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PDCD1 (programmed cell death 1)

Identity

Alias_namesSLEB2
systemic lupus erythematosus susceptibility 2
Alias_symbol (synonym)CD279
PD1
hSLE1
PD-1
Other aliashPD-1
hPD-l
HGNC (Hugo) PDCD1
LocusID (NCBI) 5133
Atlas_Id 41673
Location 2q37.3  [Link to chromosome band 2q37]
Location_base_pair Starts at 241849881 and ends at 241858906 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)

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

 


External links

Nomenclature
HGNC (Hugo)PDCD1   8760
Cards
Entrez_Gene (NCBI)PDCD1  5133  programmed cell death 1
AliasesCD279; PD-1; PD1; SLEB2; 
hPD-1; hPD-l; hSLE1
GeneCards (Weizmann)PDCD1
Ensembl hg19 (Hinxton)ENSG00000188389 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000188389 [Gene_View]  ENSG00000188389 [Sequence]  chr2:241849881-241858906 [Contig_View]  PDCD1 [Vega]
ICGC DataPortalENSG00000188389
TCGA cBioPortalPDCD1
AceView (NCBI)PDCD1
Genatlas (Paris)PDCD1
WikiGenes5133
SOURCE (Princeton)PDCD1
Genetics Home Reference (NIH)PDCD1
Genomic and cartography
GoldenPath hg38 (UCSC)PDCD1  -     chr2:241849881-241858906 -  2q37.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PDCD1  -     2q37.3   [Description]    (hg19-Feb_2009)
EnsemblPDCD1 - 2q37.3 [CytoView hg19]  PDCD1 - 2q37.3 [CytoView hg38]
Mapping of homologs : NCBIPDCD1 [Mapview hg19]  PDCD1 [Mapview hg38]
OMIM126200   600244   605218   
Gene and transcription
Genbank (Entrez)AI928135 AK313848 AY206416 AY238517 AY322430
RefSeq transcript (Entrez)NM_005018
RefSeq genomic (Entrez)NC_000002 NG_012110 NT_187527
Consensus coding sequences : CCDS (NCBI)PDCD1
Cluster EST : UnigeneHs.158297 [ NCBI ]
CGAP (NCI)Hs.158297
Alternative Splicing GalleryENSG00000188389
Gene ExpressionPDCD1 [ NCBI-GEO ]   PDCD1 [ EBI - ARRAY_EXPRESS ]   PDCD1 [ SEEK ]   PDCD1 [ MEM ]
Gene Expression Viewer (FireBrowse)PDCD1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5133
GTEX Portal (Tissue expression)PDCD1
Human Protein AtlasENSG00000188389-PDCD1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ15116   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ15116  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ15116
Splice isoforms : SwissVarQ15116
PhosPhoSitePlusQ15116
Domaine pattern : Prosite (Expaxy)IG_LIKE (PS50835)   
Domains : Interpro (EBI)Ig-like_dom    Ig-like_dom_sf    Ig-like_fold    Ig_sub    Ig_V-set   
Domain families : Pfam (Sanger)V-set (PF07686)   
Domain families : Pfam (NCBI)pfam07686   
Domain families : Smart (EMBL)IG (SM00409)  IGv (SM00406)  
Conserved Domain (NCBI)PDCD1
DMDM Disease mutations5133
Blocks (Seattle)PDCD1
PDB (SRS)2M2D    3RRQ    4ZQK    5B8C    5GGR    5GGS    5IUS    5JXE    5WT9   
PDB (PDBSum)2M2D    3RRQ    4ZQK    5B8C    5GGR    5GGS    5IUS    5JXE    5WT9   
PDB (IMB)2M2D    3RRQ    4ZQK    5B8C    5GGR    5GGS    5IUS    5JXE    5WT9   
PDB (RSDB)2M2D    3RRQ    4ZQK    5B8C    5GGR    5GGS    5IUS    5JXE    5WT9   
Structural Biology KnowledgeBase2M2D    3RRQ    4ZQK    5B8C    5GGR    5GGS    5IUS    5JXE    5WT9   
SCOP (Structural Classification of Proteins)2M2D    3RRQ    4ZQK    5B8C    5GGR    5GGS    5IUS    5JXE    5WT9   
