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PTPN13 protein tyrosine phosphatase non-receptor type 13 [ Homo sapiens (human) ]

Gene ID: 5783, updated on 12-Oct-2019

Summary

Official Symbol
PTPN13provided by HGNC
Official Full Name
protein tyrosine phosphatase non-receptor type 13provided by HGNC
Primary source
HGNC:HGNC:9646
See related
Ensembl:ENSG00000163629 MIM:600267
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PNP1; FAP-1; PTP1E; PTPL1; PTPLE; PTP-BL; hPTP1E; PTP-BAS
Summary
The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP is a large intracellular protein. It has a catalytic PTP domain at its C-terminus and two major structural domains: a region with five PDZ domains and a FERM domain that binds to plasma membrane and cytoskeletal elements. This PTP was found to interact with, and dephosphorylate, Fas receptor and IkappaBalpha through the PDZ domains. This suggests it has a role in Fas mediated programmed cell death. This PTP was also shown to interact with GTPase-activating protein, and thus may function as a regulator of Rho signaling pathways. Four alternatively spliced transcript variants, which encode distinct proteins, have been reported. [provided by RefSeq, Oct 2008]
Expression
Broad expression in skin (RPKM 27.0), ovary (RPKM 14.2) and 18 other tissues See more
Orthologs

Genomic context

See PTPN13 in Genome Data Viewer
Location:
4q21.3
Exon count:
48
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (86594307..86815176)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (87515468..87736332)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene mitogen-activated protein kinase 10 Neighboring gene RN7SK pseudogene 96 Neighboring gene microRNA 4452 Neighboring gene uncharacterized LOC107986189 Neighboring gene solute carrier family 10 member 6 Neighboring gene ribosomal protein L6 pseudogene 13

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association study on dimethylarginines reveals novel AGXT2 variants associated with heart rate variability but not with overall mortality.
NHGRI GWA Catalog

Pathways from BioSystems

  • Apoptosis, organism-specific biosystem (from KEGG)
    Apoptosis, organism-specific biosystemApoptosis is a genetically programmed process for the elimination of damaged or redundant cells by activation of caspases (aspartate-specific cysteine proteases). The onset of apoptosis is controlled...
  • Apoptosis, conserved biosystem (from KEGG)
    Apoptosis, conserved biosystemApoptosis is a genetically programmed process for the elimination of damaged or redundant cells by activation of caspases (aspartate-specific cysteine proteases). The onset of apoptosis is controlled...
  • Apoptosis Modulation and Signaling, organism-specific biosystem (from WikiPathways)
    Apoptosis Modulation and Signaling, organism-specific biosystemApoptosis, or cell death program, can be activated by various mechanisms within the extrinsic and the intrinsic pathway. While activation of cell death receptors leads to the engagement of the extrin...
  • Ectoderm Differentiation, organism-specific biosystem (from WikiPathways)
    Ectoderm Differentiation, organism-specific biosystemModel depicting ectoderm specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell lin...
  • Ephrin B reverse signaling, organism-specific biosystem (from Pathway Interaction Database)
    Ephrin B reverse signaling, organism-specific biosystem
    Ephrin B reverse signaling
  • Fc-epsilon receptor I signaling in mast cells, organism-specific biosystem (from Pathway Interaction Database)
    Fc-epsilon receptor I signaling in mast cells, organism-specific biosystem
    Fc-epsilon receptor I signaling in mast cells
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
    Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
  • PI Metabolism, organism-specific biosystem (from REACTOME)
    PI Metabolism, organism-specific biosystemPhosphatidylinositol (PI), a membrane phospholipid, can be reversibly phosphorylated at the 3, 4, and 5 positions of the inositol ring to generate seven phosphoinositides: phosphatidylinositol 3-phos...
  • Phospholipid metabolism, organism-specific biosystem (from REACTOME)
    Phospholipid metabolism, organism-specific biosystemPhospholipids contain a polar head group and two long-chain fatty acyl moieties, one of which is generally unsaturated. The head group is a glycerol or serine phosphate attached to a polar group such...
  • Synthesis of PIPs at the plasma membrane, organism-specific biosystem (from REACTOME)
    Synthesis of PIPs at the plasma membrane, organism-specific biosystemAt the plasma membrane, subsequent phosphorylation of phosphatidylinositol 4-phosphate (PI4P) produces phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) and phosphatidylinositol 3,4,5-trisphosphate (...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp686J1497

