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Open reading frame (ORF) annotation in the exon skipping event | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon | |
Gene summary for TOPBP1 |
Gene summary |
Gene information | Gene symbol | TOPBP1 | Gene ID | 11073 |
Gene name | DNA topoisomerase II binding protein 1 | |
Synonyms | TOP2BP1 | |
Cytomap | 3q22.1 | |
Type of gene | protein-coding | |
Description | DNA topoisomerase 2-binding protein 1DNA topoisomerase II-beta-binding protein 1topoisomerase (DNA) II binding protein 1 | |
Modification date | 20180523 | |
UniProtAcc | Q92547 | |
Context | PubMed: TOPBP1 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
TOPBP1 | GO:0006974 | cellular response to DNA damage stimulus | 12773567 |
TOPBP1 | GO:0010212 | response to ionizing radiation | 12773567 |
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Exon skipping events across known transcript of Ensembl for TOPBP1 from UCSC genome browser |
Skipped exons in TCGA and GTEx 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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Gene isoform structures and expression levels for TOPBP1 |
Expression levels of gene isoforms across TCGA. |
Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for TOPBP1 |
Information of exkip skipping event in TCGA. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
exon_skip_388636 | 3 | 133319416:133320237:133327378:133327540:133327716:133327806 | 133327378:133327540 | ENSG00000163781.8 | ENST00000260810.5 |
exon_skip_388637 | 3 | 133329847:133329985:133331232:133331396:133335657:133335769 | 133331232:133331396 | ENSG00000163781.8 | ENST00000260810.5 |
exon_skip_388639 | 3 | 133331232:133331396:133335657:133335769:133336003:133336170 | 133335657:133335769 | ENSG00000163781.8 | ENST00000260810.5 |
exon_skip_388640 | 3 | 133336003:133336170:133337056:133337277:133338998:133339191 | 133337056:133337277 | ENSG00000163781.8 | ENST00000260810.5 |
exon_skip_388646 | 3 | 133342154:133342301:133342895:133343019:133347205:133347235 | 133342895:133343019 | ENSG00000163781.8 | ENST00000513818.1,ENST00000260810.5 |
exon_skip_388648 | 3 | 133368777:133368787:133371306:133371391:133372188:133372312 | 133371306:133371391 | ENSG00000163781.8 | ENST00000572787.1 |
exon_skip_388649 | 3 | 133368777:133368787:133371306:133371458:133372188:133372312 | 133371306:133371458 | ENSG00000163781.8 | ENST00000508524.1 |
exon_skip_388650 | 3 | 133368777:133368787:133371306:133371473:133372188:133372312 | 133371306:133371473 | ENSG00000163781.8 | ENST00000260810.5 |
exon_skip_388653 | 3 | 133368777:133368787:133372188:133372368:133374133:133374330 | 133372188:133372368 | ENSG00000163781.8 | ENST00000511439.1 |
exon_skip_388654 | 3 | 133371306:133371473:133372188:133372368:133374133:133374330 | 133372188:133372368 | ENSG00000163781.8 | ENST00000260810.5 |
exon_skip_388659 | 3 | 133377859:133377994:133379887:133379978:133380612:133380737 | 133379887:133379978 | ENSG00000163781.8 | ENST00000260810.5 |
PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for TOPBP1 |
Information of exkip skipping event in GTEx |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
exon_skip_388636 | 3 | 133319416:133320237:133327378:133327540:133327716:133327806 | 133327378:133327540 | ENSG00000163781.8 | ENST00000260810.5 |
exon_skip_388637 | 3 | 133329847:133329985:133331232:133331396:133335657:133335769 | 133331232:133331396 | ENSG00000163781.8 | ENST00000260810.5 |
exon_skip_388639 | 3 | 133331232:133331396:133335657:133335769:133336003:133336170 | 133335657:133335769 | ENSG00000163781.8 | ENST00000260810.5 |
exon_skip_388640 | 3 | 133336003:133336170:133337056:133337277:133338998:133339191 | 133337056:133337277 | ENSG00000163781.8 | ENST00000260810.5 |
exon_skip_388646 | 3 | 133342154:133342301:133342895:133343019:133347205:133347235 | 133342895:133343019 | ENSG00000163781.8 | ENST00000260810.5,ENST00000513818.1 |
exon_skip_388648 | 3 | 133368777:133368787:133371306:133371391:133372188:133372312 | 133371306:133371391 | ENSG00000163781.8 | ENST00000572787.1 |
