U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 5783, updated on 7-Apr-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

Location:
4q21.3
Exon count:
49
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (86594315..86815161)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (89923800..90144654)
105.20220307 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
  • 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_2023_10

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