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    PDCD1 programmed cell death 1 [ Homo sapiens (human) ]

    Gene ID: 5133, updated on 22-Aug-2016
    Official Symbol
    PDCD1provided by HGNC
    Official Full Name
    programmed cell death 1provided by HGNC
    Primary source
    HGNC:HGNC:8760
    See related
    Ensembl:ENSG00000188389 HPRD:02590; MIM:600244; Vega:OTTHUMG00000151342
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PD1; PD-1; CD279; SLEB2; hPD-1; hPD-l; hSLE1
    Summary
    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]
    Orthologs
    Location:
    2q37.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 2 NC_000002.12 (241849881..241858908, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (242792033..242801058, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986004 Neighboring gene uncharacterized LOC107986005 Neighboring gene uncharacterized LOC105373977 Neighboring gene receptor transporter protein 5 (putative) Neighboring gene uncharacterized LOC105373978

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120 binds and signals through CD4, which leads to T cell activation with upregulation of the CXCR5, PD-1, Fas, and FasL expression PubMed
    Nef nef HIV-1 Nef can transcriptionally induce the expression of PD-1 during infection in vitro. Nef-induced PD-1 upregulation requires its proline-rich motif and the activation of the downstream kinase p38 PubMed
    Pr55(Gag) gag The enhancement of Tim-3 and PD-1 expression by common gamma-chain IL-2 can inhibit the function of T cells re-stimulated by HIV-1 Gag and TCR PubMed
    gag Blocking the PD-1 pathway enhances Gag-specific CD4+ T cell proliferation PubMed

    Go to the HIV-1, Human Interaction Database

    • Adaptive Immune System, organism-specific biosystem (from REACTOME)
      Adaptive Immune System, organism-specific biosystemAdaptive immunity refers to antigen-specific immune response efficiently involved in clearing the pathogens. The adaptive immune system is comprised of B and T lymphocytes that express receptors with...
    • Cell adhesion molecules (CAMs), organism-specific biosystem (from KEGG)
      Cell adhesion molecules (CAMs), organism-specific biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...
    • Cell adhesion molecules (CAMs), conserved biosystem (from KEGG)
      Cell adhesion molecules (CAMs), conserved biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...
    • Costimulation by the CD28 family, organism-specific biosystem (from REACTOME)
      Costimulation by the CD28 family, organism-specific biosystemOptimal activation of T-lymphocytes requires at least two signals. A primary one is delivered by the T-cell receptor (TCR) complex after antigen recognition and additional costimulatory signals are d...
    • Immune System, organism-specific biosystem (from REACTOME)
      Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
    • PD-1 signaling, organism-specific biosystem (from REACTOME)
      PD-1 signaling, organism-specific biosystemThe Programmed cell death protein 1 (PD-1) is one of the negative regulators of TCR signaling. PD-1 may exert its effects on cell differentiation and survival directly by inhibiting early activation ...
    • T cell receptor signaling pathway, organism-specific biosystem (from KEGG)
      T cell receptor signaling pathway, organism-specific biosystemActivation of T lymphocytes is a key event for an efficient response of the immune system. It requires the involvement of the T-cell receptor (TCR) as well as costimulatory molecules such as CD28. En...
    • T cell receptor signaling pathway, conserved biosystem (from KEGG)
      T cell receptor signaling pathway, conserved biosystemActivation of T lymphocytes is a key event for an efficient response of the immune system. It requires the involvement of the T-cell receptor (TCR) as well as costimulatory molecules such as CD28. En...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    signal transducer activity TAS
    Traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    T cell costimulation TAS
    Traceable Author Statement
    more info
     
    apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    humoral immune response TAS
    Traceable Author Statement
    more info
    PubMed 
    multicellular organism development TAS
    Traceable Author Statement
    more info
    PubMed 
    negative regulation of apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of tolerance induction IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of T cell apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    external side of plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    plasma membrane TAS
    Traceable Author Statement
    more info
     
    Preferred Names
    programmed cell death protein 1
    Names
    programmed cell death 1 protein
    protein PD-1
    systemic lupus erythematosus susceptibility 2

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_012110.1 RefSeqGene

      Range
      5001..14026
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_005018.2NP_005009.2  programmed cell death protein 1 precursor

      See identical proteins and their annotated locations for NP_005009.2

      Status: REVIEWED

      Source sequence(s)
      AI928135, AY238517, CR988122, U64863
      Consensus CDS
      CCDS33428.1
      UniProtKB/Swiss-Prot
      Q15116
      UniProtKB/TrEMBL
      A0A0M3M0G7
      Related
      ENSP00000335062, OTTHUMP00000199883, ENST00000334409, OTTHUMT00000322313
      Conserved Domains (2) summary
      smart00410
      Location:39125
      IG_like; Immunoglobulin like
      pfam07686
      Location:38127
      V-set; Immunoglobulin V-set domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p7 Primary Assembly

      Range
      241849881..241858908 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017004293.1XP_016859782.1  

    2. XM_006712573.2XP_006712636.1  

      See identical proteins and their annotated locations for XP_006712636.1

      Conserved Domains (2) summary
      cd00099
      Location:42136
      IgV; Immunoglobulin variable domain (IgV)
      smart00410
      Location:39125
      IG_like; Immunoglobulin like

    Reference GRCh38.p7 ALT_REF_LOCI_1

    Genomic

    1. NT_187527.1 Reference GRCh38.p7 ALT_REF_LOCI_1

      Range
      61979..71004 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018913.2 Alternate CHM1_1.1

      Range
      242797131..242806156 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)