Human Gene PDCD4 (ENST00000280154.12_4) from GENCODE V47lift37
  Description: programmed cell death 4, transcript variant 1 (from RefSeq NM_014456.5)
Gencode Transcript: ENST00000280154.12_4
Gencode Gene: ENSG00000150593.18_9
Transcript (Including UTRs)
   Position: hg19 chr10:112,631,686-112,659,764 Size: 28,079 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg19 chr10:112,635,786-112,657,846 Size: 22,061 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:112,631,686-112,659,764)mRNA (may differ from genome)Protein (469 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PDCD4_HUMAN
DESCRIPTION: RecName: Full=Programmed cell death protein 4; AltName: Full=Neoplastic transformation inhibitor protein; AltName: Full=Nuclear antigen H731-like; AltName: Full=Protein 197/15a;
FUNCTION: Inhibits translation initiation and cap-dependent translation. May excert its function by hindering the interaction between EIF4A1 and EIF4G. Inhibits the helicase activity of EIF4A. Modulates the activation of JUN kinase. Down-regulates the expression of MAP4K1, thus inhibiting events important in driving invasion, namely, MAPK85 activation and consequent JUN-dependent transcription. May play a role in apoptosis. Tumor suppressor. Inhibits tumor promoter-induced neoplastic transformation. Binds RNA (By similarity).
SUBUNIT: Interacts (via MI domains) with EIF4A2 (By similarity). Interacts (via MI domains) with EIF4A1 (via N-terminal domain). Heterotrimer with EIF4A1; one molecule of PDCD4 binds two molecules of EIF4A1. Interacts with EIF4G1. May form a complex with EIF4A1 and EIF4G1. The interaction between PDCD4 and EIF4A1 interferes with the interaction between EIF4A1 and EIF4G. When phosphorylated, interacts with BTRC and FBXW11.
INTERACTION: P02649:APOE; NbExp=3; IntAct=EBI-935824, EBI-1222467; P49810:PSEN2; NbExp=3; IntAct=EBI-935824, EBI-2010251; P62277:RPS13; NbExp=2; IntAct=EBI-935824, EBI-351850;
SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=Shuttles between the nucleus and cytoplasm. Predominantly nuclear under normal growth conditions, and when phosphorylated at Ser-457. Exported from the nucleus in the absence of serum.
TISSUE SPECIFICITY: Up-regulated in proliferative cells. Highly expressed in epithelial cells of the mammary gland. Reduced expression in lung cancer and colon carcinoma.
INDUCTION: IL2/interleukin-2 stimulation inhibits expression, while IL12/interleukin-12 increases expression.
DOMAIN: Binds EIF4A1 via both MI domains.
PTM: Polyubiquitinated, leading to its proteasomal degradation. Rapidly degraded in response to mitogens. Phosphorylation of the phosphodegron promotes interaction with BTRC and proteasomal degradation.
PTM: Phosphorylated at Ser-67 by RPS6KB1 in response to mitogens; phosphorylation promotes proteasomal degradation of PDCD4.
SIMILARITY: Belongs to the PDCD4 family.
SIMILARITY: Contains 2 MI domains.
SEQUENCE CAUTION: Sequence=AAB42218.1; Type=Erroneous gene model prediction; Sequence=AAH15036.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence;
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/PDCD4ID41675ch10q24.html";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: PDCD4
Diseases sorted by gene-association score: tonsil cancer (6), colorectal cancer (2), lung cancer (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D013749 Tetrachlorodibenzodioxin
  • D000082 Acetaminophen
  • D010634 Phenobarbital
  • D014212 Tretinoin
  • C006253 pirinixic acid
  • C028474 1,4-bis(2-(3,5-dichloropyridyloxy))benzene
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
  • C404910 2,2-bis(4-hydroxyphenyl)-1,1,1-trichloroethane
  • C029497 2,3-bis(3'-hydroxybenzyl)butyrolactone
  • C486182 2,3-bis(4-hydroxyphenyl)-propionitrile
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 170.81 RPKM in Pancreas
Total median expression: 1420.73 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -45.20153-0.295 Picture PostScript Text
3' UTR -474.201918-0.247 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR016024 - ARM-type_fold
IPR003891 - Initiation_fac_eIF4g_MI

