Human Gene PTPN3 (ENST00000374541.4) from GENCODE V44
  Description: Homo sapiens protein tyrosine phosphatase non-receptor type 3 (PTPN3), transcript variant 1, mRNA. (from RefSeq NM_002829)
RefSeq Summary (NM_002829): The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This protein contains a C-terminal PTP domain and an N-terminal domain homologous to the band 4.1 superfamily of cytoskeletal-associated proteins. P97, a cell cycle regulator involved in a variety of membrane related functions, has been shown to be a substrate of this PTP. This PTP was also found to interact with, and be regulated by adaptor protein 14-3-3 beta. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2009].
Gencode Transcript: ENST00000374541.4
Gencode Gene: ENSG00000070159.14
Transcript (Including UTRs)
   Position: hg38 chr9:109,375,700-109,498,307 Size: 122,608 Total Exon Count: 26 Strand: -
Coding Region
   Position: hg38 chr9:109,379,556-109,463,434 Size: 83,879 Coding Exon Count: 25 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:109,375,700-109,498,307)mRNA (may differ from genome)Protein (913 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PTN3_HUMAN
DESCRIPTION: RecName: Full=Tyrosine-protein phosphatase non-receptor type 3; EC=3.1.3.48; AltName: Full=Protein-tyrosine phosphatase H1; Short=PTP-H1;
FUNCTION: May act at junctions between the membrane and the cytoskeleton. Possesses tyrosine phosphatase activity.
CATALYTIC ACTIVITY: Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate.
INTERACTION: P10912:GHR; NbExp=4; IntAct=EBI-1047946, EBI-286316; P11473:VDR; NbExp=4; IntAct=EBI-1047946, EBI-286357;
SUBCELLULAR LOCATION: Cell membrane; Peripheral membrane protein; Cytoplasmic side. Cytoplasm, cytoskeleton.
SIMILARITY: Belongs to the protein-tyrosine phosphatase family. Non-receptor class subfamily.
SIMILARITY: Contains 1 FERM domain.
SIMILARITY: Contains 1 PDZ (DHR) domain.
SIMILARITY: Contains 1 tyrosine-protein phosphatase domain.

-  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: PTPN3
Diseases sorted by gene-association score: cholangiocarcinoma, susceptibility to* (454), non-functioning pituitary adenoma (9), scott syndrome (7), functioning pituitary adenoma (6), monocarboxylate transporter 1 deficiency (5), diabetes mellitus, insulin-dependent (3), diabetes mellitus, noninsulin-dependent (1)
* = Manually curated disease association

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 13.17 RPKM in Skin - Sun Exposed (Lower leg)
Total median expression: 150.21 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 -49.70106-0.469 Picture PostScript Text
3' UTR -1149.703856-0.298 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
IPR019749 - Band_41_domain
IPR019750 - Band_41_fam
IPR014352 - FERM/acyl-CoA-bd_prot_3-hlx
IPR019748 - FERM_central
IPR019747 - FERM_CS
IPR000299 - FERM_domain
IPR018979 - FERM_N
IPR018980 - FERM_PH-like_C
IPR001478 - PDZ
IPR011993 - PH_like_dom
IPR000387 - Tyr/Dual-specificity_Pase
IPR016130 - Tyr_Pase_AS
IPR012151 - Tyr_Pase_non-rcpt_typ-3/4
IPR000242 - Tyr_Pase_rcpt/non-rcpt

Pfam Domains:
PF09380 - FERM C-terminal PH-like domain
PF00373 - FERM central domain
PF09379 - FERM N-terminal domain
PF00595 - PDZ domain (Also known as DHR or GLGF)
PF00102 - Protein-tyrosine phosphatase

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2B49 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P26045
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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
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001784 phosphotyrosine binding
GO:0004721 phosphoprotein phosphatase activity
GO:0004725 protein tyrosine phosphatase activity
GO:0005515 protein binding
GO:0008092 cytoskeletal protein binding
GO:0016787 hydrolase activity
GO:0016791 phosphatase activity
GO:0017080 sodium channel regulator activity
GO:0051117 ATPase binding

Biological Process:
GO:0006470 protein dephosphorylation
GO:0016311 dephosphorylation
GO:0035335 peptidyl-tyrosine dephosphorylation
GO:0042059 negative regulation of epidermal growth factor receptor signaling pathway
GO:0045930 negative regulation of mitotic cell cycle
GO:0051045 negative regulation of membrane protein ectodomain proteolysis
GO:0097421 liver regeneration
GO:0098902 regulation of membrane depolarization during action potential
GO:2000649 regulation of sodium ion transmembrane transporter activity

