Human Gene PTPN23 (ENST00000265562.5_4) from GENCODE V47lift37
  Description: protein tyrosine phosphatase non-receptor type 23, transcript variant 1 (from RefSeq NM_015466.4)
Gencode Transcript: ENST00000265562.5_4
Gencode Gene: ENSG00000076201.16_10
Transcript (Including UTRs)
   Position: hg19 chr3:47,422,511-47,454,925 Size: 32,415 Total Exon Count: 25 Strand: +
Coding Region
   Position: hg19 chr3:47,422,587-47,454,675 Size: 32,089 Coding Exon Count: 25 

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 (chr3:47,422,511-47,454,925)mRNA (may differ from genome)Protein (1636 aa)
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UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PTN23_HUMAN
DESCRIPTION: RecName: Full=Tyrosine-protein phosphatase non-receptor type 23; EC=3.1.3.48; AltName: Full=His domain-containing protein tyrosine phosphatase; Short=HD-PTP; AltName: Full=Protein tyrosine phosphatase TD14; Short=PTP-TD14;
FUNCTION: May act as a negative regulator of Ras-mediated mitogenic activity. Plays a role in ciliogenesis.
CATALYTIC ACTIVITY: Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate.
SUBUNIT: Interacts with GRAP2 and GRB2.
INTERACTION: O75791:GRAP2; NbExp=5; IntAct=EBI-724478, EBI-740418; P62993:GRB2; NbExp=6; IntAct=EBI-724478, EBI-401755;
SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Cytoplasmic vesicle. Endosome. Cytoplasm, cytoskeleton, cilium basal body.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the protein-tyrosine phosphatase family. Non-receptor class subfamily.
SIMILARITY: Contains 1 BRO1 domain.
SIMILARITY: Contains 2 TPR repeats.
SIMILARITY: Contains 1 tyrosine-protein phosphatase domain.
SEQUENCE CAUTION: Sequence=BAA95995.2; 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: PTPN23
Diseases sorted by gene-association score: respiratory system benign neoplasm (9)

-  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: 38.31 RPKM in Pituitary
Total median expression: 897.02 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 -41.6076-0.547 Picture PostScript Text
3' UTR -70.20250-0.281 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
IPR025304 - ALIX_V_dom
IPR004328 - BRO1_dom
IPR000387 - Tyr/Dual-specificity_Pase
IPR016130 - Tyr_Pase_AS
IPR000242 - Tyr_Pase_rcpt/non-rcpt

Pfam Domains:
PF00102 - Protein-tyrosine phosphatase
PF03097 - BRO1-like domain
PF13949 - ALIX V-shaped domain binding to HIV

SCOP Domains:
48452 - TPR-like
103657 - BAR/IMD domain-like
47266 - 4-helical cytokines
52799 - (Phosphotyrosine protein) phosphatases II

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


ModBase Predicted Comparative 3D Structure on Q9H3S7
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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 orthologNo orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
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 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004721 phosphoprotein phosphatase activity
GO:0004725 protein tyrosine phosphatase activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0016791 phosphatase activity
GO:0019901 protein kinase binding

Biological Process:
GO:0006470 protein dephosphorylation
GO:0010633 negative regulation of epithelial cell migration
GO:0015031 protein transport
GO:0016311 dephosphorylation
GO:0030030 cell projection organization
GO:0030334 regulation of cell migration
GO:0032456 endocytic recycling
GO:0035335 peptidyl-tyrosine dephosphorylation
GO:0043162 ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
GO:0045022 early endosome to late endosome transport
GO:0060271 cilium assembly
GO:0061357 positive regulation of Wnt protein secretion
GO:0071345 cellular response to cytokine stimulus
GO:1903387 positive regulation of homophilic cell adhesion
GO:1903393 positive regulation of adherens junction organization
GO:2000643 positive regulation of early endosome to late endosome transport

