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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 PTCH1 |
 Gene summary |
| Gene information | Gene symbol | PTCH1 | Gene ID | 5727 |
| Gene name | patched 1 | |
| Synonyms | BCNS|NBCCS|PTC|PTC1|PTCH | |
| Cytomap | 9q22.32 | |
| Type of gene | protein-coding | |
| Description | protein patched homolog 1 | |
| Modification date | 20200314 | |
| 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 |
| PTCH1 | GO:0010875 | positive regulation of cholesterol efflux | 21931618 |
| PTCH1 | GO:0072659 | protein localization to plasma membrane | 11278759 |
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Gene structures and expression levels for PTCH1 |
| 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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ENSG00000185920
| 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 |
| STG | UP | ENST00000429896.6 | PTCH1-207:protein_coding:PTCH1 | 3.577490e+01 | 2.225597e+00 | 1.319724e-03 | 4.450744e-02 |
| CB | UP | ENST00000375271.4 | PTCH1-202:protein_coding:PTCH1 | 8.144766e+00 | 8.794817e-01 | 1.676034e-04 | 1.146693e-03 |
| CB | UP | ENST00000429896.6 | PTCH1-207:protein_coding:PTCH1 | 8.241631e+02 | 8.944497e-01 | 5.798033e-03 | 2.224294e-02 |
| 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 PTCH1 |
| 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_102060 | chr9 | 95453478:95453620:95456276:95456413:95458013:95458293 | 95456276:95456413 |
| exon_skip_109542 | chr9 | 95469813:95469931:95474012:95474143:95476034:95476154 | 95474012:95474143 |
| exon_skip_120591 | chr9 | 95476759:95476857:95477547:95477702:95478055:95478186 | 95477547:95477702 |
| exon_skip_194368 | chr9 | 95485824:95485874:95506407:95506599:95516469:95516658 | 95506407:95506599 |
| exon_skip_201098 | chr9 | 95480544:95480588:95485685:95485874:95506407:95506599 | 95485685:95485874 |
| exon_skip_205521 | chr9 | 95469813:95469931:95474012:95474143:95476034:95476159 | 95474012:95474143 |
| exon_skip_268074 | chr9 | 95449069:95449323:95449841:95449940:95453478:95453620 | 95449841:95449940 |
| exon_skip_27476 | chr9 | 95480390:95480588:95485685:95485874:95506407:95506599 | 95485685:95485874 |
| exon_skip_34972 | chr9 | 95468938:95469153:95469813:95469931:95474012:95474143 | 95469813:95469931 |
| exon_skip_45555 | chr9 | 95469813:95469931:95476034:95476159:95476759:95476857 | 95476034:95476159 |
| exon_skip_66316 | chr9 | 95467287:95467425:95468751:95469153:95469813:95469931 | 95468751:95469153 |
| exon_skip_80216 | chr9 | 95481971:95482040:95482134:95482203:95485685:95485874 | 95482134:95482203 |
| 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 PTCH1 |
| 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 |
| ENST00000331920 | 95477547 | 95477702 | 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 |
| ENST00000331920 | 95477547 | 95477702 | 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 |
| ENST00000331920 | 95449841 | 95449940 | Frame-shift |
| ENST00000331920 | 95468751 | 95469153 | Frame-shift |
| ENST00000331920 | 95482134 | 95482203 | Frame-shift |
| ENST00000331920 | 95456276 | 95456413 | In-frame |
| ENST00000331920 | 95476034 | 95476159 | In-frame |
| ENST00000331920 | 95477547 | 95477702 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PTCH1 |
p-ENSG00000185920_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 |
| ENST00000331920 | 8074 | 1447 | 95477547 | 95477702 | 1648 | 1802 | 449 | 500 |
| 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 |
| ENST00000331920 | 8074 | 1447 | 95477547 | 95477702 | 1648 | 1802 | 449 | 500 |
| 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 |
| ENST00000331920 | 8074 | 1447 | 95477547 | 95477702 | 1648 | 1802 | 449 | 500 |
| ENST00000331920 | 8074 | 1447 | 95476034 | 95476159 | 1903 | 2027 | 534 | 575 |
| ENST00000331920 | 8074 | 1447 | 95456276 | 95456413 | 3469 | 3605 | 1056 | 1101 |
| 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 |
| Q13635 | 449 | 500 | 1 | 1447 | Chain | ID=PRO_0000205964;Note=Protein patched homolog 1 |