Cellular Component:
GO:0005737 cytoplasm
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0009898 cytoplasmic side of plasma membrane
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  BX648735 - Homo sapiens mRNA; cDNA DKFZp686N1128 (from clone DKFZp686N1128).
BX648253 - Homo sapiens mRNA; cDNA DKFZp686B07115 (from clone DKFZp686B07115).
M64572 - Human protein tyrosine phosphatase mRNA, complete cds.
BC143848 - Homo sapiens protein tyrosine phosphatase, non-receptor type 3, mRNA (cDNA clone MGC:177380 IMAGE:9052363), complete cds.
BC126117 - Homo sapiens protein tyrosine phosphatase, non-receptor type 3, mRNA (cDNA clone MGC:161395 IMAGE:8991833), complete cds.
AK316066 - Homo sapiens cDNA, FLJ78965 complete cds, highly similar to Tyrosine-protein phosphatase non-receptor type 3 (EC 3.1.3.48).
AK295875 - Homo sapiens cDNA FLJ50545 complete cds, highly similar to Tyrosine-protein phosphatase non-receptor type3 (EC 3.1.3.48).
AK304434 - Homo sapiens cDNA FLJ53589 complete cds, highly similar to Tyrosine-protein phosphatase non-receptor type3 (EC 3.1.3.48).
DQ104439 - Homo sapiens tyrosine phosphatase mRNA, complete cds, alternatively spliced.
HQ258671 - Synthetic construct Homo sapiens clone IMAGE:100072701 protein tyrosine phosphatase, non-receptor type 3 (PTPN3), transcript variant 1 (PTPN3) gene, encodes complete protein.
KJ904541 - Synthetic construct Homo sapiens clone ccsbBroadEn_13935 PTPN3 gene, encodes complete protein.
LF206475 - JP 2014500723-A/13978: Polycomb-Associated Non-Coding RNAs.
MA442052 - JP 2018138019-A/13978: Polycomb-Associated Non-Coding RNAs.
AK096975 - Homo sapiens cDNA FLJ39656 fis, clone SMINT2005956.
CR749204 - Homo sapiens mRNA; cDNA DKFZp686N0569 (from clone DKFZp686N0569).
JD069554 - Sequence 50578 from Patent EP1572962.
JD535419 - Sequence 516443 from Patent EP1572962.
JD367597 - Sequence 348621 from Patent EP1572962.
BC033716 - Homo sapiens, clone IMAGE:4452690, mRNA, partial cds.
JD357546 - Sequence 338570 from Patent EP1572962.
JD188230 - Sequence 169254 from Patent EP1572962.
JD480774 - Sequence 461798 from Patent EP1572962.
JD241147 - Sequence 222171 from Patent EP1572962.
JD344451 - Sequence 325475 from Patent EP1572962.
JD282905 - Sequence 263929 from Patent EP1572962.
JD426877 - Sequence 407901 from Patent EP1572962.
JD071577 - Sequence 52601 from Patent EP1572962.
JD067125 - Sequence 48149 from Patent EP1572962.
JD132874 - Sequence 113898 from Patent EP1572962.
JD124799 - Sequence 105823 from Patent EP1572962.
AK303608 - Homo sapiens cDNA FLJ52384 complete cds, highly similar to Tyrosine-protein phosphatase non-receptor type 3 (EC 3.1.3.48).
JD479471 - Sequence 460495 from Patent EP1572962.
JD283486 - Sequence 264510 from Patent EP1572962.
JD279394 - Sequence 260418 from Patent EP1572962.
AK296265 - Homo sapiens cDNA FLJ50413 complete cds, highly similar to Tyrosine-protein phosphatase non-receptor type3 (EC 3.1.3.48).
JD126306 - Sequence 107330 from Patent EP1572962.
AK316118 - Homo sapiens cDNA, FLJ79017 complete cds, highly similar to Tyrosine-protein phosphatase non-receptor type3 (EC 3.1.3.48).
AK296388 - Homo sapiens cDNA FLJ59556 complete cds, highly similar to Tyrosine-protein phosphatase non-receptor type3 (EC 3.1.3.48).
JD424783 - Sequence 405807 from Patent EP1572962.
JD250425 - Sequence 231449 from Patent EP1572962.
S76309 - PTPH1=cytoskeletal-associated protein tyrosine phosphatase [human, hepatocellular carcinoma cell line cHc4, mRNA Partial Mutant, 48 nt].
S39392 - Homo sapiens protein tyrosine phosphatase mRNA, partial cds.
LF206473 - JP 2014500723-A/13976: Polycomb-Associated Non-Coding RNAs.
MA442050 - JP 2018138019-A/13976: Polycomb-Associated Non-Coding RNAs.
AK308349 - Homo sapiens cDNA, FLJ98297.
LF354889 - JP 2014500723-A/162392: Polycomb-Associated Non-Coding RNAs.
MA590466 - JP 2018138019-A/162392: Polycomb-Associated Non-Coding RNAs.
LF354893 - JP 2014500723-A/162396: Polycomb-Associated Non-Coding RNAs.
MA590470 - JP 2018138019-A/162396: Polycomb-Associated Non-Coding RNAs.
LF354897 - JP 2014500723-A/162400: Polycomb-Associated Non-Coding RNAs.
MA590474 - JP 2018138019-A/162400: Polycomb-Associated Non-Coding RNAs.
BC063287 - Homo sapiens protein tyrosine phosphatase, non-receptor type 3, mRNA (cDNA clone IMAGE:30344422), with apparent retained intron.

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

Protein P26045 (Reactome details) participates in the following event(s):

R-HSA-8867047 PTPN3 dephosphorylates EPS15
R-HSA-182971 EGFR downregulation
R-HSA-177929 Signaling by EGFR
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: A0AUW9, ENST00000374541.1, ENST00000374541.2, ENST00000374541.3, NM_002829, P26045, PTN3_HUMAN, PTPH1, uc004bed.1, uc004bed.2, uc004bed.3, uc004bed.4
UCSC ID: ENST00000374541.4
RefSeq Accession: NM_002829
Protein: P26045 (aka PTN3_HUMAN)
CCDS: CCDS6776.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.