Human Gene PTPMT1 (ENST00000326674.10_4) from GENCODE V47lift37
  Description: protein tyrosine phosphatase mitochondrial 1, transcript variant 1 (from RefSeq NM_175732.3)
Gencode Transcript: ENST00000326674.10_4
Gencode Gene: ENSG00000110536.14_8
Transcript (Including UTRs)
   Position: hg19 chr11:47,587,151-47,595,013 Size: 7,863 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr11:47,587,175-47,593,181 Size: 6,007 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq 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 (chr11:47,587,151-47,595,013)mRNA (may differ from genome)Protein (201 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PTPM1_HUMAN
DESCRIPTION: RecName: Full=Phosphatidylglycerophosphatase and protein-tyrosine phosphatase 1; EC=3.1.3.27; AltName: Full=PTEN-like phosphatase; AltName: Full=Phosphoinositide lipid phosphatase; AltName: Full=Protein-tyrosine phosphatase mitochondrial 1; EC=3.1.3.16; EC=3.1.3.48; Flags: Precursor;
FUNCTION: Lipid phosphatase which dephosphorylates phosphatidylglycerophosphate (PGP) to phosphatidylglycerol (PG). PGP is an essential intermediate in the biosynthetic pathway of cardiolipin, a mitochondrial-specific phospholipid regulating the membrane integrity and activities of the organelle. Has also been shown to display phosphatase activity toward phosphoprotein substrates, specifically mediates dephosphorylation of mitochondrial proteins, thereby playing an essential role in ATP production. Has probably a preference for proteins phosphorylated on Ser and/or Thr residues compared to proteins phosphorylated on Tyr residues. Probably involved in regulation of insulin secretion in pancreatic beta cells (By similarity).
CATALYTIC ACTIVITY: Phosphatidylglycerophosphate + H(2)O = phosphatidylglycerol + phosphate.
CATALYTIC ACTIVITY: Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate.
CATALYTIC ACTIVITY: A phosphoprotein + H(2)O = a protein + phosphate.
PATHWAY: Phospholipid metabolism; phosphatidylglycerol biosynthesis; phosphatidylglycerol from CDP-diacylglycerol: step 2/2.
SUBCELLULAR LOCATION: Mitochondrion inner membrane (By similarity). Note=Associated with the inner membrane (By similarity).
SIMILARITY: Belongs to the protein-tyrosine phosphatase family. Non-receptor class dual specificity subfamily.
SIMILARITY: Contains 1 tyrosine-protein phosphatase domain.
CAUTION: Was originally erroneously termed DUSP23.
SEQUENCE CAUTION: Sequence=AAH14048.1; Type=Erroneous initiation; Sequence=AAK07545.1; 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: PTPMT1
Diseases sorted by gene-association score: cogan syndrome (2)

-  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: 106.98 RPKM in Testis
Total median expression: 1150.02 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -6.8024-0.283 Picture PostScript Text
3' UTR -547.101832-0.299 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
IPR000340 - Dual-sp_phosphatase_cat-dom
IPR024950 - DUSP
IPR000387 - Tyr/Dual-specificity_Pase
IPR016130 - Tyr_Pase_AS

Pfam Domains:
PF00782 - Dual specificity phosphatase, catalytic domain

SCOP Domains:
52799 - (Phosphotyrosine protein) phosphatases II

ModBase Predicted Comparative 3D Structure on Q8WUK0
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 orthologNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004439 phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity
GO:0004721 phosphoprotein phosphatase activity
GO:0004725 protein tyrosine phosphatase activity
GO:0005515 protein binding
GO:0008138 protein tyrosine/serine/threonine phosphatase activity
GO:0008962 phosphatidylglycerophosphatase activity
GO:0016787 hydrolase activity
GO:0016791 phosphatase activity

Biological Process:
GO:0006470 protein dephosphorylation
GO:0006629 lipid metabolic process
GO:0006655 phosphatidylglycerol biosynthetic process
GO:0008654 phospholipid biosynthetic process
GO:0016311 dephosphorylation
GO:0032049 cardiolipin biosynthetic process
GO:0035335 peptidyl-tyrosine dephosphorylation
GO:2001242 regulation of intrinsic apoptotic signaling pathway

