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

Gene ID: 27250, updated on 23-Nov-2023

Summary

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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Try the new Transcript table

Genomic context

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

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?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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

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_001199492.2NP_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:313426
    MA3; Domain in DAP-5, eIF4G, MA-3 and other proteins
  2. NM_014456.5NP_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:327440
    MA3; Domain in DAP-5, eIF4G, MA-3 and other proteins
  3. NM_145341.4NP_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:316429
    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)