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

    Gene ID: 5783, updated on 7-Oct-2018

    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; Vega:OTTHUMG00000160968
    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 current GRCh38.p12 (GCF_000001405.38) 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 RNA, 7SK small nuclear 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 Jun 15 11:32:44 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat'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 
    Process Evidence Code Pubs
    cellular response to cytokine stimulus TAS
    Traceable Author Statement
    more info
     
    peptidyl-tyrosine dephosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    phosphatidylinositol biosynthetic process TAS
    Traceable Author Statement
    more info
     
    protein dephosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of phosphatidylinositol 3-kinase signaling IDA
    Inferred from Direct Assay
    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
     
    extracellular exosome HDA PubMed 
    lamellipodium IDA
    Inferred from Direct Assay
    more info
    PubMed 
    neuron projection IEA
    Inferred from Electronic Annotation
    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_006264.2NP_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, OTTHUMP00000219449, ENST00000427191.6, OTTHUMT00000363189
      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_080683.2NP_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, OTTHUMP00000219451, ENST00000411767.6, OTTHUMT00000363191
      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_080684.2NP_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, OTTHUMP00000219450, ENST00000316707.10, OTTHUMT00000363190
      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 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p12 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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