Gene Ontology Provided by GOA

Function Evidence Code Pubs
phosphatidylinositol 3-kinase regulatory subunit binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein tyrosine phosphatase activity IDA
Inferred from Direct Assay
more info
PubMed 
protein tyrosine phosphatase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
cell body IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoskeleton IEA
Inferred from Electronic Annotation
more info
 
cytosol IDA
Inferred from Direct Assay
more info
 
extracellular exosome HDA PubMed 
fibrillar center IDA
Inferred from Direct Assay
more info
 
lamellipodium IDA
Inferred from Direct Assay
more info
PubMed 
neuron projection IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
tyrosine-protein phosphatase non-receptor type 13
Names
fas-associated protein-tyrosine phosphatase 1
hPTPE1
protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)
protein-tyrosine phosphatase 1E
protein-tyrosine phosphatase PTPL1
NP_006255.1
NP_542414.1
NP_542415.1
NP_542416.1
XP_011530467.1
XP_016864000.1
XP_016864001.1
XP_016864002.1
XP_016864003.1
XP_016864004.1
XP_016864005.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_029704.1 RefSeqGene

    Range
    5001..225862
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_006264.3NP_006255.1  tyrosine-protein phosphatase non-receptor type 13 isoform 2

    See identical proteins and their annotated locations for NP_006255.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks multiple in-frame segments of the coding region, compared to variant 4. The encoded protein (isoform 2) lacks 19 internal amino acids, compared to isoform 4.
    Source sequence(s)
    BG202767, D21210, DA625835
    Consensus CDS
    CCDS47095.1
    UniProtKB/Swiss-Prot
    Q12923
    Related
    ENSP00000408368.2, ENST00000427191.6
    Conserved Domains (10) summary
    smart00194
    Location:21952447
    PTPc; Protein tyrosine phosphatase, catalytic domain
    smart00228
    Location:14791570
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    smart00295
    Location:573781
    B41; Band 4.1 homologues
    smart00750
    Location:3190
    KIND; kinase non-catalytic C-lobe domain
    cd00047
    Location:22212447
    PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...
    cd00992
    Location:10721156
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    pfam00373
    Location:668781
    FERM_M; FERM central domain
    pfam09379
    Location:576638
    FERM_N; FERM N-terminal domain
    pfam16599
    Location:11581348
    PTN13_u3; Unstructured linker region on PTN13 protein between PDZ
    cl17171
    Location:777877
    PH-like; Pleckstrin homology-like domain
  2. NM_080683.3NP_542414.1  tyrosine-protein phosphatase non-receptor type 13 isoform 1

    See identical proteins and their annotated locations for NP_542414.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks an in-frame segment of a coding exon, compared to variant 4. The encoded protein (isoform 1) lacks 5 internal amino acids, compared to isoform 4.
    Source sequence(s)
    BG202767, D21209, DA625835
    Consensus CDS
    CCDS47094.1
    UniProtKB/Swiss-Prot
    Q12923
    Related
    ENSP00000407249.2, ENST00000411767.7
    Conserved Domains (10) summary
    smart00194
    Location:22142466
    PTPc; Protein tyrosine phosphatase, catalytic domain
    smart00228
    Location:14981589
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    smart00295
    Location:573781
    B41; Band 4.1 homologues
    smart00750
    Location:3190
    KIND; kinase non-catalytic C-lobe domain
    cd00047
    Location:22402466
    PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...
    cd00992
    Location:10911175
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    pfam00373
    Location:668781
    FERM_M; FERM central domain
    pfam09379
    Location:576638
    FERM_N; FERM N-terminal domain
    pfam16599
    Location:11771367
    PTN13_u3; Unstructured linker region on PTN13 protein between PDZ
    cl17171
    Location:777877
    PH-like; Pleckstrin homology-like domain
  3. NM_080684.3NP_542415.1  tyrosine-protein phosphatase non-receptor type 13 isoform 3

