PTPN9 protein tyrosine phosphatase non-receptor type 9 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PTPN9provided by HGNC
Official Full Name: protein tyrosine phosphatase non-receptor type 9provided by HGNC
Primary source: HGNC:HGNC:9661
See related: Ensembl:ENSG00000169410 MIM:600768; AllianceGenome:HGNC:9661
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: MEG2; PTPMEG2
Summary: The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP contains an N-terminal domain that shares a significant similarity with yeast SEC14, which is a protein that has phosphatidylinositol transfer activity and is required for protein secretion through the Golgi complex in yeast. This PTP was found to be activated by polyphosphoinositide, and is thought to be involved in signaling events regulating phagocytosis. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in thyroid (RPKM 22.0), small intestine (RPKM 10.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 15q24.2

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (75463251..75579315, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (73333337..73450019, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (75755592..75871656, complement)

Chromosome 15 - NC_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The binding of PKCepsilon and MEG2 to STAT3 regulates IL-6-mediated microglial hyperalgesia during inflammatory pain.
Title: The binding of PKCε and MEG2 to STAT3 regulates IL-6-mediated microglial hyperalgesia during inflammatory pain.
Signature of miR-21 and MEG-2 and their correlation with TGF-beta signaling in breast cancer.
Title: Signature of miR-21 and MEG-2 and their correlation with TGF-β signaling in breast cancer.
CircMMD_007 promotes oncogenic effects in the progression of lung adenocarcinoma through microRNA-197-3p/protein tyrosine phosphatase non-receptor type 9 axis.
Title: CircMMD_007 promotes oncogenic effects in the progression of lung adenocarcinoma through microRNA-197-3p/protein tyrosine phosphatase non-receptor type 9 axis.
PTPN9-mediated dephosphorylation of VTI1B promotes ATG16L1 precursor fusion and autophagosome formation.
Title: PTPN9-mediated dephosphorylation of VTI1B promotes ATG16L1 precursor fusion and autophagosome formation.
Effect of L3MBTL3/PTPN9 polymorphisms on risk to alcohol-induced ONFH in Chinese Han population.
Title: Effect of L3MBTL3/PTPN9 polymorphisms on risk to alcohol-induced ONFH in Chinese Han population.
The Critical Role of the miR-21-MEG2 Axis in Colorectal Cancer.
Title: The Critical Role of the miR-21-MEG2 Axis in Colorectal Cancer.
Low MEG2 expression is associated with metastasis of hepatocellular carcinoma.
Title: MEG2 inhibits the growth and metastasis of hepatocellular carcinoma by inhibiting AKT pathway.
Results from a study on gene expression variability markers in early-stage human embryos shows that PTPN9 is a putative expression variability marker for the 3-day, 8-cell embryo stage.
Title: Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development.
this study highlights an important role for miR-96 in the regulation of PTPN9 in breast cancer cells and may provide insight into the molecular mechanisms of breast carcinogenesis.
Title: miR-96 promotes cell proliferation, migration and invasion by targeting PTPN9 in breast cancer.
Expression of MEG2 is reversely correlated with that of miR-181a-5p in gastric cancer.
Title: MEG2 is regulated by miR-181a-5p and functions as a tumour suppressor gene to suppress the proliferation and migration of gastric cancer cells.

Submit: New GeneRIF Correction See all GeneRIFs (20)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Screening in Jurkat T-cells with a short-hairpin-RNA (shRNA) library identifies PTPN9/PTP-MEG2, a member of the protein tyrosine phosphatase family, is important for HIV-1 replication	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G32986 (e-PCR)
- UniSTS:117563

PTPN9_399 (e-PCR)
- UniSTS:277625

G10644 (e-PCR)
- UniSTS:62081

WI-7786 (e-PCR)
- UniSTS:23939

A009Y26 (e-PCR)
- UniSTS:7603

G17833 (e-PCR)
- UniSTS:11962

RH77799 (e-PCR)
- UniSTS:4283

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables histone H2AXY142 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables non-membrane spanning protein tyrosine phosphatase activity	IEA Inferred from Electronic Annotation more info
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, metal-dependent	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of neuron projection development	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within peptidyl-tyrosine dephosphorylation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of protein localization to plasma membrane	IDA Inferred from Direct Assay more info	PubMed
involved_in protein dephosphorylation	TAS Traceable Author Statement more info	PubMed
involved_in signal transduction	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in neuron projection terminus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info

General protein information

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Preferred Names: tyrosine-protein phosphatase non-receptor type 9

Names: PTPase-MEG2; protein-tyrosine phosphatase MEG2

NP_002824.1

EC 3.1.3.48

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

NM_002833.4 → NP_002824.1 tyrosine-protein phosphatase non-receptor type 9

See identical proteins and their annotated locations for NP_002824.1

Status: REVIEWED

Source sequence(s)

AC105036, AC105137, BC071574, M83738

Consensus CDS

CCDS10280.1

UniProtKB/Swiss-Prot

P43378, Q53XR9

UniProtKB/TrEMBL

Q6IQ43

Related

ENSP00000482732.1, ENST00000618819.5

Conserved Domains (3) summary

smart00516
Location:90 → 240

SEC14; Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p)

smart01100
Location:20 → 68

CRAL_TRIO_N; CRAL/TRIO, N-terminal domain

cd14543
Location:299 → 569

PTPc-N9; catalytic domain of tyrosine-protein phosphatase non-receptor type 9