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Aliases for PDCD1 Gene

Aliases for PDCD1 Gene

  • Programmed Cell Death 1 2 3
  • Systemic Lupus Erythematosus Susceptibility 2 2 3
  • Protein PD-1 3 4
  • SLEB2 3 6
  • HPD-1 3 4
  • PD1 3 4
  • Programmed Cell Death Protein 1 3
  • CD279 Antigen 4
  • CD279 3
  • HPD-L 3
  • HSLE1 3
  • PD-1 3

External Ids for PDCD1 Gene

Previous Symbols for PDCD1 Gene

  • SLEB2

Summaries for PDCD1 Gene

Entrez Gene Summary for PDCD1 Gene

  • This gene encodes a cell surface membrane protein of the immunoglobulin superfamily. This protein is expressed in pro-B-cells and is thought to play a role in their differentiation. In mice, expression of this gene is induced in the thymus when anti-CD3 antibodies are injected and large numbers of thymocytes undergo apoptosis. Mice deficient for this gene bred on a BALB/c background developed dilated cardiomyopathy and died from congestive heart failure. These studies suggest that this gene product may also be important in T cell function and contribute to the prevention of autoimmune diseases. [provided by RefSeq, Jul 2008]

GeneCards Summary for PDCD1 Gene

PDCD1 (Programmed Cell Death 1) is a Protein Coding gene. Diseases associated with PDCD1 include systemic lupus erythematosus 2 and multiple sclerosis, disease progression, modifier of. Among its related pathways are Class I MHC mediated antigen processing and presentation and B cell receptor signaling pathway (KEGG). GO annotations related to this gene include signal transducer activity.

UniProtKB/Swiss-Prot for PDCD1 Gene

  • Inhibitory cell surface receptor involved in the regulation of T-cell function during immunity and tolerance. Upon ligand binding, inhibits T-cell effector functions in an antigen-specific manner. Possible cell death inducer, in association with other factors.

Gene Wiki entry for PDCD1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDCD1 Gene

Genomics for PDCD1 Gene

Genomic Location for PDCD1 Gene

Start:
241,849,881 bp from pter
End:
241,858,908 bp from pter
Size:
9,028 bases
Orientation:
Minus strand

Genomic View for PDCD1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PDCD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDCD1 Gene

Regulatory Elements for PDCD1 Gene

Transcription factor binding sites by QIAGEN in the PDCD1 gene promoter:

Proteins for PDCD1 Gene

  • Protein details for PDCD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q15116-PDCD1_HUMAN
    Recommended name:
    Programmed cell death protein 1
    Protein Accession:
    Q15116
    Secondary Accessions:
    • O00517
    • Q8IX89

    Protein attributes for PDCD1 Gene

    Size:
    288 amino acids
    Molecular mass:
    31647 Da
    Quaternary structure:
    • Monomer.

    Three dimensional structures from OCA and Proteopedia for PDCD1 Gene

neXtProt entry for PDCD1 Gene

Proteomics data for PDCD1 Gene at MOPED

Post-translational modifications for PDCD1 Gene

  • Modification sites at PhosphoSitePlus
  • Glycosylation at Asn49, Asn58, Asn74, and Asn116

Other Protein References for PDCD1 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for PDCD1 Gene

Domains for PDCD1 Gene

Gene Families for PDCD1 Gene

HGNC:
  • CD :CD molecules
  • VSET :Immunoglobulin superfamily / V-set domain containing

Protein Domains for PDCD1 Gene

Suggested Antigen Peptide Sequences for PDCD1 Gene

Graphical View of Domain Structure for InterPro Entry

Q15116

UniProtKB/Swiss-Prot:

PDCD1_HUMAN
Domain:
  • Contains 1 Ig-like V-type (immunoglobulin-like) domain.:
    • Q15116
genes like me logo Genes that share domains with PDCD1: view

Function for PDCD1 Gene

Molecular function for PDCD1 Gene

GENATLAS Biochemistry: programmed cell death (apoptosis) 1,mouse PD1 homolog
UniProtKB/Swiss-Prot Function: Inhibitory cell surface receptor involved in the regulation of T-cell function during immunity and tolerance. Upon ligand binding, inhibits T-cell effector functions in an antigen-specific manner. Possible cell death inducer, in association with other factors.

