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

    Gene ID: 5133, updated on 26-Sep-2021

    Summary

    Official Symbol
    PDCD1provided by HGNC
    Official Full Name
    programmed cell death 1provided by HGNC
    Primary source
    HGNC:HGNC:8760
    See related
    Ensembl:ENSG00000188389 MIM:600244
    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
    Programmed cell death protein 1 (PDCD1) is an immune-inhibitory receptor expressed in activated T cells; it is involved in the regulation of T-cell functions, including those of effector CD8+ T cells. In addition, this protein can also promote the differentiation of CD4+ T cells into T regulatory cells. PDCD1 is expressed in many types of tumors including melanomas, and has demonstrated to play a role in anti-tumor immunity. Moreover, this protein has been shown to be involved in safeguarding against autoimmunity, however, it can also contribute to the inhibition of effective anti-tumor and anti-microbial immunity. [provided by RefSeq, Aug 2020]
    Expression
    Biased expression in lymph node (RPKM 8.8), spleen (RPKM 2.6) and 7 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See PDCD1 in Genome Data Viewer
    Location:
    2q37.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (241849881..241858908, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (242792036..242801046, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene neuraminidase 4 Neighboring gene uncharacterized LOC107986004 Neighboring gene uncharacterized LOC105373977 Neighboring gene receptor transporter protein 5 (putative) Neighboring gene uncharacterized LOC105373978

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    HIV-1 infection downregulates CXCR5 and PDCD1 (PD1) expression in primary germinal center T follicular helper cells PubMed

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in adaptive immune response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in humoral immune response TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in multicellular organism development TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of immune response ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of T cell apoptotic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in positive regulation of T cell apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    programmed cell death protein 1
    Names
    programmed cell death 1 protein
    protein PD-1
    systemic lupus erythematosus susceptibility 2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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
      5013..14023
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_005018.3NP_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
      ENSP00000335062.5, ENST00000334409.10
      Conserved Domains (1) summary
      cd16088
      Location:35144
      IgV_PD1; Immunoglobulin (Ig)-like domain of Programmed cell Death 1 (PD1)

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

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

    mRNA and Protein(s)

    1. XM_017004293.1XP_016859782.1  programmed cell death protein 1 isoform X1

    2. XM_006712573.2XP_006712636.1  programmed cell death protein 1 isoform X2

      See identical proteins and their annotated locations for XP_006712636.1

      Conserved Domains (2) summary
      smart00410
      Location:39125
      IG_like; Immunoglobulin like
      pfam07686
      Location:38127
      V-set; Immunoglobulin V-set domain

    Reference GRCh38.p13 ALT_REF_LOCI_1

    Genomic

    1. NT_187527.1 Reference GRCh38.p13 ALT_REF_LOCI_1

      Range
      61982..70992 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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