PTPN13 protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase) [Homo sapiens] - Gene

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Summary

Official Symbol: PTPN13provided by HGNC
Official Full Name: protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)provided by HGNC
Primary source: HGNC:9646
See related: Ensembl:ENSG00000163629; HPRD:02602; 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; DKFZp686J1497
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]

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Genomic context

Location :: 4q21.3

Sequence :: Chromosome: 4; NC_000004.11 (87515468..87736329)

See PTPN13 in Epigenomics, MapViewer

Chromosome 4 - NC_000004.11 Genomic Context describing neighboring genes

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Genomic regions, transcripts, and products

Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

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Bibliography

GeneRIFs: Gene References Into Functions What's a GeneRIF?

interaction between Tel and Tel-PdgfRbeta decreases Tel/Icsbp/Hdac3 binding to the PTPN13 cis element, resulting in increased transcription.
Title: The leukemia-associated fusion protein Tel-platelet-derived growth factor receptor β (Tel-PdgfRβ) inhibits transcriptional repression of PTPN13 gene by interferon consensus sequence binding protein (Icsbp).
The PTPL1 is an important mediator of central cellular processes such as proliferation and invasion.
Title: Downregulation of protein tyrosine phosphatase PTPL1 alters cell cycle and upregulates invasion-related genes in prostate cancer cells.
The Ret oncoprotein exerts opposing controls on Fap-1 and CD95, increasing Fap-1 expression and decreasing CD95 cell surface expression.
Title: Interplay between Ret and Fap-1 regulates CD95-mediated apoptosis in medullary thyroid cancer cells.
REVIEW: the alterations in expression and the genetic and epigenetic arguments supporting an oncogenic or an anti-oncogenic impact of PTPL1
Title: PTPN13/PTPL1: an important regulator of tumor aggressiveness.
X-ray crystal structures of PDZ2 in the absence and presence of RA-GEF2 ligand; very minor structural changes in PDZ2 accompany peptide binding
Title: Crystallographic and nuclear magnetic resonance evaluation of the impact of peptide binding to the second PDZ domain of protein tyrosine phosphatase 1E.
FAP-1 was demonstrated to be responsible for the reduced sensitivity to CD95-mediated apoptosis in cells with inhibited miR-200.
Title: miR-200c regulates induction of apoptosis through CD95 by targeting FAP-1.
PTPL1 regulates breast cancer cell aggressiveness through direct inactivation of Src kinase.
Title: PTPL1/PTPN13 regulates breast cancer cell aggressiveness through direct inactivation of Src kinase.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Transfection of FAP-1 siRNA into SW480 cells silenced the expression of FAP-1 and consequently abolished the inhibitory function of Fas/FasL-mediated apoptosis pathway, thus increasing the efficacy of chemotherapy for colon carcinoma with oxaliplatin.
Title: Silencing Fas-associated phosphatase 1 expression enhances efficiency of chemotherapy for colon carcinoma with oxaliplatin.
PTPN13 SNPs were found to influence susceptibility to a wide spectrum of cancers.
Title: Missense polymorphisms of PTPRJ and PTPN13 genes affect susceptibility to a variety of human cancers.

Submit: New GeneRIF Correction See all (37)