Gene Ontology (GO) - Molecular Function for PDCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004871 signal transducer activity TAS 1396582
GO:0005515 protein binding IPI 21982860
genes like me logo Genes that share ontologies with PDCD1: view
genes like me logo Genes that share phenotypes with PDCD1: view

Animal Models for PDCD1 Gene

MGI Knock Outs for PDCD1:

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting and HOMER Transcription for PDCD1 Gene

Localization for PDCD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDCD1 Gene

Membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PDCD1 Gene COMPARTMENTS Subcellular localization image for PDCD1 gene
Compartment Confidence
plasma membrane 4
cytosol 1
endoplasmic reticulum 1
extracellular 1
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for PDCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0009897 external side of plasma membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PDCD1: view

Pathways for PDCD1 Gene

genes like me logo Genes that share pathways with PDCD1: view

Pathways by source for PDCD1 Gene

Gene Ontology (GO) - Biological Process for PDCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006915 apoptotic process IEA --
GO:0006959 humoral immune response TAS 9332365
GO:0007165 signal transduction TAS 1396582
GO:0007275 multicellular organismal development TAS 9332365
GO:0031295 T cell costimulation TAS --
genes like me logo Genes that share ontologies with PDCD1: view

Compounds for PDCD1 Gene

(2) Novoseek inferred chemical compound relationships for PDCD1 Gene

Compound -log(P) Hits PubMed IDs
allergens 4.07 1
tyrosine 0 2
genes like me logo Genes that share compounds with PDCD1: view

Transcripts for PDCD1 Gene

mRNA/cDNA for PDCD1 Gene

(3) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(9) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PDCD1 Gene

Programmed cell death 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PDCD1 Gene

No ASD Table

Relevant External Links for PDCD1 Gene

GeneLoc Exon Structure for
PDCD1
ECgene alternative splicing isoforms for
PDCD1

Expression for PDCD1 Gene

mRNA expression in normal human tissues for PDCD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PDCD1 Gene

This gene is overexpressed in Whole Blood (6.8), Heart - Atrial Appendage (5.4), and Spleen (5.3).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for PDCD1 Gene

SOURCE GeneReport for Unigene cluster for PDCD1 Gene Hs.158297

genes like me logo Genes that share expressions with PDCD1: view

No data available for mRNA Expression by UniProt/SwissProt for PDCD1 Gene

Orthologs for PDCD1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PDCD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PDCD1 35
  • 98.37 (n)
  • 96.95 (a)
cow
(Bos Taurus)
Mammalia PDCD1 35
  • 75 (n)
  • 65.36 (a)
PDCD1 36
  • 66 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PDCD1 35
  • 75.53 (n)
  • 66.67 (a)
PDCD1 36
  • 66 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pdcd1 35
  • 70.16 (n)
  • 59.09 (a)
Pdcd1 16
Pdcd1 36
  • 60 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PDCD1 36
  • 18 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PDCD1 36
  • 30 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia LOC102550808 35
  • 70.57 (n)
  • 60.64 (a)
chicken
(Gallus gallus)
Aves PDCD1 35
  • 50.78 (n)
  • 34.47 (a)
PDCD1 36
  • 29 (a)
OneToOne
Species with no ortholog for PDCD1:
  • 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)
  • lizard (Anolis carolinensis)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for PDCD1 Gene

ENSEMBL:
Gene Tree for PDCD1 (if available)
TreeFam:
Gene Tree for PDCD1 (if available)

