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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 PTPRS |
Gene summary |
Gene information | Gene symbol | PTPRS | Gene ID | 5802 |
Gene name | protein tyrosine phosphatase receptor type S | |
Synonyms | PTPSIGMA|R-PTP-S|R-PTP-sigma | |
Cytomap | 19p13.3 | |
Type of gene | protein-coding | |
Description | receptor-type tyrosine-protein phosphatase Sprotein tyrosine phosphatase PTPsigmareceptor-type tyrosine-protein phosphatase sigma | |
Modification date | 20200322 | |
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 |
PTPRS | GO:0006470 | protein dephosphorylation | 8524829 |
PTPRS | GO:0099560 | synaptic membrane adhesion | 23345436 |
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Gene structures and expression levels for PTPRS |
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 |
PCC | DOWN | ENST00000353284.7 | PTPRS-202:protein_coding:PTPRS | 2.466541e+02 | -8.001532e-01 | 5.527735e-04 | 1.760728e-02 |
PG | UP | ENST00000588012.5 | PTPRS-205:protein_coding:PTPRS | 2.200098e+02 | 1.137139e+00 | 9.760048e-05 | 2.696370e-03 |
TC | UP | ENST00000588012.5 | PTPRS-205:protein_coding:PTPRS | 1.514802e+02 | 8.066275e-01 | 6.966467e-05 | 1.213165e-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 PTPRS |
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_101594 | chr19 | 5215498:5215595:5216720:5216767:5218420:5218532 | 5216720:5216767 |
exon_skip_117017 | chr19 | 5222123:5222220:5222689:5223297:5225727:5225844 | 5222689:5223297 |
exon_skip_124991 | chr19 | 5215505:5215595:5216720:5216767:5218420:5218532 | 5216720:5216767 |
exon_skip_143036 | chr19 | 5208237:5208391:5210469:5210594:5210679:5210805 | 5210469:5210594 |
exon_skip_155468 | chr19 | 5215367:5215412:5215498:5215595:5218420:5218532 | 5215498:5215595 |
exon_skip_156141 | chr19 | 5229491:5229684:5231310:5231615:5238919:5239063 | 5231310:5231615 |
exon_skip_180289 | chr19 | 5218420:5218532:5218787:5218798:5219310:5219405 | 5218787:5218798 |
exon_skip_205442 | chr19 | 5225727:5225844:5229491:5229684:5231310:5231424 | 5229491:5229684 |
exon_skip_215183 | chr19 | 5225727:5225844:5229316:5229342:5229491:5229684 | 5229316:5229342 |
exon_skip_222378 | chr19 | 5225727:5225844:5229316:5229342:5229491:5229521 | 5229316:5229342 |
exon_skip_236960 | chr19 | 5260805:5260822:5262964:5262972:5265008:5265196 | 5262964:5262972 |
exon_skip_242514 | chr19 | 5229316:5229342:5229491:5229684:5231310:5231424 | 5229491:5229684 |
exon_skip_262622 | chr19 | 5218787:5218798:5219310:5219467:5219939:5220016 | 5219310:5219467 |
exon_skip_267151 | chr19 | 5243901:5244482:5245776:5246045:5258017:5258127 | 5245776:5246045 |
exon_skip_279208 | chr19 | 5265008:5265196:5273442:5273583:5274199:5274344 | 5273442:5273583 |
exon_skip_296278 | chr19 | 5207922:5208057:5208237:5208391:5210469:5210594 | 5208237:5208391 |
exon_skip_33281 | chr19 | 5206774:5206842:5207922:5208057:5208237:5208391 | 5207922:5208057 |
exon_skip_3471 | chr19 | 5218420:5218532:5218787:5218798:5219310:5219467 | 5218787:5218798 |
exon_skip_35412 | chr19 | 5229316:5229342:5229491:5229684:5231310:5231615 | 5229491:5229684 |
exon_skip_48866 | chr19 | 5240199:5240332:5243901:5244482:5245776:5246045 | 5243901:5244482 |
exon_skip_88905 | chr19 | 5245776:5246045:5256108:5256119:5258017:5258127 | 5256108:5256119 |
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 |
exon_skip_101594 | MSBB_PG | 2.956391e-01 | 1.907273e-01 | 1.049118e-01 | 6.621448e-07 |
exon_skip_215183 | Mayo_TC | 3.436250e-01 | 4.882258e-01 | -1.446008e-01 | 2.687869e-06 |
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Open reading frame (ORF) annotation in the exon skipping event for PTPRS |
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 |
ENST00000587303 | 5207922 | 5208057 | Frame-shift |
ENST00000587303 | 5229491 | 5229684 | Frame-shift |
ENST00000587303 | 5273442 | 5273583 | Frame-shift |
ENST00000587303 | 5210469 | 5210594 | In-frame |
ENST00000587303 | 5216720 | 5216767 | In-frame |
ENST00000587303 | 5218787 | 5218798 | In-frame |
ENST00000587303 | 5229316 | 5229342 | In-frame |
ENST00000587303 | 5231310 | 5231615 | In-frame |
ENST00000587303 | 5243901 | 5244482 | In-frame |
ENST00000587303 | 5256108 | 5256119 | 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 |
ENST00000587303 | 5216720 | 5216767 | In-frame |
ENST00000587303 | 5218787 | 5218798 | In-frame |
ENST00000587303 | 5222689 | 5223297 | In-frame |
ENST00000587303 | 5229316 | 5229342 | In-frame |
ENST00000587303 | 5256108 | 5256119 | 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 |
