Human Gene PPP4R2 (uc003dph.1) Description and Page Index
  Description: Homo sapiens protein phosphatase 4, regulatory subunit 2 (PPP4R2), mRNA.
RefSeq Summary (NM_174907): The protein encoded by this gene is a regulatory subunit of the serine/threonine-protein phosphatase 4 complex. In addition to being required for efficient DNA double strand break repair, this complex plays a role in organization of microtubules at centrosomes and processing of spliceosomal snRNPs. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2015].
Transcript (Including UTRs)
   Position: hg19 chr3:73,046,119-73,115,011 Size: 68,893 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr3:73,046,189-73,114,873 Size: 68,685 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:73,046,119-73,115,011)mRNA (may differ from genome)Protein (417 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: PP4R2_HUMAN
DESCRIPTION: RecName: Full=Serine/threonine-protein phosphatase 4 regulatory subunit 2;
FUNCTION: Regulatory subunit of serine/threonine-protein phosphatase 4 (PP4). May regulate the activity of PPP4C at centrosomal microtubule organizing centers. Its interaction with the SMN complex leads to enhance the temporal localization of snRNPs, suggesting a role of PPP4C in maturation of spliceosomal snRNPs. 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. Mediates RPA2 dephosphorylation by recruiting PPP4C to RPA2 in a DNA damage-dependent manner. RPA2 dephosphorylation is required for the efficient RPA2-mediated recruitment of RAD51 to chromatin following double strand breaks, an essential step for DNA repair.
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-PPP4R2, PPP4C- PPP4R2-PPP4R3A and PPP4C-PPP4R2-PPP4R3B. The PPP4C-PPP4R2 complex appears to be a tetramer composed of 2 molecules of PPP4C and 2 molecules of PPP4R2. Interacts with DDX20/GEMIN3 and GEMIN4. Interacts with RPA2; this DNA damage-dependent interaction recruits PPP4C leading to RPA2 dephosphorylation.
INTERACTION: P60510:PPP4C; NbExp=8; IntAct=EBI-1048740, EBI-1046072;
SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton, centrosome. Nucleus. Note=Ionizing radiation induces relocalization to nuclear foci and colocalization with RPA2.
TISSUE SPECIFICITY: Widely expressed.
SIMILARITY: Belongs to the PPP4R2 family.
SEQUENCE CAUTION: Sequence=AAI00282.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=CAB93534.2; Type=Erroneous initiation;

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 14.99 RPKM in Nerve - Tibial
Total median expression: 426.11 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -29.1070-0.416 Picture PostScript Text
3' UTR -24.00138-0.174 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
IPR015267 - PPP4R2

Pfam Domains:
PF09184 - PPP4R2

ModBase Predicted Comparative 3D Structure on Q9NY27
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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 orthologGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
  EnsemblFlyBaseWormBase 
  Protein SequenceProtein SequenceProtein Sequence 
  AlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0019888 protein phosphatase regulator activity
GO:0030674 protein binding, bridging

Biological Process:
GO:0006397 mRNA processing
GO:0006464 cellular protein modification process
GO:0008380 RNA splicing
GO:0010569 regulation of double-strand break repair via homologous recombination
GO:0043666 regulation of phosphoprotein phosphatase activity

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005815 microtubule organizing center
GO:0005856 cytoskeleton
GO:0030289 protein phosphatase 4 complex


-  Descriptions from all associated GenBank mRNAs
  AJ271448 - Homo sapiens mRNA for protein phosphatase 4 regulatory subunit 2 (PPP4R2 gene).
LP895448 - Sequence 312 from Patent EP3253886.
AK289901 - Homo sapiens cDNA FLJ75248 complete cds.
BC100281 - Homo sapiens protein phosphatase 4, regulatory subunit 2, mRNA (cDNA clone IMAGE:6502858), partial cds.
BC110889 - Homo sapiens protein phosphatase 4, regulatory subunit 2, mRNA (cDNA clone MGC:131930 IMAGE:6503859), complete cds.
AF327345 - Homo sapiens hypothetical protein SBBI57 mRNA, complete cds.
LF384161 - JP 2014500723-A/191664: Polycomb-Associated Non-Coding RNAs.
JD406954 - Sequence 387978 from Patent EP1572962.
JD462315 - Sequence 443339 from Patent EP1572962.
BC128136 - Homo sapiens protein phosphatase 4, regulatory subunit 2, mRNA (cDNA clone MGC:149220 IMAGE:40112443), complete cds.
BC128137 - Homo sapiens protein phosphatase 4, regulatory subunit 2, mRNA (cDNA clone MGC:149221 IMAGE:40112444), complete cds.
KJ895666 - Synthetic construct Homo sapiens clone ccsbBroadEn_05060 PPP4R2 gene, encodes complete protein.
KJ903888 - Synthetic construct Homo sapiens clone ccsbBroadEn_13282 PPP4R2 gene, encodes complete protein.
AL833216 - Homo sapiens mRNA; cDNA DKFZp667B117 (from clone DKFZp667B117).
LF364656 - JP 2014500723-A/172159: Polycomb-Associated Non-Coding RNAs.
DQ579305 - Homo sapiens piRNA piR-47417, complete sequence.
LF364657 - JP 2014500723-A/172160: Polycomb-Associated Non-Coding RNAs.
JD468896 - Sequence 449920 from Patent EP1572962.
LF364658 - JP 2014500723-A/172161: Polycomb-Associated Non-Coding RNAs.
LF364659 - JP 2014500723-A/172162: Polycomb-Associated Non-Coding RNAs.
LF364660 - JP 2014500723-A/172163: Polycomb-Associated Non-Coding RNAs.
LF380983 - JP 2014500723-A/188486: Polycomb-Associated Non-Coding RNAs.
LF364661 - JP 2014500723-A/172164: Polycomb-Associated Non-Coding RNAs.
LF364662 - JP 2014500723-A/172165: Polycomb-Associated Non-Coding RNAs.
MA619738 - JP 2018138019-A/191664: Polycomb-Associated Non-Coding RNAs.
MA600233 - JP 2018138019-A/172159: Polycomb-Associated Non-Coding RNAs.
MA600234 - JP 2018138019-A/172160: Polycomb-Associated Non-Coding RNAs.
MA600235 - JP 2018138019-A/172161: Polycomb-Associated Non-Coding RNAs.
MA600236 - JP 2018138019-A/172162: Polycomb-Associated Non-Coding RNAs.
MA600237 - JP 2018138019-A/172163: Polycomb-Associated Non-Coding RNAs.
MA600238 - JP 2018138019-A/172164: Polycomb-Associated Non-Coding RNAs.
MA600239 - JP 2018138019-A/172165: Polycomb-Associated Non-Coding RNAs.
MA616560 - JP 2018138019-A/188486: Polycomb-Associated Non-Coding RNAs.

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

Protein Q9NY27 (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: A8K1I6, NM_174907, NP_777567, PP4R2_HUMAN, Q2TAJ9, Q498B8, Q8WXX6, Q9NY27, SBBI57
UCSC ID: uc003dph.1
RefSeq Accession: NM_174907
Protein: Q9NY27 (aka PP4R2_HUMAN)
CCDS: CCDS2917.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_174907.2
exon count: 9CDS single in 3' UTR: no RNA size: 1495
ORF size: 1254CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2708.00frame shift in genome: no % Coverage: 97.79
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.