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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 TOP1 |
 Gene summary |
| Gene information | Gene symbol | TOP1 | Gene ID | 7150 |
| Gene name | DNA topoisomerase I | |
| Synonyms | TOPI | |
| Cytomap | 20q12 | |
| Type of gene | protein-coding | |
| Description | DNA topoisomerase 1Scl-70 antigentopoisomerase (DNA) Itype I DNA topoisomerase | |
| 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 |
| TOP1 | GO:0006265 | DNA topological change | 14594810 |
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Gene structures and expression levels for TOP1 |
| 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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ENSG00000198900
| 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 |
| 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 TOP1 |
| 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_228383 | chr20 | 41116278:41116392:41118169:41118296:41121696:41121790 | 41118169:41118296 |
| exon_skip_267441 | chr20 | 41113970:41114155:41115371:41115439:41116278:41116392 | 41115371:41115439 |
| exon_skip_277367 | chr20 | 41029431:41029455:41061394:41061490:41076171:41076294 | 41061394:41061490 |
| exon_skip_64385 | chr20 | 41097220:41097341:41098215:41098337:41100056:41100243 | 41098215:41098337 |
| exon_skip_87041 | chr20 | 41061394:41061490:41076171:41076294:41077582:41077637 | 41076171:41076294 |
| exon_skip_90228 | chr20 | 41077582:41077637:41080085:41080180:41081165:41081240 | 41080085:41080180 |
| 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 TOP1 |
| 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 |
| ENST00000361337 | 41061394 | 41061490 | Frame-shift |
| ENST00000361337 | 41076171 | 41076294 | Frame-shift |
| ENST00000361337 | 41118169 | 41118296 | Frame-shift |
| ENST00000361337 | 41080085 | 41080180 | 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 |
| ENST00000361337 | 41076171 | 41076294 | Frame-shift |
| 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 |
| ENST00000361337 | 41061394 | 41061490 | Frame-shift |
| ENST00000361337 | 41076171 | 41076294 | Frame-shift |
| ENST00000361337 | 41118169 | 41118296 | Frame-shift |
| ENST00000361337 | 41080085 | 41080180 | In-frame |
| ENST00000361337 | 41098215 | 41098337 | In-frame |
| ENST00000361337 | 41115371 | 41115439 | In-frame |
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Infer the effects of exon skipping event on protein functional features for TOP1 |
p-ENSG00000198900_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 |
| ENST00000361337 | 3755 | 765 | 41080085 | 41080180 | 587 | 681 | 112 | 143 |
| 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 |
| ENST00000361337 | 3755 | 765 | 41080085 | 41080180 | 587 | 681 | 112 | 143 |
| ENST00000361337 | 3755 | 765 | 41098215 | 41098337 | 1104 | 1225 | 284 | 325 |
| ENST00000361337 | 3755 | 765 | 41115371 | 41115439 | 1890 | 1957 | 546 | 569 |
| 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 |
| P11387 | 112 | 143 | 2 | 765 | Chain | ID=PRO_0000145201;Note=DNA topoisomerase 1 |
| P11387 | 112 | 143 | 23 | 204 | Compositional bias | Note=Lys-rich |
| P11387 | 112 | 143 | 117 | 117 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)%3B alternate |
| P11387 | 112 | 143 | 117 | 117 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1)%3B alternate;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:25114211;Dbxref=PMID:25114211 |
| P11387 | 112 | 143 | 117 | 117 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)%3B alternate;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:25114211,ECO:0000244|PubMed:25218447,ECO:0000244|PubMed:25772364,ECO:0000244|P |
| P11387 | 112 | 143 | 134 | 134 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:25218447,ECO:0000244|PubMed:28112733;Dbxref=PMID:25218447,PMID:28112733 |
| P11387 | 112 | 143 | 112 | 112 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:20068231;Dbxref=PMID:20068231 |
| P11387 | 112 | 143 | 117 | 117 | Mutagenesis | Note=5-fold decrease in sumoylation. Localizes in both nucleoplasm and nucleoli%3B when associated with or without R-103 or R-153. Almost complete loss of sumoylation%2C concentrates in nucleoli and no clearing from nucleoli on CPT treatment%3B when assoc |
| 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 |
| P11387 | 112 | 143 | 2 | 765 | Chain | ID=PRO_0000145201;Note=DNA topoisomerase 1 |
| P11387 | 112 | 143 | 23 | 204 | Compositional bias | Note=Lys-rich |
| P11387 | 112 | 143 | 117 | 117 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)%3B alternate |
| P11387 | 112 | 143 | 117 | 117 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1)%3B alternate;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:25114211;Dbxref=PMID:25114211 |
| P11387 | 112 | 143 | 117 | 117 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)%3B alternate;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:25114211,ECO:0000244|PubMed:25218447,ECO:0000244|PubMed:25772364,ECO:0000244|P |
| P11387 | 112 | 143 | 134 | 134 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:25218447,ECO:0000244|PubMed:28112733;Dbxref=PMID:25218447,PMID:28112733 |
| P11387 | 112 | 143 | 112 | 112 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:20068231;Dbxref=PMID:20068231 |
| P11387 | 112 | 143 | 117 | 117 | Mutagenesis | Note=5-fold decrease in sumoylation. Localizes in both nucleoplasm and nucleoli%3B when associated with or without R-103 or R-153. Almost complete loss of sumoylation%2C concentrates in nucleoli and no clearing from nucleoli on CPT treatment%3B when assoc |
| P11387 | 284 | 325 | 2 | 765 | Chain | ID=PRO_0000145201;Note=DNA topoisomerase 1 |
| P11387 | 284 | 325 | 272 | 285 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1A31 |
| P11387 | 284 | 325 | 288 | 293 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1A31 |
| P11387 | 284 | 325 | 297 | 299 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1A31 |
| P11387 | 284 | 325 | 303 | 317 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1A31 |
| P11387 | 284 | 325 | 321 | 338 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1A31 |
| P11387 | 284 | 325 | 316 | 316 | Site | Note=Interaction with DNA |
| P11387 | 546 | 569 | 2 | 765 | Chain | ID=PRO_0000145201;Note=DNA topoisomerase 1 |
| P11387 | 546 | 569 | 549 | 549 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733 |
| P11387 | 546 | 569 | 545 | 553 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1A31 |
| P11387 | 546 | 569 | 554 | 557 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1A31 |
| P11387 | 546 | 569 | 564 | 567 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1A31 |
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3'-UTR located exon skipping events that lost miRNA binding sites in TOP1 |
| 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 TOP1 |
| - 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 TOP1 |
| 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 TOP1 |
| 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 TOP1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for TOP1 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| P11387 | approved|investigational | DB00762 | Irinotecan | small molecule | P11387 |
| P11387 | approved|investigational | DB01030 | Topotecan | small molecule | P11387 |
| P11387 | approved|investigational | DB05630 | Sodium stibogluconate | small molecule | P11387 |
| P11387 | approved | DB11254 | Hexylresorcinol | small molecule | P11387 |
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RelatedDiseases for TOP1 |
| 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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