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Phenotypes

Review eQTL and phenotype association data in this region using PheGenI

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Products	Interactant	Other Gene	Source	Pubs	Description
NC_000004.9	AAK11227.1		BIND	PubMed	EWS-FLI1 interacts with the PTPN13 (PTPL1) promoter.
Q12923	P25054	APC	HPRD	PubMed
Q12923	PARG1	ARHGAP29	HPRD	PubMed
Q12923	Bromodomain containing 7	BRD7	HPRD	PubMed
Q12923	P52943	CRIP2	HPRD	PubMed
Q12923	P35222	CTNNB1	HPRD	PubMed
Q12923	P98172	EFNB1	HPRD	PubMed
Q12923	P52799	EFNB2	HPRD	PubMed
Q12923	Q13158	FADD	HPRD	PubMed
Q12923	P25445	FAS	HPRD	PubMed
Q12923	P48023	FASLG	HPRD	PubMed
Q12923	P25963	NFKBIA	HPRD	PubMed
Q12923	P08138	NGFR	HPRD	PubMed
Q12923	Q00994	NGFRAP1	HPRD	PubMed
Q12923	P50479	PDLIM4	HPRD	PubMed
Q12923	Q16513	PKN2	HPRD	PubMed
Q12923	Q9HB21	PLEKHA1	HPRD	PubMed
Q12923	P17612	PRKACA	HPRD	PubMed
Q12923	Q8TEU7	RAPGEF6	HPRD	PubMed
Q12923	Q15654	TRIP6	HPRD	PubMed
Q12923	P63104	YWHAZ	HPRD	PubMed
BioGRID:111747	BioGRID:114806	ARHGAP29	BioGRID	PubMed	Reconstituted Complex
BioGRID:111747	BioGRID:246393	Apc	BioGRID	PubMed	Affinity Capture-Western; Reconstituted Complex; Two-hybrid
BioGRID:111747	BioGRID:107880	CTNNB1	BioGRID	PubMed	Biochemical Activity
BioGRID:111747	BioGRID:108267	EFNB1	BioGRID	PubMed	Reconstituted Complex
BioGRID:111747	BioGRID:106852	FASLG	BioGRID	PubMed	Reconstituted Complex
BioGRID:111747	BioGRID:108957	GHR	BioGRID	PubMed	Far Western
BioGRID:111747	BioGRID:110859	NFKBIA	BioGRID	PubMed	Reconstituted Complex
BioGRID:111747	BioGRID:111572	PKN2	BioGRID	PubMed	Affinity Capture-Western; Reconstituted Complex; Two-hybrid
BioGRID:111747	BioGRID:113164	UBC	BioGRID	PubMed	Affinity Capture-MS; Reconstituted Complex

Function	Evidence Code	Pubs
hydrolase activity	IEA Inferred from Electronic Annotation more info
protein binding	IPI Inferred from Physical Interaction more info	PubMed
protein tyrosine phosphatase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
peptidyl-tyrosine dephosphorylation	IDA Inferred from Direct Assay more info	PubMed
peptidyl-tyrosine dephosphorylation	TAS Traceable Author Statement more info	PubMed
protein dephosphorylation	TAS Traceable Author Statement 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
lamellipodium	IDA Inferred from Direct Assay more info	PubMed
neuron projection	IEA Inferred from Electronic Annotation more info
nucleus	IDA Inferred from Direct Assay more info	PubMed
plasma membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

Preferred Names: tyrosine-protein phosphatase non-receptor type 13

Names: tyrosine-protein phosphatase non-receptor type 13; hPTPE1; protein-tyrosine phosphatase 1E; protein-tyrosine phosphatase PTPL1; fas-associated protein-tyrosine phosphatase 1

NP_006255.1

EC 3.1.3.48

NP_542414.1

EC 3.1.3.48

NP_542415.1

EC 3.1.3.48

NP_542416.1

EC 3.1.3.48

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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

NG_029704.1 RefSeqGene

Range

5001..225862

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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, OTTHUMP00000219449, ENST00000427191, OTTHUMT00000363189

Conserved Domains (8) summary

cd00047
Location:2220 – 2447
Blast Score: 753

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:1072 – 1156
Blast Score: 207

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) ...

cd00836
Location:776 – 869
Blast Score: 206

FERM_C; FERM_C domain

smart00194
Location:2195 – 2447
Blast Score: 860

PTPc; Protein tyrosine phosphatase, catalytic domain

smart00295
Location:573 – 781
Blast Score: 415

B41; Band 4.1 homologues

pfam00373
Location:670 – 781
Blast Score: 295

FERM_M; FERM central domain

pfam09379
Location:576 – 664
Blast Score: 220

FERM_N; FERM N-terminal domain

cl09925
Location:3 – 190
Blast Score: 436

PKc_like; Protein Kinases, catalytic domain
NM_080683.2 → NP_542414.1 tyrosine-protein phosphatase non-receptor type 13 isoform 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, OTTHUMP00000219451, ENST00000411767, OTTHUMT00000363191

Conserved Domains (8) summary

cd00047
Location:2239 – 2466
Blast Score: 753

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:1091 – 1175
Blast Score: 207

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) ...

