Human Gene PDPR (ENST00000288050.9_4) from GENCODE V47lift37

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Description: pyruvate dehydrogenase phosphatase regulatory subunit, transcript variant 1 (from RefSeq NM_017990.5)
Gencode Transcript: ENST00000288050.9_4
Gencode Gene: ENSG00000090857.14_8
Transcript (Including UTRs)
Position: hg19 chr16:70,148,235-70,196,440 Size: 48,206 Total Exon Count: 19 Strand: +
Coding Region
Position: hg19 chr16:70,154,396-70,190,782 Size: 36,387 Coding Exon Count: 17

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species
GO Annotations	mRNA Descriptions	Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr16:70,148,235-70,196,440)			mRNA (may differ from genome)		Protein (879 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	Malacards	MGI	OMIM	PubMed	Reactome
UniProtKB	Wikipedia	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: PDPR_HUMAN DESCRIPTION: RecName: Full=Pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial; Short=PDPr; Flags: Precursor; FUNCTION: Decreases the sensitivity of PDP1 to magnesium ions, and this inhibition is reversed by the polyamine spermine (By similarity). SUBUNIT: Heterodimer of a catalytic (PDP1) and a regulatory (PDPR) subunit (By similarity). SUBCELLULAR LOCATION: Mitochondrion matrix (By similarity). SIMILARITY: Belongs to the GcvT family. CAUTION: It is uncertain whether Met-1 or Met-2 is the initiator. SEQUENCE CAUTION: Sequence=BAC02699.1; Type=Erroneous initiation; Sequence=BAF85191.1; 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

MalaCards Disease Associations


	MalaCards Gene Search: PDPR Diseases sorted by gene-association score: anismus (18)

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine D000393 Air Pollutants D010634 Phenobarbital D012999 Soman C044887 beta-methylcholine C045950 propiconazole C009277 sodium arsenate

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 15.52 RPKM in Testis Total median expression: 334.73 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

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-86.20	251	-0.343	Picture	PostScript	Text
3' UTR	-1790.10	5658	-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
IPR006076 - FAD-dep_OxRdtase
IPR013977 - GCV_T_C
IPR006222 - GCV_T_N

Pfam Domains:
PF00890 - FAD binding domain
PF01266 - FAD dependent oxidoreductase
PF01571 - Aminomethyltransferase folate-binding domain
PF08669 - Glycine cleavage T-protein C-terminal barrel domain
PF16350 - FAD dependent oxidoreductase central domain

SCOP Domains:
101790 - Aminomethyltransferase beta-barrel domain
51735 - NAD(P)-binding Rossmann-fold domains
51905 - FAD/NAD(P)-binding domain
52440 - PreATP-grasp domain
51971 - Nucleotide-binding domain
52821 - Rhodanese/Cell cycle control phosphatase
51984 - MurCD N-terminal domain
54373 - FAD-linked reductases, C-terminal domain
103025 - Folate-binding domain

ModBase Predicted Comparative 3D Structure on Q8NCN5


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0004741 [pyruvate dehydrogenase (lipoamide)] phosphatase activity GO:0016491 oxidoreductase activity Biological Process: GO:0006470 protein dephosphorylation GO:0010510 regulation of acetyl-CoA biosynthetic process from pyruvate GO:0055114 oxidation-reduction process Cellular Component: GO:0005739 mitochondrion GO:0005759 mitochondrial matrix