exon_skip_388649 | 3 | 133368777:133368787:133371306:133371458:133372188:133372312 | 133371306:133371458 | ENSG00000163781.8 | ENST00000508524.1 |
exon_skip_388650 | 3 | 133368777:133368787:133371306:133371473:133372188:133372312 | 133371306:133371473 | ENSG00000163781.8 | ENST00000260810.5 |
exon_skip_388653 | 3 | 133368777:133368787:133372188:133372368:133374133:133374330 | 133372188:133372368 | ENSG00000163781.8 | ENST00000511439.1 |
exon_skip_388654 | 3 | 133371306:133371473:133372188:133372368:133374133:133374330 | 133372188:133372368 | ENSG00000163781.8 | ENST00000260810.5 |
exon_skip_388659 | 3 | 133377859:133377994:133379887:133379978:133380612:133380737 | 133379887:133379978 | ENSG00000163781.8 | ENST00000260810.5 |
PSI values of skipped exons in GTEx. |
* Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for TOPBP1 |
Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000260810 | 133379887 | 133379978 | 3UTR-3CDS |
ENST00000260810 | 133331232 | 133331396 | Frame-shift |
ENST00000260810 | 133335657 | 133335769 | Frame-shift |
ENST00000260810 | 133337056 | 133337277 | Frame-shift |
ENST00000260810 | 133342895 | 133343019 | Frame-shift |
ENST00000260810 | 133371306 | 133371473 | Frame-shift |
ENST00000260810 | 133327378 | 133327540 | In-frame |
ENST00000260810 | 133372188 | 133372368 | In-frame |
Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000260810 | 133379887 | 133379978 | 3UTR-3CDS |
ENST00000260810 | 133331232 | 133331396 | Frame-shift |
ENST00000260810 | 133335657 | 133335769 | Frame-shift |
ENST00000260810 | 133337056 | 133337277 | Frame-shift |
ENST00000260810 | 133342895 | 133343019 | Frame-shift |
ENST00000260810 | 133371306 | 133371473 | Frame-shift |
ENST00000260810 | 133327378 | 133327540 | In-frame |
ENST00000260810 | 133372188 | 133372368 | In-frame |
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Infer the effects of exon skipping event on protein functional features for TOPBP1 |
Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
Loci of skipped exons in TCGA 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 |
ENST00000260810 | 5395 | 1522 | 133372188 | 133372368 | 875 | 1054 | 247 | 307 |
ENST00000260810 | 5395 | 1522 | 133327378 | 133327540 | 4396 | 4557 | 1421 | 1475 |
Loci of skipped exons in GTEx 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 |
ENST00000260810 | 5395 | 1522 | 133372188 | 133372368 | 875 | 1054 | 247 | 307 |
ENST00000260810 | 5395 | 1522 | 133327378 | 133327540 | 4396 | 4557 | 1421 | 1475 |
Lost protein functional features of individual exon skipping events in TCGA. |
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 |
Q92547 | 247 | 307 | 260 | 262 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OLC |
Q92547 | 247 | 307 | 282 | 284 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OLC |
Q92547 | 247 | 307 | 1 | 1522 | Chain | ID=PRO_0000072631;Note=DNA topoisomerase 2-binding protein 1 |
Q92547 | 247 | 307 | 195 | 284 | Domain | Note=BRCT 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00033 |
Q92547 | 247 | 307 | 249 | 256 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OLC |
Q92547 | 247 | 307 | 264 | 273 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OLC |
Q92547 | 247 | 307 | 279 | 281 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OLC |
Q92547 | 247 | 307 | 298 | 298 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
Q92547 | 247 | 307 | 301 | 301 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:17525332;Dbxref=PMID:17525332 |
Q92547 | 1421 | 1475 | 1435 | 1439 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3AL2 |
Q92547 | 1421 | 1475 | 1462 | 1465 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3AL2 |
Q92547 | 1421 | 1475 | 1 | 1522 | Chain | ID=PRO_0000072631;Note=DNA topoisomerase 2-binding protein 1 |
Q92547 | 1421 | 1475 | 1389 | 1486 | Domain | Note=BRCT 8;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00033 |
Q92547 | 1421 | 1475 | 1428 | 1433 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3AL2 |
Q92547 | 1421 | 1475 | 1453 | 1458 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3AL2 |
