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

Gene ID: 5780, updated on 2-Nov-2024

Summary

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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

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See PTPN9 in Genome Data Viewer
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_000015.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 1822 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6667 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:75660721-75661253 Neighboring gene nei like DNA glycosylase 1 Neighboring gene mannosidase alpha class 2C member 1 Neighboring gene SIN3 transcription regulator family member A Neighboring gene ribosomal protein L13 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6668 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:75742449-75743368 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6670 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9853 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:75744915-75745446 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:75745447-75745979 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9855 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9856 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6671 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9857 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6672 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9858 Neighboring gene Sharpr-MPRA regulatory region 2587 Neighboring gene uncharacterized LOC105370902 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:75797079-75797864 Neighboring gene small nuclear ribonucleoprotein F-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6673 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:75871223-75871821 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6675 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9859 Neighboring gene snurportin 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6676 Neighboring gene IMP U3 small nucleolar ribonucleoprotein 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. Low MEG2 expression is associated with metastasis of hepatocellular carcinoma.
    Title: MEG2 inhibits the growth and metastasis of hepatocellular carcinoma by inhibiting AKT pathway.
  8. 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.
  9. 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.
  10. 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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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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
Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
EBI GWAS Catalog

Variation

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See Variation Viewer (GRCh37.p13)

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

Potential readthrough

Included gene: SNUPN

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables non-membrane spanning protein tyrosine phosphatase activity TAS
Traceable Author Statement
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 
Process Evidence Code Pubs
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

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)

  1. 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

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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    75463251..75579315 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    73333337..73450019 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P43378.1 GenPept UniProtKB/Swiss-Prot:P43378

Gene LinkOut

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