cd00836
Location:776 – 869
Blast Score: 207

FERM_C; FERM_C domain

smart00194
Location:2214 – 2466
Blast Score: 860

PTPc; Protein tyrosine phosphatase, catalytic domain

smart00295
Location:573 – 781
Blast Score: 416

B41; Band 4.1 homologues

pfam00373
Location:670 – 781
Blast Score: 295

FERM_M; FERM central domain

pfam09379
Location:576 – 664
Blast Score: 221

FERM_N; FERM N-terminal domain

cl09925
Location:3 – 190
Blast Score: 436

PKc_like; Protein Kinases, catalytic domain
NM_080684.2 → NP_542415.1 tyrosine-protein phosphatase non-receptor type 13 isoform 3

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, OTTHUMP00000219450, ENST00000316707, OTTHUMT00000363190

Conserved Domains (8) summary

cd00047
Location:2048 – 2275
Blast Score: 751

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:900 – 984
Blast Score: 206

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) ...

cd00836
Location:776 – 869
Blast Score: 205

FERM_C; FERM_C domain

smart00194
Location:2023 – 2275
Blast Score: 857

PTPc; Protein tyrosine phosphatase, catalytic domain

smart00295
Location:573 – 781
Blast Score: 415

B41; Band 4.1 homologues

pfam00373
Location:670 – 781
Blast Score: 295

FERM_M; FERM central domain

pfam09379
Location:576 – 664
Blast Score: 219

FERM_N; FERM N-terminal domain

cl09925
Location:3 – 190
Blast Score: 438

PKc_like; Protein Kinases, catalytic domain
NM_080685.2 → NP_542416.1 tyrosine-protein phosphatase non-receptor type 13 isoform 4

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, ENST00000436978

Conserved Domains (8) summary

cd00047
Location:2244 – 2471
Blast Score: 753

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:1091 – 1175
Blast Score: 207

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) ...

cd00836
Location:776 – 869
Blast Score: 206

FERM_C; FERM_C domain

smart00194
Location:2219 – 2471
Blast Score: 860

PTPc; Protein tyrosine phosphatase, catalytic domain

smart00295
Location:573 – 781
Blast Score: 416

B41; Band 4.1 homologues

pfam00373
Location:670 – 781
Blast Score: 295

FERM_M; FERM central domain

pfam09379
Location:576 – 664
Blast Score: 221

FERM_N; FERM N-terminal domain

cl09925
Location:3 – 190
Blast Score: 436

PKc_like; Protein Kinases, catalytic domain

RefSeqs of Annotated Genomes: Build 37.3

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

Reference GRCh37.p5 Primary Assembly

Genomic

NC_000004.11 Reference GRCh37.p5 Primary Assembly

Range

87515468..87736329

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000136.1 Alternate HuRef

Range

83259993..83481272

Download

GenBank, FASTA, Sequence Viewer (Graphics)

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Related Sequences

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	AC097657.3	None
genomic	AC105413.3	AAY40972.1
genomic	AC110076.4 (94321..103210)	None
genomic	AF101267.1	None
genomic	CH471057.1	EAX05965.1
		EAX05966.1
		EAX05967.1
		EAX05968.1
genomic	JA362582.1	CCA94573.1
mRNA	AB208904.1	BAD92141.1
mRNA	AF233323.1	AAF63474.1
mRNA	AK056151.1	None
mRNA	BC039610.1	AAH39610.1
mRNA	BC139915.1	None
mRNA	BC140777.1	AAI40778.1
mRNA	BC144520.1	None
mRNA	BG202767.1	None
mRNA	BX647553.1	CAH10380.1
mRNA	D21209.1	BAA04750.1
mRNA	D21210.1	BAA04751.1
mRNA	D21211.1	BAA04752.1
mRNA	DA625835.1	None
mRNA	L34583.1	AAC41755.1
mRNA	U12128.1	AAB60339.1
mRNA	U12129.1	None
mRNA	U12131.1	None
mRNA	U12132.1	None
mRNA	X79676.1	CAA56124.1
mRNA	X80289.1	CAA56563.1

Protein Accession	Links
Protein Accession	GenPept Link	UniProtKB Link
Q12923.2	GenPept	UniProtKB/Swiss-Prot:Q12923
Q4W5F5	GenPept	UniProtKB/TrEMBL:Q4W5F5
Q59H55	GenPept	UniProtKB/TrEMBL:Q59H55
Q6AWB9	GenPept	UniProtKB/TrEMBL:Q6AWB9