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005769 early endosome
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005929 cilium
GO:0016604 nuclear body
GO:0031410 cytoplasmic vesicle
GO:0036064 ciliary basal body
GO:0042995 cell projection
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  KJ904704 - Synthetic construct Homo sapiens clone ccsbBroadEn_14098 PTPN23 gene, encodes complete protein.
AB040904 - Homo sapiens KIAA1471 mRNA for KIAA1471 protein, partial cds.
AK055157 - Homo sapiens cDNA FLJ30595 fis, clone BRAWH2008956, highly similar to Protein-tyrosine-phosphatase (EC 3.1.3.48).
AK299906 - Homo sapiens cDNA FLJ58078 complete cds, highly similar to Tyrosine-protein phosphatase non-receptortype 23 (EC 3.1.3.48).
AK295888 - Homo sapiens cDNA FLJ53444 complete cds, highly similar to Tyrosine-protein phosphatase non-receptor type 23 (EC 3.1.3.48).
AK289502 - Homo sapiens cDNA FLJ75567 complete cds, highly similar to Homo sapiens protein tyrosine phosphatase, non-receptor type 23 (PTPN23), mRNA.
AB025194 - Homo sapiens mRNA for protein tyrosine phosphatase HD-PTP, complete cds.
AF290614 - Homo sapiens clone F2896 protein tyrosine phosphatase TD14 mRNA, complete cds.
AK295877 - Homo sapiens cDNA FLJ58355 complete cds, highly similar to Tyrosine-protein phosphatase non-receptor type 23 (EC 3.1.3.48).
BC089042 - Homo sapiens protein tyrosine phosphatase, non-receptor type 23, mRNA (cDNA clone MGC:99484 IMAGE:6579163), complete cds.
BC027711 - Homo sapiens protein tyrosine phosphatase, non-receptor type 23, mRNA (cDNA clone IMAGE:4111514), partial cds.
AL110210 - Homo sapiens mRNA; cDNA DKFZp564F0923 (from clone DKFZp564F0923); partial cds.
BC020380 - Homo sapiens protein tyrosine phosphatase, non-receptor type 23, mRNA (cDNA clone IMAGE:4154022).
BC004881 - Homo sapiens protein tyrosine phosphatase, non-receptor type 23, mRNA (cDNA clone IMAGE:3831058), partial cds.
CU678784 - Synthetic construct Homo sapiens gateway clone IMAGE:100019902 5' read PTPN23 mRNA.
BT009758 - Homo sapiens protein tyrosine phosphatase, non-receptor type 23 mRNA, complete cds.
AF169350 - Homo sapiens protein tyrosine phosphatase TD14 (PTP-TD14) mRNA, partial cds.
JD116315 - Sequence 97339 from Patent EP1572962.
JD068110 - Sequence 49134 from Patent EP1572962.
JD201067 - Sequence 182091 from Patent EP1572962.
JD164588 - Sequence 145612 from Patent EP1572962.
JD228863 - Sequence 209887 from Patent EP1572962.
JD560604 - Sequence 541628 from Patent EP1572962.
JD401047 - Sequence 382071 from Patent EP1572962.
JD224737 - Sequence 205761 from Patent EP1572962.
JD107826 - Sequence 88850 from Patent EP1572962.

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

Protein Q9H3S7 (Reactome details) participates in the following event(s):

R-HSA-9008059 Interleukin-37 signaling
R-HSA-446652 Interleukin-1 family signaling
R-HSA-449147 Signaling by Interleukins
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: A8K0D7, ENST00000265562.1, ENST00000265562.2, ENST00000265562.3, ENST00000265562.4, KIAA1471, NM_015466, PTN23_HUMAN, Q7KZF8, Q8N6Z5, Q9BSR5, Q9H3S7, Q9P257, Q9UG03, Q9UMZ4, uc317ice.1, uc317ice.2
UCSC ID: ENST00000265562.5_4
RefSeq Accession: NM_015466.4
Protein: Q9H3S7 (aka PTN23_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.