Format

Send to:

Choose Destination

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

Gene ID: 5133, updated on 12-Aug-2018

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; 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]
Expression
Biased expression in lymph node (RPKM 8.8), spleen (RPKM 2.6) and 7 other tissues See more
Orthologs

Genomic context

See PDCD1 in Genome Data Viewer
Location:
2q37.3
Exon count:
6
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 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 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat'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 BioSystems

  • 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...
  • T-Cell Receptor and Co-stimulatory Signaling, organism-specific biosystem (from WikiPathways)
    T-Cell Receptor and Co-stimulatory Signaling, organism-specific biosystemThe activation and translocation of transcription factors NFAT, AP-1 and NF-kappa-B via the co-stimulatory signaling cascade triggered by MHC peptide, B7 proteins and PD-L1. The activation of NFAT in...
  • T-Cell antigen Receptor (TCR) pathway during Staphylococcus aureus infection, organism-specific biosystem (from WikiPathways)
    T-Cell antigen Receptor (TCR) pathway during Staphylococcus aureus infection, organism-specific biosystemThis pathway is based on Figure 4 of "A Model of an Integrated Immune System Pathway in Homo sapiens and Its Interaction with Superantigen Producing Expression Regulatory Pathway in Staphylococcus au...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
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 
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
 

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)

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
    ENSP00000335062.5, OTTHUMP00000199883, ENST00000334409.9, OTTHUMT00000322313
    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 Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 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.p12 ALT_REF_LOCI_1

Genomic

  1. NT_187527.1 Reference GRCh38.p12 ALT_REF_LOCI_1

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