Cellular Component:
GO:0005634 nucleus
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  AK127967 - Homo sapiens cDNA FLJ46081 fis, clone TESTI2005112, highly similar to NADH-ubiquinone oxidoreductase 30 kDa subunit, mitochondrial precursor (EC 1.6.5.3).
BC073798 - Homo sapiens cDNA clone IMAGE:4590861, partial cds.
LF383704 - JP 2014500723-A/191207: Polycomb-Associated Non-Coding RNAs.
BC107573 - Homo sapiens cDNA clone IMAGE:3931025.
AK294640 - Homo sapiens cDNA FLJ57723 complete cds, moderately similar to Protein-tyrosine phosphatase mitochondrial 1, mitochondrial precursor (EC 3.1.3.48).
BC020242 - Homo sapiens protein tyrosine phosphatase, mitochondrial 1, mRNA (cDNA clone MGC:31981 IMAGE:4591438), complete cds.
CU676524 - Synthetic construct Homo sapiens gateway clone IMAGE:100018550 5' read PTPMT1 mRNA.
HQ447910 - Synthetic construct Homo sapiens clone IMAGE:100071266; CCSB007876_01 protein tyrosine phosphatase, mitochondrial 1 (PTPMT1) gene, encodes complete protein.
EU831532 - Synthetic construct Homo sapiens clone HAIB:100066561; DKFZo004D0418 protein tyrosine phosphatase, mitochondrial 1 protein (PTPMT1) gene, encodes complete protein; nuclear gene for mitochondrial product.
AY333987 - Homo sapiens unknown mRNA.
EU831440 - Synthetic construct Homo sapiens clone HAIB:100066469; DKFZo008D0417 protein tyrosine phosphatase, mitochondrial 1 protein (PTPMT1) gene, encodes complete protein; nuclear gene for mitochondrial product.
BC014048 - Homo sapiens protein tyrosine phosphatase, mitochondrial 1, mRNA (cDNA clone IMAGE:3348134), partial cds.
AF277187 - Homo sapiens PNAS-129 mRNA, complete cds.
LF347876 - JP 2014500723-A/155379: Polycomb-Associated Non-Coding RNAs.
LF347874 - JP 2014500723-A/155377: Polycomb-Associated Non-Coding RNAs.
JD325213 - Sequence 306237 from Patent EP1572962.
JD503449 - Sequence 484473 from Patent EP1572962.
JD233205 - Sequence 214229 from Patent EP1572962.
JD213954 - Sequence 194978 from Patent EP1572962.
JD482372 - Sequence 463396 from Patent EP1572962.
JD333927 - Sequence 314951 from Patent EP1572962.
JD342863 - Sequence 323887 from Patent EP1572962.
JD094635 - Sequence 75659 from Patent EP1572962.
JD297902 - Sequence 278926 from Patent EP1572962.
JD506986 - Sequence 488010 from Patent EP1572962.
JD061658 - Sequence 42682 from Patent EP1572962.
JD127006 - Sequence 108030 from Patent EP1572962.
CU678157 - Synthetic construct Homo sapiens gateway clone IMAGE:100019755 3' read KBTBD4 mRNA.
JD308589 - Sequence 289613 from Patent EP1572962.
JD068212 - Sequence 49236 from Patent EP1572962.
JD051863 - Sequence 32887 from Patent EP1572962.
JD073158 - Sequence 54182 from Patent EP1572962.
JD509853 - Sequence 490877 from Patent EP1572962.
JD163348 - Sequence 144372 from Patent EP1572962.
JD554088 - Sequence 535112 from Patent EP1572962.
JD075985 - Sequence 57009 from Patent EP1572962.
JD168667 - Sequence 149691 from Patent EP1572962.
JD213589 - Sequence 194613 from Patent EP1572962.
LF347872 - JP 2014500723-A/155375: Polycomb-Associated Non-Coding RNAs.
JD355506 - Sequence 336530 from Patent EP1572962.
JD364763 - Sequence 345787 from Patent EP1572962.
MA619281 - JP 2018138019-A/191207: Polycomb-Associated Non-Coding RNAs.
MA583453 - JP 2018138019-A/155379: Polycomb-Associated Non-Coding RNAs.
MA583451 - JP 2018138019-A/155377: Polycomb-Associated Non-Coding RNAs.
MA583449 - JP 2018138019-A/155375: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
PWY-5269 - cardiolipin biosynthesis

Reactome (by CSHL, EBI, and GO)

Protein Q8WUK0 (Reactome details) participates in the following event(s):

R-HSA-1483197 PTPMT1 dephosphorylates PGP to PG
R-HSA-1483148 Synthesis of PG
R-HSA-1483206 Glycerophospholipid biosynthesis
R-HSA-1483257 Phospholipid metabolism
R-HSA-556833 Metabolism of lipids
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: E9PAT8, ENST00000326674.1, ENST00000326674.2, ENST00000326674.3, ENST00000326674.4, ENST00000326674.5, ENST00000326674.6, ENST00000326674.7, ENST00000326674.8, ENST00000326674.9, MOSP, NM_175732, PLIP, PNAS-129, PTPM1_HUMAN, PTPMT1 , Q7Z557, Q8WUK0, Q96CR2, Q9BXV8, uc317scp.1, uc317scp.2
UCSC ID: ENST00000326674.10_4
RefSeq Accession: NM_175732.3
Protein: Q8WUK0 (aka PTPM1_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.