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Open reading frame (ORF) annotation in the exon skipping event | |
3'-UTR located exon skipping events lost miRNA binding sites | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
Gene summary for PTPRT |
Gene summary |
Gene information | Gene symbol | PTPRT | Gene ID | 11122 |
Gene name | protein tyrosine phosphatase receptor type T | |
Synonyms | RPTPrho | |
Cytomap | 20q12-q13.11 | |
Type of gene | protein-coding | |
Description | receptor-type tyrosine-protein phosphatase TR-PTP-TRPTP-rhoreceptor protein tyrosine phosphatasereceptor-type tyrosine-protein phosphatase rho | |
Modification date | 20200313 | |
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 |
PTPRT | GO:0006470 | protein dephosphorylation | 16973135 |
PTPRT | GO:0007156 | homophilic cell adhesion via plasma membrane adhesion molecules | 18644975 |
PTPRT | GO:0035335 | peptidyl-tyrosine dephosphorylation | 17360477 |
PTPRT | GO:0071354 | cellular response to interleukin-6 | 17360477 |
PTPRT | GO:1904893 | negative regulation of STAT cascade | 17360477 |
PTPRT | GO:1990264 | peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity | 24846175 |
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Gene structures and expression levels for PTPRT |
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. |
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. |
Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
TC | DOWN | ENST00000373187.5 | PTPRT-203:protein_coding:PTPRT | 2.132228e+01 | -1.184339e+01 | 7.612400e-12 | 2.090083e-09 |
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 PTPRT |
Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
All exon skipping events in AD cohorts. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
exon_skip_107682 | chr20 | 42780218:42780299:42791195:42791466:42885807:42885932 | 42791195:42791466 |
exon_skip_133683 | chr20 | 42199240:42199388:42236229:42236258:42248687:42248822 | 42236229:42236258 |
exon_skip_23951 | chr20 | 42448220:42448329:42472266:42472562:42677866:42678159 | 42472266:42472562 |
exon_skip_68445 | chr20 | 42248687:42248822:42270397:42270453:42282489:42282525 | 42270397:42270453 |
exon_skip_73558 | chr20 | 42352084:42352285:42448220:42448329:42472266:42472562 | 42448220:42448329 |
exon_skip_97049 | chr20 | 42115199:42115315:42116039:42116098:42118403:42118500 | 42116039:42116098 |
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 PTPRT |
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 |
ENST00000373193 | 42448220 | 42448329 | Frame-shift |
ENST00000373193 | 42791195 | 42791466 | Frame-shift |
ENST00000373193 | 42270397 | 42270453 | In-frame |
ENST00000373193 | 42472266 | 42472562 | 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 |
ENST00000373193 | 42791195 | 42791466 | Frame-shift |
ENST00000373193 | 42270397 | 42270453 | In-frame |
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 |
ENST00000373193 | 42270397 | 42270453 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PTPRT |
p-ENSG00000196090_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 |
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 |
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 PTPRT |
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 PTPRT |
- 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 PTPRT |
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 PTPRT |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
HCC | exon_skip_68445 | rs11086830 | chr20:42349891 | 2.631549e-04 | 2.027165e-02 |
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Correlation with RNA binding proteins (RBPs) for PTPRT |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
IFG | LIN28A | exon_skip_133683 | 4.001288e-01 | 3.487550e-02 |
IFG | HNRNPK | exon_skip_68445 | -6.217079e-01 | 4.131359e-04 |
IFG | HNRNPL | exon_skip_68445 | -4.442341e-01 | 1.787127e-02 |
IFG | RBM4B | exon_skip_68445 | -4.373482e-01 | 1.994819e-02 |
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RelatedDrugs for PTPRT |
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 PTPRT |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |