Human Gene PDP2 (uc002eqk.2)
  Description: Homo sapiens pyruvate dehyrogenase phosphatase catalytic subunit 2 (PDP2), mRNA.
RefSeq Summary (NM_020786): This gene is a mitochondrial protein that functions as a phosphatase and is involved in the enzymatic resetting of the pyruvate dehydrogenase complex. Alternative splicing results in multiple transcript variants encoding the same protein. [provided by RefSeq, Aug 2016]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments.
Transcript (Including UTRs)
   Position: hg19 chr16:66,914,383-66,925,002 Size: 10,620 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg19 chr16:66,918,188-66,919,777 Size: 1,590 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:66,914,383-66,925,002)mRNA (may differ from genome)Protein (529 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PDP2_HUMAN
DESCRIPTION: RecName: Full=[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 2, mitochondrial; Short=PDP 2; EC=3.1.3.43; AltName: Full=Pyruvate dehydrogenase phosphatase catalytic subunit 2; Short=PDPC 2; Flags: Precursor;
FUNCTION: Catalyzes the dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex (By similarity).
CATALYTIC ACTIVITY: [Pyruvate dehydrogenase (acetyl-transferring)] phosphate + H(2)O = [pyruvate dehydrogenase (acetyl-transferring)] + phosphate.
COFACTOR: Binds 2 magnesium ions per subunit (By similarity).
SUBUNIT: Heterodimer of a catalytic subunit and a FAD protein of unknown function (By similarity).
SUBCELLULAR LOCATION: Mitochondrion matrix (By similarity).
SIMILARITY: Belongs to the PP2C family.
SEQUENCE CAUTION: Sequence=BAA92586.1; Type=Erroneous initiation;

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PDP2
CDC HuGE Published Literature: PDP2

-  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: 2.81 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 60.22 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 -90.30215-0.420 Picture PostScript Text
3' UTR -1859.025225-0.356 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
IPR001932 - PP2C-like
IPR000222 - PP2C_Mn2_Asp60_BS
IPR015655 - Protein_Pase_2C

Pfam Domains:
PF00481 - Protein phosphatase 2C

SCOP Domains:
81606 - Protein serine/threonine phosphatase 2C, catalytic domain

ModBase Predicted Comparative 3D Structure on Q9P2J9
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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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003824 catalytic activity
GO:0004721 phosphoprotein phosphatase activity
GO:0004722 protein serine/threonine phosphatase activity
GO:0004741 [pyruvate dehydrogenase (lipoamide)] phosphatase activity
GO:0016787 hydrolase activity
GO:0043169 cation binding
GO:0046872 metal ion binding

Biological Process:
GO:0006470 protein dephosphorylation
GO:0010510 regulation of acetyl-CoA biosynthetic process from pyruvate