Descriptions from all associated GenBank mRNAs


	AB082521 - Homo sapiens mRNA for KIAA1990 protein. LF384459 - JP 2014500723-A/191962: Polycomb-Associated Non-Coding RNAs. AK292502 - Homo sapiens cDNA FLJ76952 complete cds, highly similar to Homo sapiens pyruvate dehydrogenase phosphatase regulatory subunit (PDPR), mRNA. AK302987 - Homo sapiens cDNA FLJ50312 complete cds, highly similar to Homo sapiens pyruvate dehydrogenase phosphatase regulatory subunit (PDPR), mRNA. BX538153 - Homo sapiens mRNA; cDNA DKFZp686J1643 (from clone DKFZp686J1643). BC090941 - Homo sapiens pyruvate dehydrogenase phosphatase regulatory subunit, mRNA (cDNA clone IMAGE:3101638), with apparent retained intron. AB384342 - Synthetic construct DNA, clone: pF1KSDA1990, Homo sapiens KIAA1990 gene for pyruvate dehydrogenase phosphatase regulatory subunit, complete cds, without stop codon, in Flexi system. JD234478 - Sequence 215502 from Patent EP1572962. JD341317 - Sequence 322341 from Patent EP1572962. JD454544 - Sequence 435568 from Patent EP1572962. JD076311 - Sequence 57335 from Patent EP1572962. JD433378 - Sequence 414402 from Patent EP1572962. JD483358 - Sequence 464382 from Patent EP1572962. JD107970 - Sequence 88994 from Patent EP1572962. LF374645 - JP 2014500723-A/182148: Polycomb-Associated Non-Coding RNAs. JD527915 - Sequence 508939 from Patent EP1572962. DQ580564 - Homo sapiens piRNA piR-48676, complete sequence. JD102620 - Sequence 83644 from Patent EP1572962. JD470108 - Sequence 451132 from Patent EP1572962. JD486718 - Sequence 467742 from Patent EP1572962. JD086192 - Sequence 67216 from Patent EP1572962. CR627404 - Homo sapiens mRNA; cDNA DKFZp686A088 (from clone DKFZp686A088). AK000941 - Homo sapiens cDNA FLJ10079 fis, clone HEMBA1001896, weakly similar to DIMETHYLGLYCINE DEHYDROGENASE PRECURSOR (EC 1.5.99.2). JD299797 - Sequence 280821 from Patent EP1572962. JD482783 - Sequence 463807 from Patent EP1572962. DQ600352 - Homo sapiens piRNA piR-38418, complete sequence. LF374648 - JP 2014500723-A/182151: Polycomb-Associated Non-Coding RNAs. LF374649 - JP 2014500723-A/182152: Polycomb-Associated Non-Coding RNAs. LF374650 - JP 2014500723-A/182153: Polycomb-Associated Non-Coding RNAs. DQ577133 - Homo sapiens piRNA piR-45245, complete sequence. LF374651 - JP 2014500723-A/182154: Polycomb-Associated Non-Coding RNAs. DQ581599 - Homo sapiens piRNA piR-49711, complete sequence. LF374652 - JP 2014500723-A/182155: Polycomb-Associated Non-Coding RNAs. AK316384 - Homo sapiens cDNA, FLJ79283 complete cds, highly similar to Homo sapiens pyruvate dehydrogenase phosphatase regulatory subunit (PDPR), mRNA. AK093391 - Homo sapiens cDNA FLJ36072 fis, clone TESTI2019669, highly similar to Homo sapiens pyruvate dehydrogenase phosphatase regulatory subunit (PDPR), mRNA. AX748094 - Sequence 1619 from Patent EP1308459. LF374654 - JP 2014500723-A/182157: Polycomb-Associated Non-Coding RNAs. LF374655 - JP 2014500723-A/182158: Polycomb-Associated Non-Coding RNAs. BX537614 - Homo sapiens mRNA; cDNA DKFZp686D16130 (from clone DKFZp686D16130). DQ579602 - Homo sapiens piRNA piR-47714, complete sequence. JD397478 - Sequence 378502 from Patent EP1572962. JD403121 - Sequence 384145 from Patent EP1572962. JD520011 - Sequence 501035 from Patent EP1572962. JD393966 - Sequence 