Human Gene PPP4C (ENST00000279387.12_4) from GENCODE V47lift37
  Description: protein phosphatase 4 catalytic subunit, transcript variant 2 (from RefSeq NM_002720.3)
Gencode Transcript: ENST00000279387.12_4
Gencode Gene: ENSG00000149923.14_9
Transcript (Including UTRs)
   Position: hg19 chr16:30,087,315-30,096,697 Size: 9,383 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr16:30,087,699-30,096,383 Size: 8,685 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:30,087,315-30,096,697)mRNA (may differ from genome)Protein (307 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PP4C_HUMAN
DESCRIPTION: RecName: Full=Serine/threonine-protein phosphatase 4 catalytic subunit; Short=PP4C; Short=Pp4; EC=3.1.3.16; AltName: Full=Protein phosphatase X; Short=PP-X;
FUNCTION: Protein phosphatase that is involved in many processes such as microtubule organization at centrosomes, maturation of spliceosomal snRNPs, apoptosis, DNA repair, tumor necrosis factor (TNF)-alpha signaling, activation of c-Jun N-terminal kinase MAPK8, regulation of histone acetylation, DNA damage checkpoint signaling, NF-kappa-B activation and cell migration. The PPP4C- PPP4R1 PP4 complex may play a role in dephosphorylation and regulation of HDAC3. The PPP4C-PPP4R2-PPP4R3A PP4 complex specifically dephosphorylates H2AFX phosphorylated on Ser-140 (gamma-H2AFX) generated during DNA replication and required for DNA double strand break repair. Dephosphorylates NDEL1 at CDK1 phosphorylation sites and negatively regulates CDK1 activity in interphase (By similarity). In response to DNA damage, catalyzes RPA2 dephosphorylation, an essential step for DNA repair since it allows the efficient RPA2-mediated recruitment of RAD51 to chromatin.
CATALYTIC ACTIVITY: A phosphoprotein + H(2)O = a protein + phosphate.
COFACTOR: Binds 1 iron ion per subunit (By similarity).
COFACTOR: Binds 1 manganese ion per subunit (By similarity).
SUBUNIT: Serine/threonine-protein phosphatase 4 (PP4) occurs in different assemblies of the catalytic and one or more regulatory subunits. Component of the PP4 complexes PPP4C-PPP4R1, PPP4C- PPP4R2, PPP4C-PPP4R2-PPP4R3A, PPP4C-PPP4R2-PPP4R3B and PPP4C- PPP4R4. The PPP4C-PPP4R2 complex appears to be a tetramer composed of 2 molecules of PPP4C and 2 molecules of PPP4R2. Interacts with REL, NFKB1/p50 and RELA. Interacts with SMN1 AND GEMIN4. Interacts with IRS4 (phosphorylated). Interacts with SMEK1/PPP4R3A; the interaction requires PP4R2. Interacts with HDAC3.
INTERACTION: P78318:IGBP1; NbExp=7; IntAct=EBI-1046072, EBI-1055954; P30153:PPP2R1A; NbExp=3; IntAct=EBI-1046072, EBI-302388; Q8TF05:PPP4R1; NbExp=5; IntAct=EBI-1046072, EBI-1056262; Q9NY27:PPP4R2; NbExp=8; IntAct=EBI-1046072, EBI-1048740; Q6NUP7:PPP4R4; NbExp=6; IntAct=EBI-1046072, EBI-1774189; O75663:TIPRL; NbExp=2; IntAct=EBI-1046072, EBI-1054735;
SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Cytoplasm, cytoskeleton, centrosome.
SIMILARITY: Belongs to the PPP phosphatase family. PP-4 (PP-X) subfamily.