CATH (Classification of proteins structures)2M2D    3RRQ    4ZQK    5B8C    5GGR    5GGS    5IUS    5JXE    5WT9   
SuperfamilyQ15116
Human Protein Atlas [tissue]ENSG00000188389-PDCD1 [tissue]
Peptide AtlasQ15116
HPRD02590
IPIIPI00014830   IPI00384107   IPI00816146   IPI00893105   
Protein Interaction databases
DIP (DOE-UCLA)Q15116
IntAct (EBI)Q15116
FunCoupENSG00000188389
BioGRIDPDCD1
STRING (EMBL)PDCD1
ZODIACPDCD1
Ontologies - Pathways
QuickGOQ15116
Ontology : AmiGOnegative regulation of tolerance induction  protein binding  plasma membrane  apoptotic process  humoral immune response  multicellular organism development  external side of plasma membrane  integral component of membrane  T cell costimulation  negative regulation of apoptotic process  positive regulation of T cell apoptotic process  
Ontology : EGO-EBInegative regulation of tolerance induction  protein binding  plasma membrane  apoptotic process  humoral immune response  multicellular organism development  external side of plasma membrane  integral component of membrane  T cell costimulation  negative regulation of apoptotic process  positive regulation of T cell apoptotic process  
Pathways : KEGGCell adhesion molecules (CAMs)    T cell receptor signaling pathway   
NDEx NetworkPDCD1
Atlas of Cancer Signalling NetworkPDCD1
Wikipedia pathwaysPDCD1
Orthology - Evolution
OrthoDB5133
GeneTree (enSembl)ENSG00000188389
Phylogenetic Trees/Animal Genes : TreeFamPDCD1
HOVERGENQ15116
HOGENOMQ15116
Homologs : HomoloGenePDCD1
Homology/Alignments : Family Browser (UCSC)PDCD1
Gene fusions - Rearrangements
Fusion : QuiverPDCD1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPDCD1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PDCD1
dbVarPDCD1
ClinVarPDCD1
1000_GenomesPDCD1 
Exome Variant ServerPDCD1
ExAC (Exome Aggregation Consortium)ENSG00000188389
GNOMAD BrowserENSG00000188389
Varsome BrowserPDCD1
Genetic variants : HAPMAP5133
Genomic Variants (DGV)PDCD1 [DGVbeta]
DECIPHERPDCD1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPDCD1 
Mutations
ICGC Data PortalPDCD1 
TCGA Data PortalPDCD1 
Broad Tumor PortalPDCD1
OASIS PortalPDCD1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPDCD1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPDCD1
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
BioMutasearch PDCD1
DgiDB (Drug Gene Interaction Database)PDCD1
DoCM (Curated mutations)PDCD1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PDCD1 (select a term)
intoGenPDCD1
Cancer3DPDCD1(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM126200    600244    605218   
Orphanet
DisGeNETPDCD1
MedgenPDCD1
Genetic Testing Registry PDCD1
NextProtQ15116 [Medical]
TSGene5133
GENETestsPDCD1
Target ValidationPDCD1
Huge Navigator PDCD1 [HugePedia]
snp3D : Map Gene to Disease5133
BioCentury BCIQPDCD1
ClinGenPDCD1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5133
Chemical/Pharm GKB GenePA33110
Clinical trialPDCD1
Miscellaneous
canSAR (ICR)PDCD1 (select the gene name)
Probes
Litterature
PubMed499 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePDCD1
EVEXPDCD1
GoPubMedPDCD1
iHOPPDCD1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Tue Nov 6 11:29:04 CET 2018

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