ENST00000587303 | 5208237 | 5208391 | Frame-shift |
ENST00000587303 | 5219310 | 5219467 | Frame-shift |
ENST00000587303 | 5229491 | 5229684 | Frame-shift |
ENST00000587303 | 5273442 | 5273583 | Frame-shift |
ENST00000587303 | 5216720 | 5216767 | In-frame |
ENST00000587303 | 5218787 | 5218798 | In-frame |
ENST00000587303 | 5229316 | 5229342 | In-frame |
ENST00000587303 | 5256108 | 5256119 | In-frame |
ENST00000587303 | 5262964 | 5262972 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PTPRS |
p-ENSG00000105426_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 |
ENST00000587303 | 6370 | 1948 | 5243901 | 5244482 | 1089 | 1669 | 329 | 523 |
ENST00000587303 | 6370 | 1948 | 5231310 | 5231615 | 1950 | 2254 | 616 | 718 |
ENST00000587303 | 6370 | 1948 | 5216720 | 5216767 | 4149 | 4195 | 1349 | 1365 |
ENST00000587303 | 6370 | 1948 | 5210469 | 5210594 | 5462 | 5586 | 1787 | 1828 |
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 |
ENST00000587303 | 6370 | 1948 | 5222689 | 5223297 | 2595 | 3202 | 831 | 1034 |
ENST00000587303 | 6370 | 1948 | 5216720 | 5216767 | 4149 | 4195 | 1349 | 1365 |
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 |
ENST00000587303 | 6370 | 1948 | 5216720 | 5216767 | 4149 | 4195 | 1349 | 1365 |
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 |
Q13332 | 329 | 523 | 339 | 343 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX |
Q13332 | 329 | 523 | 348 | 351 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX |
Q13332 | 329 | 523 | 361 | 370 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX |
Q13332 | 329 | 523 | 377 | 382 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX |
Q13332 | 329 | 523 | 384 | 389 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX |
Q13332 | 329 | 523 | 397 | 405 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX |
Q13332 | 329 | 523 | 410 | 413 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX |
Q13332 | 329 | 523 | 417 | 420 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX |
Q13332 | 329 | 523 | 431 | 441 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX |
Q13332 | 329 | 523 | 443 | 448 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX |
Q13332 | 329 | 523 | 457 | 466 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX |
Q13332 | 329 | 523 | 475 | 479 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX |
Q13332 | 329 | 523 | 482 | 488 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX |
Q13332 | 329 | 523 | 496 | 507 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX |
Q13332 | 329 | 523 | 516 | 524 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX |
Q13332 | 329 | 523 | 30 | 1948 | Chain | ID=PRO_0000025462;Note=Receptor-type tyrosine-protein phosphatase S |
Q13332 | 329 | 523 | 334 | 424 | Domain | Note=Fibronectin type-III 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 |
Q13332 | 329 | 523 | 429 | 523 | Domain | Note=Fibronectin type-III 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 |
Q13332 | 329 | 523 | 472 | 474 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX |
Q13332 | 329 | 523 | 428 | 429 | Sequence conflict | Note=SA->RP;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q13332 | 329 | 523 | 30 | 1282 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q13332 | 616 | 718 | 617 | 1034 | Alternative sequence | ID=VSP_050023;Note=In isoform PTPS-F4-7 and isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
Q13332 | 616 | 718 | 30 | 1948 | Chain | ID=PRO_0000025462;Note=Receptor-type tyrosine-protein phosphatase S |
Q13332 | 616 | 718 | 641 | 644 | Compositional bias | Note=Poly-Pro |
Q13332 | 616 | 718 | 527 | 616 | Domain | Note=Fibronectin type-III 3;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 |
Q13332 | 616 | 718 | 621 | 718 | Domain | Note=Fibronectin type-III 4;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 |
Q13332 | 616 | 718 | 30 | 1282 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q13332 | 1349 | 1365 | 1350 | 1365 | Alternative sequence | ID=VSP_050026;Note=In isoform PTPS-MEB%2C isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:8992885;Dbxref=PMID:15489334,PMID:8992885 |
Q13332 | 1349 | 1365 | 30 | 1948 | Chain | ID=PRO_0000025462;Note=Receptor-type tyrosine-protein phosphatase S |
Q13332 | 1349 | 1365 | 1304 | 1948 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q13332 | 1787 | 1828 | 1796 | 1798 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2FH7 |
Q13332 | 1787 | 1828 | 1800 | 1802 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2FH7 |