Pfam Domains:
PF02847 - MA3 domain

SCOP Domains:
48371 - ARM repeat
48726 - Immunoglobulin

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2GGF - NMR MuPIT 2KZT - NMR MuPIT 2RG8 - X-ray MuPIT 2ZU6 - X-ray MuPIT 3EIJ - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q53EL6
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0006915 apoptotic process
GO:0007569 cell aging
GO:0030509 BMP signaling pathway
GO:0034393 positive regulation of smooth muscle cell apoptotic process
GO:0035722 interleukin-12-mediated signaling pathway
GO:0043066 negative regulation of apoptotic process
GO:0043508 negative regulation of JUN kinase activity
GO:0045786 negative regulation of cell cycle
GO:0045892 negative regulation of transcription, DNA-templated
GO:0050729 positive regulation of inflammatory response
GO:0051246 regulation of protein metabolic process
GO:0060940 epithelial to mesenchymal transition involved in cardiac fibroblast development
GO:0071222 cellular response to lipopolysaccharide
GO:1900016 negative regulation of cytokine production involved in inflammatory response
GO:1901224 positive regulation of NIK/NF-kappaB signaling
GO:1904706 negative regulation of vascular smooth muscle cell proliferation
GO:1904761 negative regulation of myofibroblast differentiation
GO:1905064 negative regulation of vascular smooth muscle cell differentiation
GO:1905461 positive regulation of vascular associated smooth muscle cell apoptotic process
GO:2000353 positive regulation of endothelial cell apoptotic process

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  LF213822 - JP 2014500723-A/21325: Polycomb-Associated Non-Coding RNAs.
AK312540 - Homo sapiens cDNA, FLJ92910, highly similar to Homo sapiens programmed cell death 4 (neoplastic transformation inhibitor) (PDCD4), transcript variant 1, mRNA.
AK315295 - Homo sapiens cDNA, FLJ96314, highly similar to Homo sapiens programmed cell death 4 (neoplastic transformation inhibitor) (PDCD4), transcript variant 2, mRNA.
AK296753 - Homo sapiens cDNA FLJ58014 complete cds, highly similar to Homo sapiens programmed cell death 4, transcript variant 1, mRNA.
AK223623 - Homo sapiens mRNA for programmed cell death 4 isoform 1 variant, clone: FCC134E07.
BC026104 - Homo sapiens programmed cell death 4 (neoplastic transformation inhibitor), mRNA (cDNA clone MGC:33046 IMAGE:4798293), complete cds.
BC031049 - Homo sapiens programmed cell death 4 (neoplastic transformation inhibitor), mRNA (cDNA clone MGC:33047 IMAGE:5277621), complete cds.
BC015036 - Homo sapiens programmed cell death 4 (neoplastic transformation inhibitor), mRNA (cDNA clone IMAGE:3921489), partial cds.
JD211167 - Sequence 192191 from Patent EP1572962.
JD216900 - Sequence 197924 from Patent EP1572962.
DL492497 - Novel nucleic acids.
JD264253 - Sequence 245277 from Patent EP1572962.
DL490967 - Novel nucleic acids.
U96628 - Homo sapiens nuclear antigen H731-like protein mRNA, complete cds.
BX537500 - Homo sapiens mRNA; cDNA DKFZp686B11166 (from clone DKFZp686B11166).
BX647834 - Homo sapiens mRNA; cDNA DKFZp779I201 (from clone DKFZp779I201).
AB590295 - Synthetic construct DNA, clone: pFN21AE1311, Homo sapiens PDCD4 gene for programmed cell death 4, without stop codon, in Flexi system.
DQ891645 - Synthetic construct clone IMAGE:100004275; FLH178937.01X; RZPDo839A11130D programmed cell death 4 (neoplastic transformation inhibitor) (PDCD4) gene, encodes complete protein.
DQ894834 - Synthetic construct Homo sapiens clone IMAGE:100009294; FLH178933.01L; RZPDo839A11129D programmed cell death 4 (neoplastic transformation inhibitor) (PDCD4) gene, encodes complete protein.
KJ904729 - Synthetic construct Homo sapiens clone ccsbBroadEn_14123 PDCD4 gene, encodes complete protein.
BX641168 - Homo sapiens mRNA; cDNA DKFZp686B16243 (from clone DKFZp686B16243).
JD023565 - Sequence 4589 from Patent EP1572962.
LX153091 - JP 2017511694-A/83: COMPOSITIONS AND METHODS OF USING MICRORNA INHIBITORS.
HZ043073 - JP 2015510401-A/163: MESENCHYMAL STEM CELLS FOR IN VITRO MODELING AND CELL-BASED THERAPY OF HUMAN DISEASES AND BANKS THEREOF.
HZ081699 - JP 2015514392-A/163: MicroRNAS FOR THE GENERATION OF ASTROCYTES.
HZ409485 - JP 2015528002-A/2082: CHIRAL CONTROL.
LF404170 - JP 2015509366-A/163: GENERATION OF NEURAL STEM CELLS AND MOTOR NEURONS.
LG052819 - KR 1020150036642-A/2085: CHIRAL CONTROL.