374990 from Patent EP1572962. JD218408 - Sequence 199432 from Patent EP1572962. JD158477 - Sequence 139501 from Patent EP1572962. JD243621 - Sequence 224645 from Patent EP1572962. JD538921 - Sequence 519945 from Patent EP1572962. BX538042 - Homo sapiens mRNA; cDNA DKFZp686F09145 (from clone DKFZp686F09145). DQ581803 - Homo sapiens piRNA piR-49915, complete sequence. JD524811 - Sequence 505835 from Patent EP1572962. JD151376 - Sequence 132400 from Patent EP1572962. JD265625 - Sequence 246649 from Patent EP1572962. DQ576489 - Homo sapiens piRNA piR-44601, complete sequence. DQ594358 - Homo sapiens piRNA piR-60470, complete sequence. DQ598419 - Homo sapiens piRNA piR-36485, complete sequence. DQ574003 - Homo sapiens piRNA piR-42115, complete sequence. LF374656 - JP 2014500723-A/182159: Polycomb-Associated Non-Coding RNAs. DQ576090 - Homo sapiens piRNA piR-44202, complete sequence. LF374657 - JP 2014500723-A/182160: Polycomb-Associated Non-Coding RNAs. DQ600562 - Homo sapiens piRNA piR-38628, complete sequence. AL117440 - Homo sapiens mRNA; cDNA DKFZp434M196 (from clone DKFZp434M196). BC006246 - Homo sapiens pyruvate dehydrogenase phosphatase regulatory subunit, mRNA (cDNA clone IMAGE:3952764), partial cds. AK024608 - Homo sapiens cDNA: FLJ20955 fis, clone ADSE01984. BC032327 - Homo sapiens pyruvate dehydrogenase phosphatase regulatory subunit, mRNA (cDNA clone IMAGE:4993188), partial cds. LF374658 - JP 2014500723-A/182161: Polycomb-Associated Non-Coding RNAs. DQ580746 - Homo sapiens piRNA piR-48858, complete sequence. DQ580747 - Homo sapiens piRNA piR-48859, complete sequence. JD027388 - Sequence 8412 from Patent EP1572962. LF374659 - JP 2014500723-A/182162: Polycomb-Associated Non-Coding RNAs. DQ598706 - Homo sapiens piRNA piR-36772, complete sequence. MA620036 - JP 2018138019-A/191962: Polycomb-Associated Non-Coding RNAs. MA610222 - JP 2018138019-A/182148: Polycomb-Associated Non-Coding RNAs. MA610225 - JP 2018138019-A/182151: Polycomb-Associated Non-Coding RNAs. MA610226 - JP 2018138019-A/182152: Polycomb-Associated Non-Coding RNAs. MA610227 - JP 2018138019-A/182153: Polycomb-Associated Non-Coding RNAs. MA610228 - JP 2018138019-A/182154: Polycomb-Associated Non-Coding RNAs. MA610229 - JP 2018138019-A/182155: Polycomb-Associated Non-Coding RNAs. MA610231 - JP 2018138019-A/182157: Polycomb-Associated Non-Coding RNAs. MA610232 - JP 2018138019-A/182158: Polycomb-Associated Non-Coding RNAs. MA610233 - JP 2018138019-A/182159: Polycomb-Associated Non-Coding RNAs. MA610234 - JP 2018138019-A/182160: Polycomb-Associated Non-Coding RNAs. MA610235 - JP 2018138019-A/182161: Polycomb-Associated Non-Coding RNAs. MA610236 - JP 2018138019-A/182162: Polycomb-Associated Non-Coding RNAs.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein Q8NCN5 (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: A7E298, A8K8Y7, B3KSE1, ENST00000288050.1, ENST00000288050.2, ENST00000288050.3, ENST00000288050.4, ENST00000288050.5, ENST00000288050.6, ENST00000288050.7, ENST00000288050.8, KIAA1990, NM_017990, PDPR_HUMAN, Q6AI20, Q6AWC9, Q8NCN5, uc317kot.1, uc317kot.2 UCSC ID: ENST00000288050.9_4 RefSeq Accession: NM_017990.5 Protein: Q8NCN5 (aka PDPR_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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