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

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

Summary

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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
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Genomic context

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See PDCD4 in Genome Data Viewer
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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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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

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

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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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

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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)

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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

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