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

    Gene ID: 27250, updated on 28-Oct-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (110871928..110900006)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (111755712..111783789)
    RS_2024_09 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 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. Programmed cell death 4 mechanism of action: The model to be updated? Vikhreva PN, et al. Cell Cycle, 2017 Oct 2. PMID 28853972, Free PMC Article
    2. Tumor suppressor PDCD4 represses internal ribosome entry site-mediated translation of antiapoptotic proteins and is regulated by S6 kinase 2. Liwak U, et al. Mol Cell Biol, 2012 May. PMID 22431522, Free PMC Article
    3. The Expression of PDCD4 in Patients With Missed Abortion and Its Clinical Significance. Li Y, et al. Reprod Sci, 2017 Nov. PMID 29017439
    4. Nuclear PDCD4 Expression Defines a Subset of Luminal B-Like Breast Cancers with Good Prognosis. Madera S, et al. Horm Cancer, 2020 Oct. PMID 32632815, Free PMC Article
    5. Programmed cell death factor 4 (PDCD4), a novel therapy target for metabolic diseases besides cancer. Lu K, et al. Free Radic Biol Med, 2020 Nov 1. PMID 32745771

    See all (356) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PDCD4 and MIR-21 are promising biomarkers in the follow-up of OED in liquid biopsies.
      Title: PDCD4 and MIR-21 are promising biomarkers in the follow-up of OED in liquid biopsies.
    2. Human tumor suppressor protein Pdcd4 binds at the mRNA entry channel in the 40S small ribosomal subunit.
      Title: Human tumor suppressor protein Pdcd4 binds at the mRNA entry channel in the 40S small ribosomal subunit.
    3. PDCD4 interacting with PIK3CB and CTSZ promotes the apoptosis of multiple myeloma cells.
      Title: PDCD4 interacting with PIK3CB and CTSZ promotes the apoptosis of multiple myeloma cells.
    4. STAT1 mediated downregulation of the tumor suppressor gene PDCD4, is driven by the atypical cadherin FAT1, in glioblastoma.
      Title: STAT1 mediated downregulation of the tumor suppressor gene PDCD4, is driven by the atypical cadherin FAT1, in glioblastoma.
    5. MicroRNA-181b-5p Facilitates Thyroid Cancer Growth via Targeting Programmed Cell Death 4.
      Title: MicroRNA-181b-5p Facilitates Thyroid Cancer Growth via Targeting Programmed Cell Death 4.
    6. PDCD4 deficiency improved 4-vinylcyclohexene dioxide-induced mouse premature ovarian insufficiency.
      Title: PDCD4 deficiency improved 4-vinylcyclohexene dioxide-induced mouse premature ovarian insufficiency.
    7. Progress on the relationship between tumor suppressor PDCD4 and diseases based on the analysis of structural characteristics.
      Title: Progress on the relationship between tumor suppressor PDCD4 and diseases based on the analysis of structural characteristics.
    8. [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].
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (267)

    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_2024_08

    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.

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