MA353701 - JP 2018075017-A/163: GENERATION OF NEURAL STEM CELLS AND MOTOR NEURONS.
FR772934 - Homo sapiens microRNA hsa-miR-4680-5p.
HZ083380 - JP 2015513906-A/737: Stem Cell Microparticles.
HZ437161 - JP 2015529450-A/737: Stem Cell Microparticles.
HZ481811 - JP 2015535430-A/2317: TERMINALLY MODIFIED RNA.
HZ791742 - JP 2016504050-A/3487: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
JC172365 - Sequence 737 from Patent WO2013150303.
JC514474 - Sequence 4727 from Patent WO2014113089.
JC573176 - Sequence 737 from Patent WO2014125276.
JC582864 - Sequence 737 from Patent WO2014125277.
JE954560 - Sequence 737 from Patent WO2015052526.
JE956313 - Sequence 737 from Patent WO2015052527.
LF138065 - JP 2016507550-A/737: Method of Producing Microparticles.
LF160362 - JP 2016513950-A/428: Oligomers with improved off-target profile.
LF163030 - JP 2016513095-A/737: Stem Cell Microparticles and miRNA.
LF953782 - JP 2016534103-A/737: Stem Cell Microparticles and miRNA.
LG006127 - KR 1020150004822-A/737: STEM CELL MICROPARTICLES.
LG053823 - KR 1020150059168-A/737: STEM CELL MICROPARTICLES.
LG241062 - KR 1020160035087-A/737: STEM CELL MICROPARTICLES AND MIRNA.
LQ072062 - Sequence 2386 from Patent EP2964234.
LV471147 - JP 2016534036-A/737: Stem Cell Microparticles and miRNA.
FR772933 - Homo sapiens microRNA hsa-miR-4680-3p.
HZ043065 - JP 2015510401-A/155: MESENCHYMAL STEM CELLS FOR IN VITRO MODELING AND CELL-BASED THERAPY OF HUMAN DISEASES AND BANKS THEREOF.
HZ081691 - JP 2015514392-A/155: MicroRNAS FOR THE GENERATION OF ASTROCYTES.
HZ481810 - JP 2015535430-A/2316: TERMINALLY MODIFIED RNA.
HZ791741 - JP 2016504050-A/3486: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
JC514473 - Sequence 4726 from Patent WO2014113089.
LF160381 - JP 2016513950-A/447: Oligomers with improved off-target profile.
LF404162 - JP 2015509366-A/155: GENERATION OF NEURAL STEM CELLS AND MOTOR NEURONS.
LQ072061 - Sequence 2385 from Patent EP2964234.
MA353693 - JP 2018075017-A/155: GENERATION OF NEURAL STEM CELLS AND MOTOR NEURONS.
AL049932 - Homo sapiens mRNA; cDNA DKFZp564H2416 (from clone DKFZp564H2416).
FW573312 - JP 2010529847-A/33: Oligonucleotides for modulation of target RNA activity.
JD284833 - Sequence 265857 from Patent EP1572962.
JD310658 - Sequence 291682 from Patent EP1572962.
JD288805 - Sequence 269829 from Patent EP1572962.
JD188319 - Sequence 169343 from Patent EP1572962.
LX153092 - JP 2017511694-A/84: COMPOSITIONS AND METHODS OF USING MICRORNA INHIBITORS.
JD314184 - Sequence 295208 from Patent EP1572962.
LX153093 - JP 2017511694-A/85: COMPOSITIONS AND METHODS OF USING MICRORNA INHIBITORS.
JD420084 - Sequence 401108 from Patent EP1572962.
MA645563 - JP 2017113010-A/3487: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA733447 - JP 2017140048-A/2317: TERMINALLY MODIFIED RNA.
MA645562 - JP 2017113010-A/3486: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA733446 - JP 2017140048-A/2316: TERMINALLY MODIFIED RNA.
MA449399 - JP 2018138019-A/21325: Polycomb-Associated Non-Coding RNAs.
MP045341 - Sequence 163 from Patent EP3401394.
MP084011 - Sequence 163 from Patent EP3401393.
MP045333 - Sequence 155 from Patent EP3401394.
MP084003 - Sequence 155 from Patent EP3401393.
MA802616 - JP 2018183181-A/3487: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA802615 - JP 2018183181-A/3486: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MP129837 - Sequence 737 from Patent EP3470073.
MP162760 - Sequence 737 from Patent WO2019069093.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q53EL6 (Reactome details) participates in the following event(s):

R-HSA-8950505 Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation
R-HSA-9020591 Interleukin-12 signaling
R-HSA-447115 Interleukin-12 family signaling
R-HSA-449147 Signaling by Interleukins
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: B2RCV4, B5ME91, ENST00000280154.1, ENST00000280154.10, ENST00000280154.11, ENST00000280154.2, ENST00000280154.3, ENST00000280154.4, ENST00000280154.5, ENST00000280154.6, ENST00000280154.7, ENST00000280154.8, ENST00000280154.9, H731, NM_014456, O15501, PDCD4_HUMAN, Q53EL6, Q5VZS6, Q6PJI5, Q8TAR5, Q99834, uc317jsz.1, uc317jsz.2
UCSC ID: ENST00000280154.12_4
RefSeq Accession: NM_014456.5
Protein: Q53EL6 (aka PDCD4_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.