    See identical proteins and their annotated locations for NP_542415.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks multiple in-frame segments of the coding region, compared to variant 4. The encoded protein (isoform 3) lacks 191 internal amino acids, compared to isoform 4.
    Source sequence(s)
    BG202767, D21211, DA625835
    Consensus CDS
    CCDS47096.1
    UniProtKB/Swiss-Prot
    Q12923
    Related
    ENSP00000322675.6, ENST00000316707.10
    Conserved Domains (10) summary
    smart00194
    Location:20232275
    PTPc; Protein tyrosine phosphatase, catalytic domain
    smart00228
    Location:13071398
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    smart00295
    Location:573781
    B41; Band 4.1 homologues
    smart00750
    Location:3190
    KIND; kinase non-catalytic C-lobe domain
    cd00047
    Location:20492275
    PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...
    cd00992
    Location:900984
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    pfam00373
    Location:668781
    FERM_M; FERM central domain
    pfam09379
    Location:576638
    FERM_N; FERM N-terminal domain
    pfam16599
    Location:9861176
    PTN13_u3; Unstructured linker region on PTN13 protein between PDZ
    cl17171
    Location:777877
    PH-like; Pleckstrin homology-like domain
  4. NM_080685.2NP_542416.1  tyrosine-protein phosphatase non-receptor type 13 isoform 4

    See identical proteins and their annotated locations for NP_542416.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) encodes the longest isoform (4).
    Source sequence(s)
    BG202767, D21209, DA625835, L34583
    Consensus CDS
    CCDS47093.1
    UniProtKB/Swiss-Prot
    Q12923
    Related
    ENSP00000394794.1, ENST00000436978.5
    Conserved Domains (10) summary
    smart00194
    Location:22192471
    PTPc; Protein tyrosine phosphatase, catalytic domain
    smart00228
    Location:15031594
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    smart00295
    Location:573781
    B41; Band 4.1 homologues
    smart00750
    Location:3190
    KIND; kinase non-catalytic C-lobe domain
    cd00047
    Location:22452471
    PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...
    cd00992
    Location:10911175
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    pfam00373
    Location:668781
    FERM_M; FERM central domain
    pfam09379
    Location:576638
    FERM_N; FERM N-terminal domain
    pfam16599
    Location:11771367
    PTN13_u3; Unstructured linker region on PTN13 protein between PDZ
    cl17171
    Location:777877
    PH-like; Pleckstrin homology-like domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    86594307..86815176
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011532165.2XP_011530467.1  tyrosine-protein phosphatase non-receptor type 13 isoform X1

    Conserved Domains (10) summary
    smart00194
    Location:22362488
    PTPc; Protein tyrosine phosphatase, catalytic domain
    smart00228
    Location:15031594
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    smart00295
    Location:573781
    B41; Band 4.1 homologues
    smart00750
    Location:3190
    KIND; kinase non-catalytic C-lobe domain
    cd00047
    Location:22622488
    PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...
    cd00992
    Location:10911175
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    pfam00373
    Location:668781
    FERM_M; FERM central domain
    pfam09379
    Location:576638
    FERM_N; FERM N-terminal domain
    pfam16599
    Location:11771367
    PTN13_u3; Unstructured linker region on PTN13 protein between PDZ
    cl17171
    Location:777877
    PH-like; Pleckstrin homology-like domain
  2. XM_017008511.2XP_016864000.1  tyrosine-protein phosphatase non-receptor type 13 isoform X2

  3. XM_017008512.2XP_016864001.1  tyrosine-protein phosphatase non-receptor type 13 isoform X3

  4. XM_017008514.2XP_016864003.1  tyrosine-protein phosphatase non-receptor type 13 isoform X5

  5. XM_017008513.2XP_016864002.1  tyrosine-protein phosphatase non-receptor type 13 isoform X4

  6. XM_017008516.2XP_016864005.1  tyrosine-protein phosphatase non-receptor type 13 isoform X7

  7. XM_017008515.2XP_016864004.1  tyrosine-protein phosphatase non-receptor type 13 isoform X6

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