Q92547 | 1421 | 1475 | 1467 | 1474 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3AL2 |
Lost protein functional features of individual exon skipping events in GTEx. |
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 |
Q92547 | 247 | 307 | 260 | 262 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OLC |
Q92547 | 247 | 307 | 282 | 284 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OLC |
Q92547 | 247 | 307 | 1 | 1522 | Chain | ID=PRO_0000072631;Note=DNA topoisomerase 2-binding protein 1 |
Q92547 | 247 | 307 | 195 | 284 | Domain | Note=BRCT 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00033 |
Q92547 | 247 | 307 | 249 | 256 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OLC |
Q92547 | 247 | 307 | 264 | 273 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OLC |
Q92547 | 247 | 307 | 279 | 281 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OLC |
Q92547 | 247 | 307 | 298 | 298 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
Q92547 | 247 | 307 | 301 | 301 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:17525332;Dbxref=PMID:17525332 |
Q92547 | 1421 | 1475 | 1435 | 1439 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3AL2 |
Q92547 | 1421 | 1475 | 1462 | 1465 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3AL2 |
Q92547 | 1421 | 1475 | 1 | 1522 | Chain | ID=PRO_0000072631;Note=DNA topoisomerase 2-binding protein 1 |
Q92547 | 1421 | 1475 | 1389 | 1486 | Domain | Note=BRCT 8;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00033 |
Q92547 | 1421 | 1475 | 1428 | 1433 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3AL2 |
Q92547 | 1421 | 1475 | 1453 | 1458 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3AL2 |
Q92547 | 1421 | 1475 | 1467 | 1474 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3AL2 |
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SNVs in the skipped exons for TOPBP1 |
- Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
- Differential PSIs between mutated versus non-mutated samples. |
TOPBP1_LUSC_exon_skip_388639_psi_boxplot.png |
TOPBP1_STAD_exon_skip_388639_psi_boxplot.png |
- Non-synonymous mutations located in the skipped exons in TCGA. |
Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
LIHC | TCGA-DD-A39Y-01 | exon_skip_388636 | 133327379 | 133327540 | 133327489 | 133327489 | Frame_Shift_Del | A | - | p.S1439fs |
STAD | TCGA-BR-4361-01 | exon_skip_388639 | 133335658 | 133335769 | 133335731 | 133335731 | Frame_Shift_Del | T | - | p.K1266fs |
UCEC | TCGA-D1-A174-01 | exon_skip_388639 | 133335658 | 133335769 | 133335731 | 133335731 | Frame_Shift_Del | T | - | p.K1266fs |
LIHC | TCGA-G3-A3CJ-01 | exon_skip_388640 | 133337057 | 133337277 | 133337094 | 133337094 | Frame_Shift_Del | A | - | p.F1185fs |
LIHC | TCGA-DD-A1EG-01 | exon_skip_388640 | 133337057 | 133337277 | 133337167 | 133337167 | Frame_Shift_Del | A | - | p.L1161fs |
LIHC | TCGA-DD-A1EG-01 | exon_skip_388640 | 133337057 | 133337277 | 133337230 | 133337230 | Frame_Shift_Del | T | - | p.N1140fs |
LIHC | TCGA-G3-A3CJ-01 | exon_skip_388640 | 133337057 | 133337277 | 133337230 | 133337230 | Frame_Shift_Del | T | - | p.N1140fs |
LIHC | TCGA-DD-A3A0-01 | exon_skip_388640 | 133337057 | 133337277 | 133337234 | 133337234 | Frame_Shift_Del | G | - | p.Q1139fs |
LIHC | TCGA-DD-A3A0-01 | exon_skip_388648 | 133371307 | 133371391 | 133371359 | 133371359 | Frame_Shift_Del | T | - | p.N346fs |
LIHC | TCGA-DD-A3A0-01 | exon_skip_388649 | 133371307 | 133371458 | 133371359 | 133371359 | Frame_Shift_Del | T | - | p.N346fs |
LIHC | TCGA-DD-A3A0-01 | exon_skip_388650 | 133371307 | 133371473 | 133371359 | 133371359 | Frame_Shift_Del | T | - | p.N346fs |
LIHC | TCGA-G3-A3CJ-01 | exon_skip_388648 | 133371307 | 133371391 | 133371359 | 133371359 | Frame_Shift_Del | T | - | p.N346fs |
LIHC | TCGA-G3-A3CJ-01 | exon_skip_388649 | 133371307 | 133371458 | 133371359 | 133371359 | Frame_Shift_Del | T | - | p.N346fs |
LIHC | TCGA-G3-A3CJ-01 | exon_skip_388650 | 133371307 | 133371473 | 133371359 | 133371359 | Frame_Shift_Del | T | - | p.N346fs |
COAD | TCGA-A6-5665-01 | exon_skip_388653 exon_skip_388654 | 133372189 | 133372368 | 133372307 | 133372307 | Frame_Shift_Del | A | - | p.D269fs |
