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PTPN6 protein tyrosine phosphatase non-receptor type 6 [ Homo sapiens (human) ]

Gene ID: 5777, updated on 6-Jun-2024

Summary

Official Symbol
PTPN6provided by HGNC
Official Full Name
protein tyrosine phosphatase non-receptor type 6provided by HGNC
Primary source
HGNC:HGNC:9658
See related
Ensembl:ENSG00000111679 MIM:176883; AllianceGenome:HGNC:9658
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
HCP; HCPH; SHP1; SHP-1; HPTP1C; PTP-1C; SHP-1L; SH-PTP1
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. N-terminal part of this PTP contains two tandem Src homolog (SH2) domains, which act as protein phospho-tyrosine binding domains, and mediate the interaction of this PTP with its substrates. This PTP is expressed primarily in hematopoietic cells, and functions as an important regulator of multiple signaling pathways in hematopoietic cells. This PTP has been shown to interact with, and dephosphorylate a wide spectrum of phospho-proteins involved in hematopoietic cell signaling. Multiple alternatively spliced variants of this gene, which encode distinct isoforms, have been reported. [provided by RefSeq, Jul 2008]
Expression
Broad expression in spleen (RPKM 76.2), lymph node (RPKM 74.9) and 19 other tissues See more
Orthologs
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Genomic context

See PTPN6 in Genome Data Viewer
Location:
12p13.31
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (6946577..6961316)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (6957743..6974790)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (7055740..7070479)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902868 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7033606-7034306 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7035007-7035706 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4193 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4194 Neighboring gene atrophin 1 Neighboring gene atrophin 1 repeat instability region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4195 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr12:7052993-7053572 and GRCh37_chr12:7053573-7054152 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7054402-7055012 Neighboring gene chromosome 12 open reading frame 57 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7055013-7055621 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4196 Neighboring gene RNA, U7 small nuclear 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:7059817-7060752 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7060753-7061686 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7061687-7062621 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5897 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5898 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5899 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5901 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5903 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5906 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5907 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5908 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7069919-7070720 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7070721-7071520 Neighboring gene uncharacterized LOC105369634 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7071521-7072322 Neighboring gene MIR200C and MIR141 host gene Neighboring gene microRNA 200c

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?

HIV-1 interactions

Replication interactions

Interaction Pubs
Monocyte derived dendritic cells from HIV-infected clinical samples upregulate PTPN6 (SHP-1) expression PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables SH2 domain binding IEA
Inferred from Electronic Annotation
more info
 
enables SH3 domain binding IEA
Inferred from Electronic Annotation
more info
 
enables cell adhesion molecule binding IEA
Inferred from Electronic Annotation
more info
 
enables non-membrane spanning protein tyrosine phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables phosphorylation-dependent protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables phosphotyrosine residue binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables phosphotyrosine residue binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables phosphotyrosine residue binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein tyrosine phosphatase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables protein tyrosine phosphatase activity TAS
Traceable Author Statement
more info
 
enables transmembrane receptor protein tyrosine phosphatase activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in B cell receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in G protein-coupled receptor signaling pathway TAS
Traceable Author Statement
more info
PubMed 
involved_in MAPK cascade IEA
Inferred from Electronic Annotation
more info
 
involved_in T cell costimulation TAS
Traceable Author Statement
more info
 
involved_in T cell proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in T cell receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cytokine-mediated signaling pathway TAS
Traceable Author Statement
more info
 
involved_in epididymis development IEA
Inferred from Electronic Annotation
more info
 
involved_in hematopoietic progenitor cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in intracellular signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in megakaryocyte development IEA
Inferred from Electronic Annotation
more info
 
involved_in mitotic cell cycle IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in natural killer cell mediated cytotoxicity IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of MAPK cascade IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of T cell proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of T cell receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of angiogenesis IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of cell population proliferation NAS
Non-traceable Author Statement
more info
PubMed 
involved_in negative regulation of humoral immune response mediated by circulating immunoglobulin IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of inflammatory response to wounding IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of interleukin-6 production ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of mast cell activation involved in immune response IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of peptidyl-tyrosine phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of tumor necrosis factor production ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in peptidyl-tyrosine dephosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in peptidyl-tyrosine dephosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in peptidyl-tyrosine phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in platelet aggregation IEA
Inferred from Electronic Annotation
more info
 
