U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    PDCD4 programmed cell death 4 [ Homo sapiens (human) ]

    Gene ID: 27250, updated on 5-Mar-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    PDCD4provided by HGNC
    Official Full Name
    programmed cell death 4provided by HGNC
    Primary source
    HGNC:HGNC:8763
    See related
    Ensembl:ENSG00000150593 MIM:608610; AllianceGenome:HGNC:8763
    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
    H731
    Summary
    This gene is a tumor suppressor and encodes a protein that binds to the eukaryotic translation initiation factor 4A1 and inhibits its function by preventing RNA binding. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2010]
    Expression
    Ubiquitous expression in colon (RPKM 80.4), thyroid (RPKM 70.8) and 25 other tissues See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    Location:
    10q25.2
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (110871928..110900006)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (111755712..111783789)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (112631686..112659764)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902500 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4055 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2822 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4057 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2823 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:112630184-112630794 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2825 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2824 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2826 Neighboring gene PDCD4 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4058 Neighboring gene microRNA 4680 Neighboring gene BBSome interacting protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2827 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:112678563-112679102 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2828 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2829 Neighboring gene SHOC2 leucine rich repeat scaffold protein Neighboring gene ribosomal protein L13a pseudogene 6 Neighboring gene microRNA 548e

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Induction of premature senescence and a less-fibrogenic phenotype by programmed cell death 4 knockdown in the human hepatic stellate cell line Lieming Xu-2. Perveen R, et al. Hum Cell, 2023 Mar. PMID 36522523, Free PMC Article
    2. Downregulation of PDCD4 by deSUMOylation associates with the progression of gestational trophoblastic disease. Wang YX, et al. Placenta, 2022 Dec. PMID 36370491
    3. Discovery of a novel role of tumor suppressor PDCD4 in stimulation of translation termination. Shuvalova E, et al. J Biol Chem, 2021 Nov. PMID 34606825, Free PMC Article
    4. Low PDCD4 Expression Is Associated With Poor Prognosis of Colorectal Carcinoma. Kim JY, et al. Appl Immunohistochem Mol Morphol, 2021 Oct 1. PMID 34029220
    5. MicroRNA-16, Programmed Cell Death Protein-4 (PDCD-4) and Polycystic Ovarian Syndrome. Zehra N, et al. J Coll Physicians Surg Pak, 2020 Aug. PMID 32893806

    See all (340) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. [PDCD4 knockdown ameliorates lipopolysaccharide-induced endothelial cell damage by improving mitochondrial dynamics].
      Title: [PDCD4 knockdown ameliorates lipopolysaccharide-induced endothelial cell damage by improving mitochondrial dynamics].
    2. Upregulated MicroRNA-21 Drives the Proliferation of Lymphatic Malformation Endothelial Cells by Inhibiting PDCD4.
      Title: Upregulated MicroRNA-21 Drives the Proliferation of Lymphatic Malformation Endothelial Cells by Inhibiting PDCD4.
    3. PRMT5 knockdown enhances cell viability and suppresses cell apoptosis, oxidative stress, inflammation and endothelial dysfunction in ox-LDL-induced vascular endothelial cells via interacting with PDCD4.
      Title: PRMT5 knockdown enhances cell viability and suppresses cell apoptosis, oxidative stress, inflammation and endothelial dysfunction in ox-LDL-induced vascular endothelial cells via interacting with PDCD4.
    4. Cryo-EM Structure of Human Tumor Suppressor Protein Pdcd4 Bound to the Ribosome.
      Title: Cryo-EM Structure of Human Tumor Suppressor Protein Pdcd4 Bound to the Ribosome.
    5. Gastric Cancer Growth Modulated by circSNTB2/miR-6938-5p/G0S2 and PDCD4.
      Title: Gastric Cancer Growth Modulated by circSNTB2/miR-6938-5p/G0S2 and PDCD4.
    6. MiR-93-5p inhibits retinal neurons apoptosis by regulating PDCD4 in acute ocular hypertension model.
      Title: MiR-93-5p inhibits retinal neurons apoptosis by regulating PDCD4 in acute ocular hypertension model.
    7. Induction of premature senescence and a less-fibrogenic phenotype by programmed cell death 4 knockdown in the human hepatic stellate cell line Lieming Xu-2.
      Title: Induction of premature senescence and a less-fibrogenic phenotype by programmed cell death 4 knockdown in the human hepatic stellate cell line Lieming Xu-2.
    8. Tumor Suppressor p53 Down-Regulates Programmed Cell Death Protein 4 (PDCD4) Expression.
      Title: Tumor Suppressor p53 Down-Regulates Programmed Cell Death Protein 4 (PDCD4) Expression.
    9. eIF4A/PDCD4 Pathway, a Factor for Doxorubicin Chemoresistance in a Triple-Negative Breast Cancer Cell Model.
      Title: eIF4A/PDCD4 Pathway, a Factor for Doxorubicin Chemoresistance in a Triple-Negative Breast Cancer Cell Model.
    10. Downregulation of PDCD4 by deSUMOylation associates with the progression of gestational trophoblastic disease.
      Title: Downregulation of PDCD4 by deSUMOylation associates with the progression of gestational trophoblastic disease.
    Submit: New GeneRIF Correction See all GeneRIFs (261)

