Human Gene PPP6C (ENST00000373547.9_6) from GENCODE V47lift37
  Description: protein phosphatase 6 catalytic subunit, transcript variant 2 (from RefSeq NM_002721.5)
Gencode Transcript: ENST00000373547.9_6
Gencode Gene: ENSG00000119414.12_10
Transcript (Including UTRs)
   Position: hg19 chr9:127,908,852-127,952,082 Size: 43,231 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr9:127,911,952-127,951,997 Size: 40,046 Coding Exon Count: 7 

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 (chr9:127,908,852-127,952,082)mRNA (may differ from genome)Protein (305 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PPP6_HUMAN
DESCRIPTION: RecName: Full=Serine/threonine-protein phosphatase 6 catalytic subunit; Short=PP6C; EC=3.1.3.16;
FUNCTION: Catalytic subunit of protein phosphatase 6 (PP6). PP6 is a component of a signaling pathway regulating cell cycle progression in response to IL2 receptor stimulation. N-terminal domain restricts G1 to S phase progression in cancer cells, in part through control of cyclin D1. Downregulates MAP3K7 kinase activation of the IL1 signaling pathway by dephosphorylation of MAP3K7.
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: Protein phosphatase 6 (PP6) holoenzyme is proposed to be a heterotrimeric complex formed by the catalytic subunit, a SAPS domain-containing subunit (PP6R) and an ankyrin repeat-domain containing regulatory subunit (ARS). Interacts with IGBP1, MAP3K7, NFKBIE, PPP6R1, PPP6R2 and PPP6R3.
INTERACTION: O15084:ANKRD28; NbExp=3; IntAct=EBI-359751, EBI-359567; P78318:IGBP1; NbExp=8; IntAct=EBI-359751, EBI-1055954; Q9UPN7:PPP6R1; NbExp=5; IntAct=EBI-359751, EBI-359745; O75170:PPP6R2; NbExp=2; IntAct=EBI-359751, EBI-359739; Q5H9R7:PPP6R3; NbExp=2; IntAct=EBI-359751, EBI-355498;
SUBCELLULAR LOCATION: Cytoplasm.
TISSUE SPECIFICITY: Ubiquitously expressed in all tissues tested with highest expression levels in testis, heart, kidney, brain, stomach, liver and skeletal muscle and lowest in placenta, lung colon and spleen.
INDUCTION: Regulated by IL2/interleukin-2 in peripheral blood T cells.
SIMILARITY: Belongs to the PPP phosphatase family. PP-6 (PP-V) 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


-  MalaCards Disease Associations
  MalaCards Gene Search: PPP6C
Diseases sorted by gene-association score: pineal parenchymal tumor of intermediate differentiation (2), hereditary wilms' tumor (2), usher syndrome, type 1c (2), spinocerebellar ataxia 12 (1)

-  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: 22.80 RPKM in Muscle - Skeletal
Total median expression: 743.32 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 -37.9085-0.446 Picture PostScript Text
3' UTR -704.403100-0.227 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 O00743
FrontTopSide
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 orthologGenome Browser
Gene DetailsGene Details Gene Details Gene Details
Gene SorterGene Sorter Gene Sorter Gene Sorter
 RGDEnsembl  SGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
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:0000082 G1/S transition of mitotic cell cycle
GO:0002376 immune system process
GO:0006470 protein dephosphorylation
GO:0007049 cell cycle
GO:0045087 innate immune response
GO:0048208 COPII vesicle coating

Cellular Component:
GO:0000139 Golgi membrane
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AK295752 - Homo sapiens cDNA FLJ50777 complete cds, highly similar to Serine/threonine-protein phosphatase 6 (EC 3.1.3.16).
AK299087 - Homo sapiens cDNA FLJ53085 complete cds, highly similar to Serine/threonine-protein phosphatase 6 (EC 3.1.3.16).
AF035158 - Homo sapiens serine/threonine protein phosphatase catalytic subunit mRNA, complete cds.
E11434 - cDNA encoding human protein phosphatase.
BC006990 - Homo sapiens protein phosphatase 6, catalytic subunit, mRNA (cDNA clone MGC:12249 IMAGE:3684339), complete cds.
X92972 - H.sapiens mRNA for protein phosphatase 6.
AK295190 - Homo sapiens cDNA FLJ51845 complete cds, highly similar to Serine/threonine-protein phosphatase 6 (EC 3.1.3.16).
AK316527 - Homo sapiens cDNA, FLJ79426 complete cds, highly similar to Serine/threonine-protein phosphatase 6 (EC 3.1.3.16).
AK312332 - Homo sapiens cDNA, FLJ92648, Homo sapiens protein phosphatase 6, catalytic subunit (PPP6C),mRNA.
KJ891876 - Synthetic construct Homo sapiens clone ccsbBroadEn_01270 PPP6C gene, encodes complete protein.
BT019708 - Homo sapiens protein phosphatase 6, catalytic subunit mRNA, complete cds.
AB385530 - Synthetic construct DNA, clone: pF1KB3951, Homo sapiens PPP6C gene for serine/threonine-protein phosphatase 6, complete cds, without stop codon, in Flexi system.
KU178271 - Homo sapiens protein phosphatase 6 catalytic subunit isoform 1 (PPP6C) mRNA, partial cds.
KU178272 - Homo sapiens protein phosphatase 6 catalytic subunit isoform 2 (PPP6C) mRNA, complete cds, alternatively spliced.
JD522017 - Sequence 503041 from Patent EP1572962.
JD504685 - Sequence 485709 from Patent EP1572962.
JD241325 - Sequence 222349 from Patent EP1572962.
JD300210 - Sequence 281234 from Patent EP1572962.
JD566672 - Sequence 547696 from Patent EP1572962.
JD084110 - Sequence 65134 from Patent EP1572962.
JD504507 - Sequence 485531 from Patent EP1572962.
JD244424 - Sequence 225448 from Patent EP1572962.
JD264335 - Sequence 245359 from Patent EP1572962.
JD024337 - Sequence 5361 from Patent EP1572962.
JD035600 - Sequence 16624 from Patent EP1572962.
JD031487 - Sequence 12511 from Patent EP1572962.
JD538589 - Sequence 519613 from Patent EP1572962.
JD417036 - Sequence 398060 from Patent EP1572962.

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

Protein O00743 (Reactome details) participates in the following event(s):

R-HSA-5694421 PP6 dephosphorylates SEC24
R-HSA-204005 COPII-mediated vesicle transport
R-HSA-199977 ER to Golgi Anterograde Transport
R-HSA-199991 Membrane Trafficking
R-HSA-948021 Transport to the Golgi and subsequent modification
R-HSA-5653656 Vesicle-mediated transport
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: B2R5V6, B7Z2W9, B7Z5K9, ENST00000373547.1, ENST00000373547.2, ENST00000373547.3, ENST00000373547.4, ENST00000373547.5, ENST00000373547.6, ENST00000373547.7, ENST00000373547.8, NM_002721, O00743, PPP6, PPP6C , PPP6_HUMAN, Q5U0A2, Q9UIC9, uc318kvy.1, uc318kvy.2
UCSC ID: ENST00000373547.9_6
RefSeq Accession: NM_002721.5
Protein: O00743 (aka PPP6_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.