Paralogs for PDCD1 Gene

Selected SIMAP similar genes for PDCD1 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with PDCD1: view

No data available for Paralogs for PDCD1 Gene

Variants for PDCD1 Gene

Sequence variations from dbSNP and Humsavar for PDCD1 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type MAF
rs2227981 -- 241,851,121(-) TCAGC(C/G/T)GACGG synonymous-codon, reference
rs2227982 - 241,851,281(-) CTCAG(C/T)CGTGC reference, missense
rs4973695 -- 241,856,119(-) GGGGG(G/T)TTTTG intron-variant
rs5839828 -- 241,859,601(-) CCCCC(-/C)GTCAG upstream-variant-2KB
rs5839829 -- 241,853,267(-) GGGGA(-/A)CTGGC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PDCD1 Gene

Variant ID Type Subtype PubMed ID
nsv876226 CNV Loss 21882294
dgv4493n71 CNV Loss 21882294
dgv4495n71 CNV Loss 21882294
dgv165e55 CNV Loss 17911159
nsv876255 CNV Loss 21882294
dgv4499n71 CNV Gain 21882294
nsv470533 CNV Loss 18288195
dgv4500n71 CNV Loss 21882294
dgv4501n71 CNV Loss 21882294
nsv821942 CNV Gain 20364138

Relevant External Links for PDCD1 Gene

HapMap Linkage Disequilibrium report
PDCD1
Human Gene Mutation Database (HGMD)
PDCD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDCD1 Gene

Disorders for PDCD1 Gene

(2) OMIM Diseases for PDCD1 Gene (600244)

UniProtKB/Swiss-Prot

PDCD1_HUMAN
  • Systemic lupus erythematosus 2 (SLEB2) [MIM:605218]: A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys and serosal membranes. It is of unknown etiology, but is thought to represent a failure of the regulatory mechanisms of the autoimmune system. The disease is marked by a wide range of system dysfunctions, an elevated erythrocyte sedimentation rate, and the formation of LE cells in the blood or bone marrow. {ECO:0000269 PubMed:12402038}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

(1) University of Copenhagen DISEASES for PDCD1 Gene

(24) Novoseek inferred disease relationships for PDCD1 Gene

Disease -log(P) Hits PubMed IDs
infection chronic 59.6 5
autoimmune diseases 55.4 12
autoimmunity 54.6 6
lupus erythematosus systemic 54 19
virus infection 51.6 15

Relevant External Links for PDCD1

Genetic Association Database (GAD)
PDCD1
Human Genome Epidemiology (HuGE) Navigator
PDCD1
genes like me logo Genes that share disorders with PDCD1: view

Publications for PDCD1 Gene

  1. A regulatory polymorphism in PDCD1 is associated with susceptibility to systemic lupus erythematosus in humans. (PMID: 12402038) Prokunina L. … Alarcon-Riquelme M.E. (Nat. Genet. 2002) 2 3 4 23 48
  2. Role of an intronic polymorphism in the PDCD1 gene with the risk of sporadic systemic lupus erythematosus and the occurrence of antiphospholipid antibodies. (PMID: 15322919) Sanghera D.K. … Kamboh M.I. (Hum. Genet. 2004) 3 23 48
  3. The human PD-1 gene: complete cDNA, genomic organization, and developmentally regulated expression in B cell progenitors. (PMID: 9332365) Finger L.R. … Billips L.D. (Gene 1997) 3 4 23
  4. A new haplotype of PDCD1 is associated with rheumatoid arthritis in Hong Kong Chinese. (PMID: 15818672) Kong E.K. … Lau Y.L. (Arthritis Rheum. 2005) 3 23 48
  5. A PD-1 polymorphism is associated with disease progression in multiple sclerosis. (PMID: 15912506) Kroner A. … Wiendl H. (Ann. Neurol. 2005) 3 23 48

Products for PDCD1 Gene

Sources for PDCD1 Gene

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