    Phenotypes

    Go to the top of the page Help

    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • MGC33046, MGC33047

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in BMP signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cellular response to lipopolysaccharide ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in epithelial to mesenchymal transition involved in cardiac fibroblast development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of JUN kinase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of cytokine production involved in inflammatory response ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of myofibroblast differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of vascular associated smooth muscle cell differentiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of vascular associated smooth muscle cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of endothelial cell apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of inflammatory response ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of non-canonical NF-kappaB signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of vascular associated smooth muscle cell apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to alkaloid IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to hormone IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    programmed cell death protein 4
    Names
    neoplastic transformation inhibitor protein
    nuclear antigen H731
    programmed cell death 4 (neoplastic transformation inhibitor)
    protein 197/15a

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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.

    mRNA and Protein(s)

    1. NM_001199492.2 → NP_001186421.1  programmed cell death protein 4 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The resulting protein (isoform 3) is shorter, compared to isoform 1.
      Source sequence(s)
      AK296753, AL136368, AL158163, BX647834
      UniProtKB/TrEMBL
      B4DKX4
      Conserved Domains (1) summary
      smart00544
      Location:313 → 426
      MA3; Domain in DAP-5, eIF4G, MA-3 and other proteins

    2. NM_014456.5 → NP_055271.2  programmed cell death protein 4 isoform 1

      See identical proteins and their annotated locations for NP_055271.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AL136368, AL158163, BC026104, BX647834, DB241608
      Consensus CDS
      CCDS7567.1
      UniProtKB/Swiss-Prot
      B2RCV4, B5ME91, O15501, Q53EL6, Q5VZS6, Q6PJI5, Q8TAR5, Q99834
      UniProtKB/TrEMBL
      B2R6E2
      Related
      ENSP00000280154.7, ENST00000280154.12
      Conserved Domains (1) summary
      smart00544
      Location:327 → 440
      MA3; Domain in DAP-5, eIF4G, MA-3 and other proteins

    3. NM_145341.4 → NP_663314.1  programmed cell death protein 4 isoform 2

      See identical proteins and their annotated locations for NP_663314.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) includes an alternate exon in the 5' coding region and utilizes a downstream start codon, compared to variant 1. The resulting protein (isoform 2) has a shorter and distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK315295, AL136368, AL158163, BX647834
      Consensus CDS
      CCDS44478.1
      UniProtKB/TrEMBL
      B2R6E2
      Related
      ENSP00000376816.2, ENST00000393104.6
      Conserved Domains (1) summary
      smart00544
      Location:316 → 429
      MA3; Domain in DAP-5, eIF4G, MA-3 and other proteins

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      110871928..110900006
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      111755712..111783789
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q53EL6.2 GenPept UniProtKB/Swiss-Prot:Q53EL6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Other Literature Sources
    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous