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    PTPN7 protein tyrosine phosphatase non-receptor type 7 [ Homo sapiens (human) ]

    Gene ID: 5778, updated on 14-Nov-2024

    Summary

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    Official Symbol
    PTPN7provided by HGNC
    Official Full Name
    protein tyrosine phosphatase non-receptor type 7provided by HGNC
    Primary source
    HGNC:HGNC:9659
    See related
    Ensembl:ENSG00000143851 MIM:176889; AllianceGenome:HGNC:9659
    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
    LPTP; HEPTP; PTPNI; BPTP-4; LC-PTP
    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 gene is preferentially expressed in a variety of hematopoietic cells, and is an early response gene in lymphokine stimulated cells. The non-catalytic N-terminus of this PTP can interact with MAP kinases and suppress the MAP kinase activities. This PTP was shown to be involved in the regulation of T cell antigen receptor (TCR) signaling, which was thought to function through dephosphorylating the molecules related to MAP kinase pathway. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2010]
    Expression
    Biased expression in bone marrow (RPKM 19.6), lymph node (RPKM 18.1) and 11 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PTPN7 in Genome Data Viewer
    Location:
    1q32.1
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (202147013..202161588, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (201404580..201419169, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (202116141..202130716, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371683 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202099011-202099794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202099795-202100578 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:202104477-202104684 Neighboring gene G protein-coupled receptor 37 like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1697 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1698 Neighboring gene ARF like GTPase 8A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1699 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2327 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2329 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202132551-202133219 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202133799-202134299 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202134943-202135522 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202152613-202153112 Neighboring gene protein tyrosine phosphatase receptor type V, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202153807-202154336 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202154337-202154866 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1700 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:202161513-202162316 Neighboring gene small nucleolar RNA U13 Neighboring gene leucine rich repeat containing G protein-coupled receptor 6

    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. PTPN7 regulates platelet functional responses downstream of GPCR agonists, but not GPVI agonists, through inhibition of ERK activation and thromboxane generation.
      Title: The protein tyrosine phosphatase PTPN7 is a negative regulator of ERK activation and thromboxane generation in platelets.
    2. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants that affect length/height in infancy/early childhood in Vietnamese-Korean families.
    3. Interactions at the active site between KIM (kinase interaction motif)-phosphatases and their substrates are predominantly nonspecific, with the majority of the KIM-phosphatase residues coordinating the peptide backbone rather than residue side chains.
      Title: Structural basis of substrate recognition by hematopoietic tyrosine phosphatase.
    4. structure of the protein tyrosine phosphatase catalytic domain of HePTP, residues 44-339
      Title: Structure of the hematopoietic tyrosine phosphatase (HePTP) catalytic domain: structure of a KIM phosphatase with phosphate bound at the active site.
    5. determined high-resolution structures of all of the human family members of Mitogen-Activated Protein Kinase-specific protein tyrosine phosphatases
      Title: Crystal structures and inhibitor identification for PTPN5, PTPRR and PTPN7: a family of human MAPK-specific protein tyrosine phosphatases.
    Submit: New GeneRIF Correction

    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
    Genome-wide association studies identify four ER negative-specific breast cancer risk loci.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ18703

    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 TAS
    Traceable Author Statement
    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, metal-dependent IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in MAPK cascade TAS
    Traceable Author Statement
    more info
    		  
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 cytoplasmic side of plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in microtubule cytoskeleton IDA
    Inferred from Direct Assay
    more info
    		  
    located_in mitotic spindle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    tyrosine-protein phosphatase non-receptor type 7
    Names
    dual specificity phosphatase 1
    hematopoietic protein-tyrosine phosphatase
    protein-tyrosine phosphatase LC-PTP
    protein-tyrosine phosphatase, nonreceptor-type, stress induced
    NP_001186726.1
    NP_001351806.1
    NP_001351807.1
    NP_002823.4
    NP_542155.1
    XP_011508121.1
    XP_011508122.1
    XP_011508125.1
    XP_047282252.1
    XP_047282253.1
    XP_047282262.1
    XP_054193897.1
    XP_054193898.1
    XP_054193899.1
    XP_054193900.1
    XP_054193901.1
    XP_054193902.1

    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_001199797.2 → NP_001186726.1  tyrosine-protein phosphatase non-receptor type 7 isoform 3

      See identical proteins and their annotated locations for NP_001186726.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks a segment in the 5' region, resulting in an upstream AUG start codon, as compared to variant 1. The resulting isoform (3) has a shorter and distinct N-terminus, as compared to isoform 1.
      Source sequence(s)
      AK302869, AL592300, DC399028
      UniProtKB/TrEMBL
      B4DZD9, J3KR55
      Conserved Domains (2) summary
      smart00194
      Location:170 → 422
      PTPc; Protein tyrosine phosphatase, catalytic domain
      cd00047
      Location:196 → 422
      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 ...

    2. NM_001364877.2 → NP_001351806.1  tyrosine-protein phosphatase non-receptor type 7 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AL592300
      UniProtKB/TrEMBL
      B4DVF0
      Conserved Domains (1) summary
      cd00047
      Location:121 → 347
      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 ...

    3. NM_001364878.1 → NP_001351807.1  tyrosine-protein phosphatase non-receptor type 7 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AL592300, BT009848, DC399028
      Consensus CDS
      CCDS1423.3
      UniProtKB/Swiss-Prot
      B3KXE1, P35236, Q53XK4, Q5SXQ0, Q5SXQ1, Q9BV05
      UniProtKB/TrEMBL
      B4DVF0
      Related
      ENSP00000418416.2, ENST00000477554.6
      Conserved Domains (1) summary
      cd14612
      Location:105 → 350
      PTPc-N7; catalytic domain of tyrosine-protein phosphatase non-receptor type 7

    4. NM_002832.4 → NP_002823.4  tyrosine-protein phosphatase non-receptor type 7 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AL592300
      Consensus CDS
      CCDS1423.3
      UniProtKB/Swiss-Prot
      B3KXE1, P35236, Q53XK4, Q5SXQ0, Q5SXQ1, Q9BV05
      UniProtKB/TrEMBL
      B4DVF0
      Related
      ENSP00000509436.1, ENST00000691036.1
      Conserved Domains (1) summary
      cd14612
      Location:105 → 350
      PTPc-N7; catalytic domain of tyrosine-protein phosphatase non-receptor type 7

    5. NM_080588.3 → NP_542155.1  tyrosine-protein phosphatase non-receptor type 7 isoform 2

      See identical proteins and their annotated locations for NP_542155.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an exon from the 5' end and contains an alternate 5' segment which includes an AUG start codon, as compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus, as compared to isoform 1.
      Source sequence(s)
      AL592300, BC001746
      Consensus CDS
      CCDS1422.1
      UniProtKB/TrEMBL
      J3KR55
      Related
      ENSP00000356248.4, ENST00000367279.8
      Conserved Domains (2) summary
      smart00194
      Location:135 → 387
      PTPc; Protein tyrosine phosphatase, catalytic domain
      cd00047
      Location:161 → 387
      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 ...

    RNA

    1. NR_037663.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an internal segment in the CDS, resulting in frame-shift and a premature stop codon, as compared to variant 1. The transcript is a nonsense-mediated mRNA decay candidate, and probably does not make a functional protein.
      Source sequence(s)
      AK301051, AL592300

    2. NR_037664.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks an exon in the CDS, resulting in frame-shift and a premature stop codon, as compared to variant 1. The transcript is a nonsense-mediated mRNA decay candidate, and probably does not make a functional protein.
      Source sequence(s)
      AK293186, AL592300

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      202147013..202161588 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047426297.1 → XP_047282253.1  tyrosine-protein phosphatase non-receptor type 7 isoform X4

    2. XM_047426296.1 → XP_047282252.1  tyrosine-protein phosphatase non-receptor type 7 isoform X3

    3. XM_011509820.3 → XP_011508122.1  tyrosine-protein phosphatase non-receptor type 7 isoform X2

      Conserved Domains (2) summary
      smart00194
      Location:90 → 388
      PTPc; Protein tyrosine phosphatase, catalytic domain
      cd00047
      Location:116 → 388
      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 ...

    4. XM_011509819.2 → XP_011508121.1  tyrosine-protein phosphatase non-receptor type 7 isoform X1

      Related
      ENSP00000309116.5, ENST00000309017.9
      Conserved Domains (2) summary
      smart00194
      Location:201 → 499
      PTPc; Protein tyrosine phosphatase, catalytic domain
      cd00047
      Location:227 → 499
      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 ...

    5. XM_047426306.1 → XP_047282262.1  tyrosine-protein phosphatase non-receptor type 7 isoform X6

    6. XM_011509823.2 → XP_011508125.1  tyrosine-protein phosphatase non-receptor type 7 isoform X5

      Conserved Domains (2) summary
      smart00194
      Location:201 → 307
      PTPc; Protein tyrosine phosphatase, catalytic domain
      cl21483
      Location:227 → 307
      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 ...

    RNA

    1. XR_007062439.1 RNA Sequence

    2. XR_921906.2 RNA Sequence

    3. XR_007062440.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      201404580..201419169 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337924.1 → XP_054193899.1  tyrosine-protein phosphatase non-receptor type 7 isoform X3

    2. XM_054337923.1 → XP_054193898.1  tyrosine-protein phosphatase non-receptor type 7 isoform X2

    3. XM_054337922.1 → XP_054193897.1  tyrosine-protein phosphatase non-receptor type 7 isoform X1

    4. XM_054337927.1 → XP_054193902.1  tyrosine-protein phosphatase non-receptor type 7 isoform X6

    5. XM_054337925.1 → XP_054193900.1  tyrosine-protein phosphatase non-receptor type 7 isoform X4

    6. XM_054337926.1 → XP_054193901.1  tyrosine-protein phosphatase non-receptor type 7 isoform X5

    RNA

    1. XR_008486131.1 RNA Sequence

    2. XR_008486130.1 RNA Sequence

    3. XR_008486132.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_080589.1: Suppressed sequence

      Description
      NM_080589.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P35236.3 GenPept UniProtKB/Swiss-Prot:P35236

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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