Cellular Component:
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix


-  Descriptions from all associated GenBank mRNAs
  AK292539 - Homo sapiens cDNA FLJ75807 complete cds, highly similar to Homo sapiens pyruvate dehydrogenase phosphatase isoenzyme 2 (PDP2), mRNA.
LP896026 - Sequence 890 from Patent EP3253886.
LF208262 - JP 2014500723-A/15765: Polycomb-Associated Non-Coding RNAs.
AB037769 - Homo sapiens KIAA1348 mRNA for KIAA1348 protein.
JD323850 - Sequence 304874 from Patent EP1572962.
JD342967 - Sequence 323991 from Patent EP1572962.
BC028030 - Homo sapiens pyruvate dehydrogenase phosphatase isoenzyme 2, mRNA (cDNA clone MGC:40210 IMAGE:5241881), complete cds.
AB384184 - Synthetic construct DNA, clone: pF1KSDA1348, Homo sapiens PDP2 gene for (pyruvate dehydrogenase)-phosphatase 2, complete cds, without stop codon, in Flexi system.
HQ448317 - Synthetic construct Homo sapiens clone IMAGE:100071733; CCSB009578_03 pyruvate dehydrogenase phosphatase isoenzyme 2 (PDP2) gene, encodes complete protein.
KJ894436 - Synthetic construct Homo sapiens clone ccsbBroadEn_03830 PDP2 gene, encodes complete protein.
LF374019 - JP 2014500723-A/181522: Polycomb-Associated Non-Coding RNAs.
LF374020 - JP 2014500723-A/181523: Polycomb-Associated Non-Coding RNAs.
LF374021 - JP 2014500723-A/181524: Polycomb-Associated Non-Coding RNAs.
JD507052 - Sequence 488076 from Patent EP1572962.
LF374022 - JP 2014500723-A/181525: Polycomb-Associated Non-Coding RNAs.
LF374023 - JP 2014500723-A/181526: Polycomb-Associated Non-Coding RNAs.
JD168101 - Sequence 149125 from Patent EP1572962.
JD268217 - Sequence 249241 from Patent EP1572962.
JD201931 - Sequence 182955 from Patent EP1572962.
JD193668 - Sequence 174692 from Patent EP1572962.
JD261825 - Sequence 242849 from Patent EP1572962.
LF374024 - JP 2014500723-A/181527: Polycomb-Associated Non-Coding RNAs.
JD535680 - Sequence 516704 from Patent EP1572962.
JD327615 - Sequence 308639 from Patent EP1572962.
LF374025 - JP 2014500723-A/181528: Polycomb-Associated Non-Coding RNAs.
JD325195 - Sequence 306219 from Patent EP1572962.
JD151196 - Sequence 132220 from Patent EP1572962.
LF374026 - JP 2014500723-A/181529: Polycomb-Associated Non-Coding RNAs.
JD132509 - Sequence 113533 from Patent EP1572962.
JD351352 - Sequence 332376 from Patent EP1572962.
JD044342 - Sequence 25366 from Patent EP1572962.
JD322181 - Sequence 303205 from Patent EP1572962.
JD555708 - Sequence 536732 from Patent EP1572962.
JD228122 - Sequence 209146 from Patent EP1572962.
JD550832 - Sequence 531856 from Patent EP1572962.
JD046970 - Sequence 27994 from Patent EP1572962.
JD229683 - Sequence 210707 from Patent EP1572962.
JD536014 - Sequence 517038 from Patent EP1572962.
JD081668 - Sequence 62692 from Patent EP1572962.
JD235272 - Sequence 216296 from Patent EP1572962.
JD563233 - Sequence 544257 from Patent EP1572962.
JD286018 - Sequence 267042 from Patent EP1572962.
JD246897 - Sequence 227921 from Patent EP1572962.
JD246896 - Sequence 227920 from Patent EP1572962.
JD193972 - Sequence 174996 from Patent EP1572962.
JD238073 - Sequence 219097 from Patent EP1572962.
JD238075 - Sequence 219099 from Patent EP1572962.
JD238074 - Sequence 219098 from Patent EP1572962.
JD171556 - Sequence 152580 from Patent EP1572962.
JD249097 - Sequence 230121 from Patent EP1572962.
JD368280 - Sequence 349304 from Patent EP1572962.
JD498315 - Sequence 479339 from Patent EP1572962.
JD179742 - Sequence 160766 from Patent EP1572962.
JD127976 - Sequence 109000 from Patent EP1572962.
JD211159 - Sequence 192183 from Patent EP1572962.
JD421987 - Sequence 403011 from Patent EP1572962.
JD161677 - Sequence 142701 from Patent EP1572962.
JD547691 - Sequence 528715 from Patent EP1572962.
JD547692 - Sequence 528716 from Patent EP1572962.
AK098273 - Homo sapiens cDNA FLJ40954 fis, clone UTERU2010525.
JD531269 - Sequence 512293 from Patent EP1572962.
JD352513 - Sequence 333537 from Patent EP1572962.
JD524736 - Sequence 505760 from Patent EP1572962.
JD337647 - Sequence 318671 from Patent EP1572962.
JD213190 - Sequence 194214 from Patent EP1572962.
JD463156 - Sequence 444180 from Patent EP1572962.
JD463157 - Sequence 444181 from Patent EP1572962.
LF374027 - JP 2014500723-A/181530: Polycomb-Associated Non-Coding RNAs.
JD140075 - Sequence 121099 from Patent EP1572962.
JD471577 - Sequence 452601 from Patent EP1572962.
JD249971 - Sequence 230995 from Patent EP1572962.
JD249972 - Sequence 230996 from Patent EP1572962.
JD127517 - Sequence 108541 from Patent EP1572962.
JD545033 - Sequence 526057 from Patent EP1572962.
JD220458 - Sequence 201482 from Patent EP1572962.
JD060283 - Sequence 41307 from Patent EP1572962.
JD430111 - Sequence 411135 from Patent EP1572962.
JD529086 - Sequence 510110 from Patent EP1572962.
JD169130 - Sequence 150154 from Patent EP1572962.
JD169131 - Sequence 150155 from Patent EP1572962.
JD169132 - Sequence 150156 from Patent EP1572962.
MA443839 - JP 2018138019-A/15765: Polycomb-Associated Non-Coding RNAs.
MA609596 - JP 2018138019-A/181522: Polycomb-Associated Non-Coding RNAs.
MA609597 - JP 2018138019-A/181523: Polycomb-Associated Non-Coding RNAs.
MA609598 - JP 2018138019-A/181524: Polycomb-Associated Non-Coding RNAs.
MA609599 - JP 2018138019-A/181525: Polycomb-Associated Non-Coding RNAs.
MA609600 - JP 2018138019-A/181526: Polycomb-Associated Non-Coding RNAs.
MA609601 - JP 2018138019-A/181527: Polycomb-Associated Non-Coding RNAs.
MA609602 - JP 2018138019-A/181528: Polycomb-Associated Non-Coding RNAs.
MA609603 - JP 2018138019-A/181529: Polycomb-Associated Non-Coding RNAs.
MA609604 - JP 2018138019-A/181530: Polycomb-Associated Non-Coding RNAs.

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

Protein Q9P2J9 (Reactome details) participates in the following event(s):

R-HSA-204169 PDP dephosphorylates p-lipo-PDH
R-HSA-204174 Regulation of pyruvate dehydrogenase (PDH) complex
R-HSA-70268 Pyruvate metabolism
R-HSA-71406 Pyruvate metabolism and Citric Acid (TCA) cycle
R-HSA-1428517 The citric acid (TCA) cycle and respiratory electron transport
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: A8K924, KIAA1348, NM_020786, NP_065837, PDP2_HUMAN, Q9P2J9
UCSC ID: uc002eqk.2
RefSeq Accession: NM_020786
Protein: Q9P2J9 (aka PDP2_HUMAN)
CCDS: CCDS10822.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_020786.2
exon count: 2CDS single in 3' UTR: no RNA size: 7042
ORF size: 1590CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3380.00frame shift in genome: no % Coverage: 99.83
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.