hg38 (UCSC)CD3D  -     chr11:118339074-118342744 -  11q23.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)CD3D  -     11q23.3   [Description]    (hg19-Feb_2009)
CD3D - 11q23.3 [CytoView hg19]  CD3D - 11q23.3 [CytoView hg38]
Mapping of homologs : NCBICD3D [Mapview hg19]  CD3D [Mapview hg38]
OMIM186790   615617   
Gene and transcription
Genbank (Entrez)AK093775 AK311971 BC039035 BC070321 CD014058
RefSeq transcript (Entrez)NM_000732 NM_001040651
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)CD3D
Cluster EST : UnigeneHs.504048 [ NCBI ]
CGAP (NCI)Hs.504048
Alternative Splicing GalleryENSG00000167286
Gene ExpressionCD3D [ NCBI-GEO ]   CD3D [ EBI - ARRAY_EXPRESS ]   CD3D [ SEEK ]   CD3D [ MEM ]
Gene Expression Viewer (FireBrowse)CD3D [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)915
GTEX Portal (Tissue expression)CD3D
Human Protein AtlasENSG00000167286-CD3D [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP04234   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP04234  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP04234
Splice isoforms : SwissVarP04234
PhosPhoSitePlusP04234
Domaine pattern : Prosite (Expaxy)ITAM_1 (PS51055)   
Domains : Interpro (EBI)CD3_esu/gsu/dsu    CD3D    Ig-like_dom_sf    Ig-like_fold    Ig_4    Phos_immunorcpt_sig_ITAM   
Domain families : Pfam (Sanger)Ig_4 (PF16680)    ITAM (PF02189)   
Domain families : Pfam (NCBI)pfam16680    pfam02189   
Domain families : Smart (EMBL)ITAM (SM00077)  
Conserved Domain (NCBI)CD3D
DMDM Disease mutations915
Blocks (Seattle)CD3D
PDB (RSDB)1XIW   
PDB Europe1XIW   
PDB (PDBSum)1XIW   
PDB (IMB)1XIW   
Structural Biology KnowledgeBase1XIW   
SCOP (Structural Classification of Proteins)1XIW   
CATH (Classification of proteins structures)1XIW   
SuperfamilyP04234
Human Protein Atlas [tissue]ENSG00000167286-CD3D [tissue]
Peptide AtlasP04234
HPRD01730
IPIIPI00022934   IPI00981421   IPI00980733   IPI00759573   
Protein Interaction databases
DIP (DOE-UCLA)P04234
IntAct (EBI)P04234
FunCoupENSG00000167286
BioGRIDCD3D
STRING (EMBL)CD3D
ZODIACCD3D
Ontologies - Pathways
QuickGOP04234
Ontology : AmiGOadaptive immune response  transcription coactivator activity  transmembrane signaling receptor activity  transmembrane signaling receptor activity  cytoplasm  plasma membrane  cell surface receptor signaling pathway  cell surface receptor signaling pathway  external side of plasma membrane  integral component of membrane  T cell differentiation  T cell differentiation  clathrin-coated vesicle membrane  T cell receptor complex  T cell receptor complex  alpha-beta T cell receptor complex  protein homodimerization activity  positive thymic T cell selection  positive thymic T cell selection  positive regulation of transcription by RNA polymerase II  protein heterodimerization activity  regulation of immune response  T cell receptor signaling pathway  protein homooligomerization  membrane organization  
Ontology : EGO-EBIadaptive immune response  transcription coactivator activity  transmembrane signaling receptor activity  transmembrane signaling receptor activity  cytoplasm  plasma membrane  cell surface receptor signaling pathway  cell surface receptor signaling pathway  external side of plasma membrane  integral component of membrane  T cell differentiation  T cell differentiation  clathrin-coated vesicle membrane  T cell receptor complex  T cell receptor complex  alpha-beta T cell receptor complex  protein homodimerization activity  positive thymic T cell selection  positive thymic T cell selection  positive regulation of transcription by RNA polymerase II  protein heterodimerization activity  regulation of immune response  T cell receptor signaling pathway  protein homooligomerization  membrane organization  
Pathways : KEGGHematopoietic cell lineage    T cell receptor signaling pathway    Chagas disease (American trypanosomiasis)    Measles    HTLV-I infection    Primary immunodeficiency   
NDEx NetworkCD3D
Atlas of Cancer Signalling NetworkCD3D
Wikipedia pathwaysCD3D
Orthology - Evolution
OrthoDB915
GeneTree (enSembl)ENSG00000167286
Phylogenetic Trees/Animal Genes : TreeFamCD3D
HOGENOMP04234
Homologs : HomoloGeneCD3D
Homology/Alignments : Family Browser (UCSC)CD3D
Gene fusions - Rearrangements
Fusion : MitelmanCAT/CD3D [11p13/11q23.3]  [t(11;11)(p13;q23)]  
Fusion : MitelmanSIK3/CD3D [11q23.3/11q23.3]  [t(11;11)(q23;q23)]  
Fusion PortalCAT 11p13 CD3D 11q23.3 OV
Fusion PortalSIK3 11q23.3 CD3D 11q23.3 LUAD
Fusion : QuiverCD3D
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCD3D [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CD3D
dbVarCD3D
ClinVarCD3D
1000_GenomesCD3D 
Exome Variant ServerCD3D
ExAC (Exome Aggregation Consortium)ENSG00000167286
GNOMAD BrowserENSG00000167286
Varsome BrowserCD3D
Genetic variants : HAPMAP915
Genomic Variants (DGV)CD3D [DGVbeta]
DECIPHERCD3D [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCD3D 
Mutations
ICGC Data PortalCD3D 
TCGA Data PortalCD3D 
Broad Tumor PortalCD3D
OASIS PortalCD3D [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCD3D  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCD3D
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)**PUBLIC** CCHMC Molecular Genetics Laboratory Mutation Database
BioMutasearch CD3D
DgiDB (Drug Gene Interaction Database)CD3D
DoCM (Curated mutations)CD3D (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CD3D (select a term)
intoGenCD3D
Cancer3DCD3D(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM186790    615617   
Orphanet17831   
DisGeNETCD3D
MedgenCD3D
Genetic Testing Registry CD3D
NextProtP04234 [Medical]
TSGene915
GENETestsCD3D
Target ValidationCD3D
Huge Navigator CD3D [HugePedia]
snp3D : Map Gene to Disease915
BioCentury BCIQCD3D
ClinGenCD3D
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD915
Chemical/Pharm GKB GenePA26215
Clinical trialCD3D
Miscellaneous
canSAR (ICR)CD3D (select the gene name)
DataMed IndexCD3D
Probes
Litterature
PubMed111 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCD3D
EVEXCD3D
GoPubMedCD3D
iHOPCD3D
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Thu Mar 21 15:39:43 CET 2019
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