involved_in platelet formation IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of cell adhesion mediated by integrin IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of cell population proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in protein dephosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of B cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of ERK1 and ERK2 cascade IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of G1/S transition of mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of apoptotic process TAS
Traceable Author Statement
more info
PubMed 
involved_in regulation of release of sequestered calcium ion into cytosol IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of type I interferon-mediated signaling pathway TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
part_of alpha-beta T cell receptor complex IEA
Inferred from Electronic Annotation
more info
 
located_in cell-cell junction 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 cytosol TAS
Traceable Author Statement
more info
 
located_in extracellular exosome HDA PubMed 
located_in extracellular region TAS
Traceable Author Statement
more info
 
located_in membrane TAS
Traceable Author Statement
more info
PubMed 
located_in nucleolus IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
part_of protein-containing complex IMP
Inferred from Mutant Phenotype
more info
PubMed 
located_in specific granule lumen TAS
Traceable Author Statement
more info
 
located_in tertiary granule lumen TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
tyrosine-protein phosphatase non-receptor type 6
Names
hematopoietic cell phosphatase
hematopoietic cell protein-tyrosine phosphatase
protein-tyrosine phosphatase 1C
protein-tyrosine phosphatase SHP-1
NP_002822.2
NP_536858.1
NP_536859.1
XP_011519290.1
XP_024304874.1
XP_047285187.1
XP_047285188.1
XP_054228689.1
XP_054228690.1
XP_054228691.1
XP_054228692.1
XP_054228693.1

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.

mRNA and Protein(s)

  1. NM_002831.6NP_002822.2  tyrosine-protein phosphatase non-receptor type 6 isoform 1

    See identical proteins and their annotated locations for NP_002822.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript and encodes the shortest isoform (1, also known as SHP-1).
    Source sequence(s)
    U47924
    Consensus CDS
    CCDS44820.1
    UniProtKB/Swiss-Prot
    A8K306, G3V0F8, P29350, Q969V8, Q9UK67
    UniProtKB/TrEMBL
    Q53EL0
    Related
    ENSP00000326010.9, ENST00000318974.14
    Conserved Domains (3) summary
    cd09931
    Location:109215
    SH2_C-SH2_SHP_like; C-terminal Src homology 2 (C-SH2) domain found in SH2 domain Phosphatases (SHP) proteins
    cd10340
    Location:3101
    SH2_N-SH2_SHP_like; N-terminal Src homology 2 (N-SH2) domain found in SH2 domain Phosphatases (SHP) proteins
    cd14606
    Location:253518
    PTPc-N6; catalytic domain of tyrosine-protein phosphatase non-receptor type 6
  2. NM_080548.5NP_536858.1  tyrosine-protein phosphatase non-receptor type 6 isoform 2

    See identical proteins and their annotated locations for NP_536858.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate 5' terminal exon compared to transcript variant 1, resulting in an isoform (2) with a distinct and longer (by 2 aa) N-terminus, compared to isoform 1.
    Source sequence(s)
    U47924
    Consensus CDS
    CCDS41744.1
    UniProtKB/TrEMBL
    Q53EL0, Q53XS4
    Related
    ENSP00000382376.1, ENST00000399448.5
    Conserved Domains (3) summary
    cd09931
    Location:111217
    SH2_C-SH2_SHP_like; C-terminal Src homology 2 (C-SH2) domain found in SH2 domain Phosphatases (SHP) proteins
    cd10340
    Location:6103
    SH2_N-SH2_SHP_like; N-terminal Src homology 2 (N-SH2) domain found in SH2 domain Phosphatases (SHP) proteins
    cd00047
    Location:274516
    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_080549.4NP_536859.1  tyrosine-protein phosphatase non-receptor type 6 isoform 3

    See identical proteins and their annotated locations for NP_536859.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate 5' terminal exon, and an alternate acceptor splice site at the penultimate exon, compared to transcript variant 1, resulting in a longer isoform (3, also known as 70 kDa SHP-1L protein) with distinct N_ and C_ termini, compared to isoform 1.
    Source sequence(s)
    U47924
    Consensus CDS
    CCDS44821.1
    UniProtKB/TrEMBL
    Q53EL0
    Related
    ENSP00000391592.1, ENST00000456013.5
    Conserved Domains (4) summary
    cd09931
    Location:109215
    SH2_C-SH2_SHP_like; C-terminal Src homology 2 (C-SH2) domain found in SH2 domain Phosphatases (SHP) proteins
    cd10340
    Location:3101
    SH2_N-SH2_SHP_like; N-terminal Src homology 2 (N-SH2) domain found in SH2 domain Phosphatases (SHP) proteins
    smart00194
    Location:243514
    PTPc; Protein tyrosine phosphatase, catalytic domain
    cd00047
    Location:272514
    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 ...

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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    6946577..6961316
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011520988.2XP_011519290.1  tyrosine-protein phosphatase non-receptor type 6 isoform X1

    See identical proteins and their annotated locations for XP_011519290.1

    UniProtKB/TrEMBL
    Q53EL0, Q53XS4
    Conserved Domains (3) summary
    cd09931
    Location:111217
    SH2_C-SH2_SHP_like; C-terminal Src homology 2 (C-SH2) domain found in SH2 domain Phosphatases (SHP) proteins
    cd10340
    Location:6103
    SH2_N-SH2_SHP_like; N-terminal Src homology 2 (N-SH2) domain found in SH2 domain Phosphatases (SHP) proteins
    cd00047
    Location:274516
    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. XM_047429231.1XP_047285187.1  tyrosine-protein phosphatase non-receptor type 6 isoform X3

    UniProtKB/TrEMBL
    Q53EL0
  3. XM_024449106.1XP_024304874.1  tyrosine-protein phosphatase non-receptor type 6 isoform X2

    UniProtKB/Swiss-Prot
    A8K306, G3V0F8, P29350, Q969V8, Q9UK67
    UniProtKB/TrEMBL
    Q53EL0
    Conserved Domains (3) summary
    cd09931
    Location:109215
    SH2_C-SH2_SHP_like; C-terminal Src homology 2 (C-SH2) domain found in SH2 domain Phosphatases (SHP) proteins
    cd10340
    Location:3101
    SH2_N-SH2_SHP_like; N-terminal Src homology 2 (N-SH2) domain found in SH2 domain Phosphatases (SHP) proteins
    cd14606
    Location:253518
    PTPc-N6; catalytic domain of tyrosine-protein phosphatase non-receptor type 6
  4. XM_047429232.1XP_047285188.1  tyrosine-protein phosphatase non-receptor type 6 isoform X4

    UniProtKB/TrEMBL
    Q53EL0

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    6957743..6974790
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054372714.1XP_054228689.1  tyrosine-protein phosphatase non-receptor type 6 isoform X1

    UniProtKB/TrEMBL
    Q53EL0, Q53XS4
  2. XM_054372716.1XP_054228691.1  tyrosine-protein phosphatase non-receptor type 6 isoform X3

    UniProtKB/TrEMBL
    Q53EL0
  3. XM_054372715.1XP_054228690.1  tyrosine-protein phosphatase non-receptor type 6 isoform X2

    UniProtKB/Swiss-Prot
    A8K306, G3V0F8, P29350, Q969V8, Q9UK67
    UniProtKB/TrEMBL
    Q53EL0
  4. XM_054372717.1XP_054228692.1  tyrosine-protein phosphatase non-receptor type 6 isoform X4

    UniProtKB/TrEMBL
    Q53EL0
  5. XM_054372718.1XP_054228693.1  tyrosine-protein phosphatase non-receptor type 6 isoform X5

    UniProtKB/TrEMBL
    B4DTD7