-  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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           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: 75.52 RPKM in Whole Blood
Total median expression: 1538.07 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 -76.90164-0.469 Picture PostScript Text
3' UTR -99.20314-0.316 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
IPR004843 - Metallo_PEstase_dom
IPR006186 - Ser/Thr-sp_prot-phosphatase

Pfam Domains:
PF00149 - Calcineurin-like phosphoesterase

SCOP Domains:
56300 - Metallo-dependent phosphatases

ModBase Predicted Comparative 3D Structure on P60510
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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    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004704 NF-kappaB-inducing kinase activity
GO:0004721 phosphoprotein phosphatase activity
GO:0004722 protein serine/threonine phosphatase activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0046872 metal ion binding

Biological Process:
GO:0006470 protein dephosphorylation
GO:0010569 regulation of double-strand break repair via homologous recombination
GO:0038061 NIK/NF-kappaB signaling

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005815 microtubule organizing center
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0030289 protein phosphatase 4 complex


-  Descriptions from all associated GenBank mRNAs
  JC506661 - Sequence 29 from Patent EP2733220.
JC737773 - Sequence 29 from Patent WO2014075939.
JC506666 - Sequence 34 from Patent EP2733220.
JC737778 - Sequence 34 from Patent WO2014075939.
JC506674 - Sequence 42 from Patent EP2733220.
JC737786 - Sequence 42 from Patent WO2014075939.
JC506688 - Sequence 56 from Patent EP2733220.
JC737800 - Sequence 56 from Patent WO2014075939.
X70218 - Homo sapiens mRNA for protein phosphatase X.
BC001416 - Homo sapiens protein phosphatase 4 (formerly X), catalytic subunit, mRNA (cDNA clone MGC:1882 IMAGE:3140324), complete cds.
AF097996 - Homo sapiens protein phosphatase X (PPX) mRNA, complete cds.
AB464104 - Synthetic construct DNA, clone: pF1KB6411, Homo sapiens PPP4C gene for protein phosphatase 4 (formerly X) catalytic subunit, without stop codon, in Flexi system.
DQ891947 - Synthetic construct clone IMAGE:100004577; FLH181677.01X; RZPDo839F12136D protein phosphatase 4 (formerly X), catalytic subunit (PPP4C) gene, encodes complete protein.
DQ895134 - Synthetic construct Homo sapiens clone IMAGE:100009594; FLH181673.01L; RZPDo839F12135D protein phosphatase 4 (formerly X), catalytic subunit (PPP4C) gene, encodes complete protein.
CU674696 - Synthetic construct Homo sapiens gateway clone IMAGE:100018816 5' read PPP4C mRNA.
KJ891873 - Synthetic construct Homo sapiens clone ccsbBroadEn_01267 PPP4C gene, encodes complete protein.
BT019746 - Homo sapiens protein phosphatase 4 (formerly X), catalytic subunit mRNA, complete cds.
GQ891342 - Homo sapiens clone HEL-S-113d epididymis secretory sperm binding protein mRNA, complete cds.
JD124781 - Sequence 105805 from Patent EP1572962.
JD306579 - Sequence 287603 from Patent EP1572962.
JD368218 - Sequence 349242 from Patent EP1572962.
JD161437 - Sequence 142461 from Patent EP1572962.
JD120881 - Sequence 101905 from Patent EP1572962.
JD175026 - Sequence 156050 from Patent EP1572962.
JD145968 - Sequence 126992 from Patent EP1572962.
JD337978 - Sequence 319002 from Patent EP1572962.
JD251684 - Sequence 232708 from Patent EP1572962.
JD090844 - Sequence 71868 from Patent EP1572962.
JD254081 - Sequence 235105 from Patent EP1572962.
JD254311 - Sequence 235335 from Patent EP1572962.

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

Protein P60510 (Reactome details) participates in the following event(s):

R-HSA-5687758 PPP4C:PPP4R2 dephosphorylates RPA2
R-HSA-5693607 Processing of DNA double-strand break ends
R-HSA-5693567 HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA)
R-HSA-5693538 Homology Directed Repair
R-HSA-5693532 DNA Double-Strand Break Repair
R-HSA-73894 DNA Repair

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000279387.1, ENST00000279387.10, ENST00000279387.11, ENST00000279387.2, ENST00000279387.3, ENST00000279387.4, ENST00000279387.5, ENST00000279387.6, ENST00000279387.7, ENST00000279387.8, ENST00000279387.9, NM_002720, P33172, P60510, PP4C_HUMAN, PPP4, PPX, uc317jrv.1, uc317jrv.2
UCSC ID: ENST00000279387.12_4
RefSeq Accession: NM_002720.3
Protein: P60510 (aka PP4C_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.