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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for PTPN6 |
 Gene summary |
| Gene information | Gene symbol | PTPN6 | Gene ID | 5777 |
| Gene name | protein tyrosine phosphatase non-receptor type 6 | |
| Synonyms | HCP|HCPH|HPTP1C|PTP-1C|SH-PTP1|SHP-1|SHP-1L|SHP1 | |
| Cytomap | 12p13.31 | |
| Type of gene | protein-coding | |
| Description | tyrosine-protein phosphatase non-receptor type 6hematopoietic cell phosphatasehematopoietic cell protein-tyrosine phosphataseprotein-tyrosine phosphatase 1Cprotein-tyrosine phosphatase SHP-1 | |
| Modification date | 20200320 | |
| UniProtAcc | ||
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| PTPN6 | GO:0006470 | protein dephosphorylation | 11266449 |
| PTPN6 | GO:0018108 | peptidyl-tyrosine phosphorylation | 9285411|18802077 |
| PTPN6 | GO:0030154 | cell differentiation | 11266449 |
| PTPN6 | GO:0070372 | regulation of ERK1 and ERK2 cascade | 11266449 |
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Gene structures and expression levels for PTPN6 |
| Skipped exons in the ROSMAP, MSBB, and Mayo based on Ensembl gene isoform structure. * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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ENSG00000111679
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| PG | UP | ENST00000543744.1 | PTPN6-222:retained_intron:PTPN6 | 3.285791e+00 | 1.030611e+00 | 2.969789e-06 | 2.033673e-04 |
| PG | UP | ENST00000542761.5 | PTPN6-218:retained_intron:PTPN6 | 9.669537e-01 | 1.174706e+00 | 4.758176e-04 | 8.520781e-03 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PTPN6 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_150639 | chr12 | 6952113:6952177:6954805:6954994:6955151:6955173 | 6954805:6954994 |
| exon_skip_229836 | chr12 | 6951375:6951520:6951609:6951731:6951983:6952177 | 6951609:6951731 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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Open reading frame (ORF) annotation in the exon skipping event for PTPN6 |
| Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000318974 | 6951609 | 6951731 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000318974 | 6954805 | 6954994 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for PTPN6 |
p-ENSG00000111679_img4.png |
| Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000318974 | 2262 | 595 | 6951609 | 6951731 | 254 | 375 | 3 | 43 |
| Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| Lost protein functional features of individual exon skipping events in ROSMAP. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| P29350 | 3 | 43 | 1 | 39 | Alternative sequence | ID=VSP_005129;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:1652101;Dbxref=PMID:1652101 |
| P29350 | 3 | 43 | 1 | 3 | Alternative sequence | ID=VSP_007775;Note=In isoform 2. MVR->MLSRG;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| P29350 | 3 | 43 | 40 | 44 | Alternative sequence | ID=VSP_005130;Note=In isoform 3. SLSVR->MLSRG;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:1652101;Dbxref=PMID:1652101 |
| P29350 | 3 | 43 | 26 | 31 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2B3O |
| P29350 | 3 | 43 | 33 | 45 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2B3O |
| P29350 | 3 | 43 | 1 | 595 | Chain | ID=PRO_0000094758;Note=Tyrosine-protein phosphatase non-receptor type 6 |
| P29350 | 3 | 43 | 4 | 100 | Domain | Note=SH2 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00191 |
| P29350 | 3 | 43 | 11 | 21 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2B3O |
| P29350 | 3 | 43 | 10 | 10 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P81718 |
| P29350 | 3 | 43 | 6 | 6 | Sequence conflict | Note=H->L;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Lost protein functional features of individual exon skipping events in MSBB. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Lost protein functional features of individual exon skipping events in Mayo. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
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3'-UTR located exon skipping events that lost miRNA binding sites in PTPN6 |
| 3'-UTR exon skipping evnets lost miRNA binding. |
| Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
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SNVs in the skipped exons for PTPN6 |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Depth of Coverage in the skipped exon of the mutated samples. |
| - Sashimi plot in the skipped exon of the mutated samples. |
| - Non-synonymous mutations located in the skipped exons. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| - Non-synonymous mutations located in the skipped exons in CCLE. |
| Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
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AD stage-associated exon skippint events for PTPN6 |
| Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
| AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PTPN6 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for PTPN6 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for PTPN6 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for PTPN6 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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