| Q13635 | 449 | 500 | 438 | 598 | Domain | Note=SSD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00199 |
| Q13635 | 449 | 500 | 458 | 472 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13635 | 449 | 500 | 494 | 501 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13635 | 449 | 500 | 437 | 457 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13635 | 449 | 500 | 473 | 493 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| Q13635 | 449 | 500 | 1 | 1447 | Chain | ID=PRO_0000205964;Note=Protein patched homolog 1 |
| Q13635 | 449 | 500 | 438 | 598 | Domain | Note=SSD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00199 |
| Q13635 | 449 | 500 | 458 | 472 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13635 | 449 | 500 | 494 | 501 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13635 | 449 | 500 | 437 | 457 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13635 | 449 | 500 | 473 | 493 | Transmembrane | Note=Helical;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 |
| Q13635 | 449 | 500 | 1 | 1447 | Chain | ID=PRO_0000205964;Note=Protein patched homolog 1 |
| Q13635 | 449 | 500 | 438 | 598 | Domain | Note=SSD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00199 |
| Q13635 | 449 | 500 | 458 | 472 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13635 | 449 | 500 | 494 | 501 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13635 | 449 | 500 | 437 | 457 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13635 | 449 | 500 | 473 | 493 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13635 | 534 | 575 | 1 | 1447 | Chain | ID=PRO_0000205964;Note=Protein patched homolog 1 |
| Q13635 | 534 | 575 | 438 | 598 | Domain | Note=SSD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00199 |
| Q13635 | 534 | 575 | 523 | 547 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13635 | 534 | 575 | 569 | 577 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13635 | 534 | 575 | 548 | 568 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13635 | 1056 | 1101 | 1 | 1447 | Chain | ID=PRO_0000205964;Note=Protein patched homolog 1 |
| Q13635 | 1056 | 1101 | 1069 | 1069 | Natural variant | ID=VAR_010979;Note=In BCNS. G->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8981943;Dbxref=PMID:8981943 |
| Q13635 | 1056 | 1101 | 1083 | 1083 | Natural variant | ID=VAR_007846;Note=In BCNS. V->VV;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9620294;Dbxref=PMID:9620294 |
| Q13635 | 1056 | 1101 | 1077 | 1083 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13635 | 1056 | 1101 | 1056 | 1076 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13635 | 1056 | 1101 | 1084 | 1104 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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3'-UTR located exon skipping events that lost miRNA binding sites in PTCH1 |
| 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 PTCH1 |
| - 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 PTCH1 |
| 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 PTCH1 |
| 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 PTCH1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | NUP42 | exon_skip_109542 | 4.105263e-01 | 9.290636e-08 |
| CB | RALYL | exon_skip_109542 | 5.006178e-01 | 2.444269e-11 |
| TC | ILF2 | exon_skip_109542 | 4.689999e-01 | 1.611133e-09 |
| TC | KHDRBS2 | exon_skip_109542 | 5.204838e-01 | 1.019336e-11 |
| TC | NUP42 | exon_skip_109542 | 5.302806e-01 | 3.521111e-12 |
| TC | RALYL | exon_skip_109542 | 5.327178e-01 | 2.688552e-12 |
| TC | HNRNPL | exon_skip_109542 | 4.435881e-01 | 1.462497e-08 |
| TC | EWSR1 | exon_skip_109542 | 4.214292e-01 | 8.684313e-08 |
| TC | ESRP1 | exon_skip_109542 | 4.723738e-01 | 1.185637e-09 |
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RelatedDrugs for PTCH1 |
| 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 PTCH1 |
| 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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