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

    Gene ID: 5783, updated on 3-Nov-2024

    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; AllianceGenome:HGNC:9646
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PTPN13 in Genome Data Viewer
    Location:
    4q21.3
    Exon count:
    49
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (86594315..86815161)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (89923800..90144654)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (87515468..87736314)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene mitogen-activated protein kinase 10 Neighboring gene RN7SK pseudogene 96 Neighboring gene NANOG hESC enhancer GRCh37_chr4:87353806-87354348 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:87374354-87374902 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:87393729-87394298 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:87398123-87398623 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:87403957-87404713 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21695 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:87468519-87469019 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:87515119-87515705 Neighboring gene microRNA 4452 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:87651683-87652182 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr4:87778666-87779166 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 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

    EBI GWAS Catalog

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • DKFZp686J1497

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphatidylinositol 3-kinase regulatory subunit binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables phosphatidylinositol 3-kinase regulatory subunit binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein tyrosine phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein tyrosine phosphatase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein tyrosine phosphatase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cell body IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in fibrillar center IDA
    Inferred from Direct Assay
    more info
     
    located_in lamellipodium IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in 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
    XP_047271992.1
    XP_047271993.1
    XP_047271994.1
    XP_047271995.1
    XP_047271996.1
    XP_047271997.1
    XP_047271998.1
    XP_047271999.1
    XP_047272000.1
    XP_047272001.1
    XP_047272002.1
    XP_047272003.1
    XP_047272004.1
    XP_054206615.1
    XP_054206616.1
    XP_054206617.1
    XP_054206618.1
    XP_054206619.1
    XP_054206620.1
    XP_054206621.1
    XP_054206622.1
    XP_054206623.1
    XP_054206624.1
    XP_054206625.1
    XP_054206626.1
    XP_054206627.1
    XP_054206628.1
    XP_054206629.1
    XP_054206630.1
    XP_054206631.1
    XP_054206632.1
    XP_054206633.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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..225847
      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/TrEMBL
      Q59H55
      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
      B2RTR0, Q12923, Q15159, Q15263, Q15264, Q15265, Q15674, Q16826, Q8IWH7, Q9NYN9, Q9UDA8
      UniProtKB/TrEMBL
      Q59H55
      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/TrEMBL
      Q59H55
      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_080685.3NP_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/TrEMBL
      Q59H55
      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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      86594315..86815161
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011532165.3XP_011530467.1  tyrosine-protein phosphatase non-receptor type 13 isoform X1

      UniProtKB/TrEMBL
      Q59H55
      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_017008511.3XP_016864000.1  tyrosine-protein phosphatase non-receptor type 13 isoform X2

      UniProtKB/TrEMBL
      Q59H55
    3. XM_017008512.3XP_016864001.1  tyrosine-protein phosphatase non-receptor type 13 isoform X3

      UniProtKB/TrEMBL
      Q59H55
    4. XM_017008514.3XP_016864003.1  tyrosine-protein phosphatase non-receptor type 13 isoform X5

      UniProtKB/TrEMBL
      Q59H55
    5. XM_017008513.3XP_016864002.1  tyrosine-protein phosphatase non-receptor type 13 isoform X4

      UniProtKB/TrEMBL
      Q59H55
    6. XM_017008516.3XP_016864005.1  tyrosine-protein phosphatase non-receptor type 13 isoform X8

      UniProtKB/TrEMBL
      Q59H55
    7. XM_047416041.1XP_047271997.1  tyrosine-protein phosphatase non-receptor type 13 isoform X13

    8. XM_047416038.1XP_047271994.1  tyrosine-protein phosphatase non-receptor type 13 isoform X10

    9. XM_017008515.3XP_016864004.1  tyrosine-protein phosphatase non-receptor type 13 isoform X7

      UniProtKB/TrEMBL
      Q59H55
    10. XM_047416039.1XP_047271995.1  tyrosine-protein phosphatase non-receptor type 13 isoform X11

    11. XM_047416037.1XP_047271993.1  tyrosine-protein phosphatase non-receptor type 13 isoform X9

    12. XM_047416042.1XP_047271998.1  tyrosine-protein phosphatase non-receptor type 13 isoform X14

    13. XM_047416040.1XP_047271996.1  tyrosine-protein phosphatase non-receptor type 13 isoform X12

    14. XM_047416044.1XP_047272000.1  tyrosine-protein phosphatase non-receptor type 13 isoform X16

    15. XM_047416043.1XP_047271999.1  tyrosine-protein phosphatase non-receptor type 13 isoform X15

    16. XM_047416045.1XP_047272001.1  tyrosine-protein phosphatase non-receptor type 13 isoform X17

    17. XM_047416047.1XP_047272003.1  tyrosine-protein phosphatase non-receptor type 13 isoform X19

    18. XM_047416046.1XP_047272002.1  tyrosine-protein phosphatase non-receptor type 13 isoform X18

    19. XM_047416048.1XP_047272004.1  tyrosine-protein phosphatase non-receptor type 13 isoform X20

    20. XM_047416036.1XP_047271992.1  tyrosine-protein phosphatase non-receptor type 13 isoform X6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      89923800..90144654
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054350640.1XP_054206615.1  tyrosine-protein phosphatase non-receptor type 13 isoform X1

    2. XM_054350641.1XP_054206616.1  tyrosine-protein phosphatase non-receptor type 13 isoform X2

    3. XM_054350642.1XP_054206617.1  tyrosine-protein phosphatase non-receptor type 13 isoform X3

    4. XM_054350644.1XP_054206619.1  tyrosine-protein phosphatase non-receptor type 13 isoform X5

    5. XM_054350643.1XP_054206618.1  tyrosine-protein phosphatase non-receptor type 13 isoform X4

    6. XM_054350646.1XP_054206621.1  tyrosine-protein phosphatase non-receptor type 13 isoform X8

    7. XM_054350651.1XP_054206626.1  tyrosine-protein phosphatase non-receptor type 13 isoform X13

    8. XM_054350648.1XP_054206623.1  tyrosine-protein phosphatase non-receptor type 13 isoform X10

    9. XM_054350645.1XP_054206620.1  tyrosine-protein phosphatase non-receptor type 13 isoform X7

    10. XM_054350649.1XP_054206624.1  tyrosine-protein phosphatase non-receptor type 13 isoform X11

    11. XM_054350647.1XP_054206622.1  tyrosine-protein phosphatase non-receptor type 13 isoform X9

    12. XM_054350652.1XP_054206627.1  tyrosine-protein phosphatase non-receptor type 13 isoform X14

    13. XM_054350650.1XP_054206625.1  tyrosine-protein phosphatase non-receptor type 13 isoform X12

    14. XM_054350654.1XP_054206629.1  tyrosine-protein phosphatase non-receptor type 13 isoform X16

    15. XM_054350653.1XP_054206628.1  tyrosine-protein phosphatase non-receptor type 13 isoform X15

    16. XM_054350655.1XP_054206630.1  tyrosine-protein phosphatase non-receptor type 13 isoform X17

    17. XM_054350657.1XP_054206632.1  tyrosine-protein phosphatase non-receptor type 13 isoform X19

    18. XM_054350656.1XP_054206631.1  tyrosine-protein phosphatase non-receptor type 13 isoform X18

    19. XM_054350658.1XP_054206633.1  tyrosine-protein phosphatase non-receptor type 13 isoform X20