COAD | TCGA-AA-3713-01 | exon_skip_388659 | 133379888 | 133379978 | 133379900 | 133379900 | Frame_Shift_Del | A | - | p.K25fs |
ESCA | TCGA-L5-A43J-01 | exon_skip_388659 | 133379888 | 133379978 | 133379900 | 133379900 | Frame_Shift_Del | A | - | p.F24fs |
ESCA | TCGA-L5-A43J-01 | exon_skip_388659 | 133379888 | 133379978 | 133379900 | 133379900 | Frame_Shift_Del | A | - | p.K25fs |
LIHC | TCGA-DD-A1EG-01 | exon_skip_388659 | 133379888 | 133379978 | 133379900 | 133379900 | Frame_Shift_Del | A | - | p.F24fs |
UCEC | TCGA-BS-A0UF-01 | exon_skip_388637 | 133331233 | 133331396 | 133331328 | 133331328 | Nonsense_Mutation | G | A | p.R1314* |
READ | TCGA-EI-6512-01 | exon_skip_388639 | 133335658 | 133335769 | 133335718 | 133335718 | Nonsense_Mutation | G | A | p.Q1271X |
LUSC | TCGA-60-2713-01 | exon_skip_388639 | 133335658 | 133335769 | 133335770 | 133335770 | Splice_Site | C | G | p.I1254_splice |
UCEC | TCGA-AP-A054-01 | exon_skip_388650 | 133371307 | 133371473 | 133371475 | 133371475 | Splice_Site | T | C | e7-2 |
- Depth of coverage in the three exons composing exon skipping event |
- 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 |
HEC59_ENDOMETRIUM | 133335658 | 133335769 | 133335731 | 133335731 | Frame_Shift_Del | T | - | p.K1266fs |
SNGM_ENDOMETRIUM | 133379888 | 133379978 | 133379900 | 133379900 | Frame_Shift_Del | A | - | p.F24fs |
SW48_LARGE_INTESTINE | 133379888 | 133379978 | 133379900 | 133379900 | Frame_Shift_Del | A | - | p.F24fs |
SNUC5_LARGE_INTESTINE | 133379888 | 133379978 | 133379900 | 133379900 | Frame_Shift_Del | A | - | p.F24fs |
ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 133327379 | 133327540 | 133327488 | 133327489 | Frame_Shift_Ins | - | A | p.S1439fs |
HEC1A_ENDOMETRIUM | 133335658 | 133335769 | 133335730 | 133335731 | Frame_Shift_Ins | - | T | p.Q1267fs |
SNU175_LARGE_INTESTINE | 133379888 | 133379978 | 133379899 | 133379900 | Frame_Shift_Ins | - | A | p.K25fs |
HARA_LUNG | 133331233 | 133331396 | 133331291 | 133331291 | Missense_Mutation | T | G | p.K1326T |
HCC366_LUNG | 133335658 | 133335769 | 133335762 | 133335762 | Missense_Mutation | G | A | p.T1256M |
NCIH630_LARGE_INTESTINE | 133337057 | 133337277 | 133337087 | 133337087 | Missense_Mutation | G | C | p.P1188A |
SW1417_LARGE_INTESTINE | 133337057 | 133337277 | 133337171 | 133337171 | Missense_Mutation | T | C | p.N1160D |
GB1_CENTRAL_NERVOUS_SYSTEM | 133371307 | 133371473 | 133371344 | 133371344 | Missense_Mutation | G | T | p.A351E |
GB1_CENTRAL_NERVOUS_SYSTEM | 133371307 | 133371391 | 133371344 | 133371344 | Missense_Mutation | G | T | p.A351E |
GB1_CENTRAL_NERVOUS_SYSTEM | 133371307 | 133371458 | 133371344 | 133371344 | Missense_Mutation | G | T | p.A351E |
MG63_BONE | 133371307 | 133371473 | 133371449 | 133371449 | Missense_Mutation | T | C | p.N316S |
MG63_BONE | 133371307 | 133371458 | 133371449 | 133371449 | Missense_Mutation | T | C | p.N316S |
SKMEL31_SKIN | 133372189 | 133372368 | 133372215 | 133372215 | Missense_Mutation | G | C | p.P299R |
SKOV3_OVARY | 133372189 | 133372368 | 133372227 | 133372227 | Missense_Mutation | T | C | p.N295S |
AN3CA_ENDOMETRIUM | 133372189 | 133372368 | 133372321 | 133372321 | Missense_Mutation | T | C | p.T264A |
SCMCRM2_SOFT_TISSUE | 133379888 | 133379978 | 133379950 | 133379950 | Missense_Mutation | G | C | p.P8A |
SNU81_LARGE_INTESTINE | 133331233 | 133331396 | 133331328 | 133331328 | Nonsense_Mutation | G | A | p.R1314* |
NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 133337057 | 133337277 | 133337215 | 133337215 | Nonsense_Mutation | C | T | p.W1145* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TOPBP1 |
sQTL information located at the skipped exons. |
Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TOPBP1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TOPBP1 |
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RelatedDrugs for TOPBP1 |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for TOPBP1 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |
TOPBP1 | C0023434 | Chronic Lymphocytic Leukemia | 1 | CTD_human |