Q13332 | 1787 | 1828 | 1805 | 1814 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2FH7 |
Q13332 | 1787 | 1828 | 1816 | 1827 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2FH7 |
Q13332 | 1787 | 1828 | 30 | 1948 | Chain | ID=PRO_0000025462;Note=Receptor-type tyrosine-protein phosphatase S |
Q13332 | 1787 | 1828 | 1680 | 1939 | Domain | Note=Tyrosine-protein phosphatase 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00160 |
Q13332 | 1787 | 1828 | 1304 | 1948 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q13332 | 1787 | 1828 | 1828 | 1830 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2FH7 |
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 |
Q13332 | 831 | 1034 | 617 | 1034 | Alternative sequence | ID=VSP_050023;Note=In isoform PTPS-F4-7 and isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
Q13332 | 831 | 1034 | 30 | 1948 | Chain | ID=PRO_0000025462;Note=Receptor-type tyrosine-protein phosphatase S |
Q13332 | 831 | 1034 | 723 | 831 | Domain | Note=Fibronectin type-III 5;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 |
Q13332 | 831 | 1034 | 832 | 930 | Domain | Note=Fibronectin type-III 6;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 |
Q13332 | 831 | 1034 | 931 | 1033 | Domain | Note=Fibronectin type-III 7;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 |
Q13332 | 831 | 1034 | 940 | 940 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q13332 | 831 | 1034 | 996 | 996 | Natural variant | ID=VAR_035649;Note=In a colorectal cancer sample%3B somatic mutation. T->M;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16959974;Dbxref=dbSNP:rs775778266,PMID:16959974 |
Q13332 | 831 | 1034 | 910 | 910 | Sequence conflict | Note=R->P;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q13332 | 831 | 1034 | 995 | 995 | Sequence conflict | Note=L->V;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q13332 | 831 | 1034 | 30 | 1282 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q13332 | 1349 | 1365 | 1350 | 1365 | Alternative sequence | ID=VSP_050026;Note=In isoform PTPS-MEB%2C isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:8992885;Dbxref=PMID:15489334,PMID:8992885 |
Q13332 | 1349 | 1365 | 30 | 1948 | Chain | ID=PRO_0000025462;Note=Receptor-type tyrosine-protein phosphatase S |
Q13332 | 1349 | 1365 | 1304 | 1948 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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 |
Q13332 | 1349 | 1365 | 1350 | 1365 | Alternative sequence | ID=VSP_050026;Note=In isoform PTPS-MEB%2C isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:8992885;Dbxref=PMID:15489334,PMID:8992885 |
Q13332 | 1349 | 1365 | 30 | 1948 | Chain | ID=PRO_0000025462;Note=Receptor-type tyrosine-protein phosphatase S |
Q13332 | 1349 | 1365 | 1304 | 1948 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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3'-UTR located exon skipping events that lost miRNA binding sites in PTPRS |
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 PTPRS |
- 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 PTPRS |
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 PTPRS |
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 PTPRS |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
DLPFC | RBFOX2 | exon_skip_101594 | -6.891958e-01 | 4.266881e-48 |
HCC | HNRNPF | exon_skip_215183 | -4.246304e-01 | 4.220527e-12 |
HCC | RBM6 | exon_skip_88905 | -4.687485e-01 | 4.802952e-16 |
IFG | RBFOX2 | exon_skip_101594 | -6.897886e-01 | 4.888553e-05 |
PCC | RBFOX2 | exon_skip_101594 | -5.768743e-01 | 5.023076e-20 |
PCC | HNRNPF | exon_skip_101594 | 5.141488e-01 | 1.444070e-15 |
PG | RBFOX2 | exon_skip_101594 | -6.739776e-01 | 2.991903e-26 |
PG | PCBP1 | exon_skip_101594 | -4.772294e-01 | 4.384872e-12 |
PG | ILF2 | exon_skip_101594 | -4.817569e-01 | 2.572229e-12 |
PG | HNRNPK | exon_skip_101594 | -4.786278e-01 | 3.721976e-12 |
PG | SRSF9 | exon_skip_101594 | -4.056868e-01 | 7.663841e-09 |
TC | RBFOX2 | exon_skip_101594 | -7.536655e-01 | 3.106391e-30 |
TC | HNRNPH2 | exon_skip_215183 | 5.036711e-01 | 1.667034e-10 |
TC | HNRNPF | exon_skip_215183 | -4.405113e-01 | 4.109678e-08 |
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RelatedDrugs for PTPRS |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Q13332 | approved | DB00630 | Alendronic acid | small molecule | Q13332 |
Q13332 | approved | DB01077 | Etidronic acid | small molecule | Q13332 |
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RelatedDiseases for PTPRS |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |