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Center for Computational Systems Medicine
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Gene summary

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Gene structures and expression levels

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Exon skipping events with PSIs in TCGA

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Exon skipping events with PSIs in GTEx

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Open reading frame (ORF) annotation in the exon skipping event

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Exon skipping events in the canonical protein sequence

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SNVs in the skipped exons with depth of coverage

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

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Related drugs with this gene

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Related diseases with this gene

Gene summary for TOPBP1

check button Gene summary
Gene informationGene symbol

TOPBP1

Gene ID

11073

Gene nameDNA topoisomerase II binding protein 1
SynonymsTOP2BP1
Cytomap

3q22.1

Type of geneprotein-coding
DescriptionDNA topoisomerase 2-binding protein 1DNA topoisomerase II-beta-binding protein 1topoisomerase (DNA) II binding protein 1
Modification date20180523
UniProtAcc

Q92547

ContextPubMed: TOPBP1 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract]
- Title (PMID)

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed 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

check buttonSkipped 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.
all structure

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Gene isoform structures and expression levels for TOPBP1

check button Expression levels of gene isoforms across TCGA.
gencode gene structure

check button Expression levels of gene isoforms across GTEx.
gencode gene structure


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Exon skipping events with PSIs in TCGA for TOPBP1

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_3886363133319416:133320237:133327378:133327540:133327716:133327806133327378:133327540ENSG00000163781.8ENST00000260810.5
exon_skip_3886373133329847:133329985:133331232:133331396:133335657:133335769133331232:133331396ENSG00000163781.8ENST00000260810.5
exon_skip_3886393133331232:133331396:133335657:133335769:133336003:133336170133335657:133335769ENSG00000163781.8ENST00000260810.5
exon_skip_3886403133336003:133336170:133337056:133337277:133338998:133339191133337056:133337277ENSG00000163781.8ENST00000260810.5
exon_skip_3886463133342154:133342301:133342895:133343019:133347205:133347235133342895:133343019ENSG00000163781.8ENST00000513818.1,ENST00000260810.5
exon_skip_3886483133368777:133368787:133371306:133371391:133372188:133372312133371306:133371391ENSG00000163781.8ENST00000572787.1
exon_skip_3886493133368777:133368787:133371306:133371458:133372188:133372312133371306:133371458ENSG00000163781.8ENST00000508524.1
exon_skip_3886503133368777:133368787:133371306:133371473:133372188:133372312133371306:133371473ENSG00000163781.8ENST00000260810.5
exon_skip_3886533133368777:133368787:133372188:133372368:133374133:133374330133372188:133372368ENSG00000163781.8ENST00000511439.1
exon_skip_3886543133371306:133371473:133372188:133372368:133374133:133374330133372188:133372368ENSG00000163781.8ENST00000260810.5
exon_skip_3886593133377859:133377994:133379887:133379978:133380612:133380737133379887:133379978ENSG00000163781.8ENST00000260810.5

check button PSI values of skipped exons in TCGA.
psi tcga

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Exon skipping events with PSIs in GTEx for TOPBP1

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_3886363133319416:133320237:133327378:133327540:133327716:133327806133327378:133327540ENSG00000163781.8ENST00000260810.5
exon_skip_3886373133329847:133329985:133331232:133331396:133335657:133335769133331232:133331396ENSG00000163781.8ENST00000260810.5
exon_skip_3886393133331232:133331396:133335657:133335769:133336003:133336170133335657:133335769ENSG00000163781.8ENST00000260810.5
exon_skip_3886403133336003:133336170:133337056:133337277:133338998:133339191133337056:133337277ENSG00000163781.8ENST00000260810.5
exon_skip_3886463133342154:133342301:133342895:133343019:133347205:133347235133342895:133343019ENSG00000163781.8ENST00000260810.5,ENST00000513818.1
exon_skip_3886483133368777:133368787:133371306:133371391:133372188:133372312133371306:133371391ENSG00000163781.8ENST00000572787.1
exon_skip_3886493133368777:133368787:133371306:133371458:133372188:133372312133371306:133371458ENSG00000163781.8ENST00000508524.1
exon_skip_3886503133368777:133368787:133371306:133371473:133372188:133372312133371306:133371473ENSG00000163781.8ENST00000260810.5
exon_skip_3886533133368777:133368787:133372188:133372368:133374133:133374330133372188:133372368ENSG00000163781.8ENST00000511439.1
exon_skip_3886543133371306:133371473:133372188:133372368:133374133:133374330133372188:133372368ENSG00000163781.8ENST00000260810.5
exon_skip_3886593133377859:133377994:133379887:133379978:133380612:133380737133379887:133379978ENSG00000163781.8ENST00000260810.5

check button PSI values of skipped exons in GTEx.
psi gtex

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for TOPBP1

check button Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000002608101333798871333799783UTR-3CDS
ENST00000260810133331232133331396Frame-shift
ENST00000260810133335657133335769Frame-shift
ENST00000260810133337056133337277Frame-shift
ENST00000260810133342895133343019Frame-shift
ENST00000260810133371306133371473Frame-shift
ENST00000260810133327378133327540In-frame
ENST00000260810133372188133372368In-frame

check button Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000002608101333798871333799783UTR-3CDS
ENST00000260810133331232133331396Frame-shift
ENST00000260810133335657133335769Frame-shift
ENST00000260810133337056133337277Frame-shift
ENST00000260810133342895133343019Frame-shift
ENST00000260810133371306133371473Frame-shift
ENST00000260810133327378133327540In-frame
ENST00000260810133372188133372368In-frame

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Infer the effects of exon skipping event on protein functional features for TOPBP1

check button Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.
prot feature distribution

check button Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST00000260810539515221333721881333723688751054247307
ENST00000260810539515221333273781333275404396455714211475

check button Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST00000260810539515221333721881333723688751054247307
ENST00000260810539515221333273781333275404396455714211475

check button 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 featureDescription of feature
Q92547247307260262Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OLC
Q92547247307282284Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OLC
Q9254724730711522ChainID=PRO_0000072631;Note=DNA topoisomerase 2-binding protein 1
Q92547247307195284DomainNote=BRCT 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00033
Q92547247307249256HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OLC
Q92547247307264273HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OLC
Q92547247307279281HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OLC
Q92547247307298298Modified residueNote=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163
Q92547247307301301Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:17525332;Dbxref=PMID:17525332
Q925471421147514351439Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3AL2
Q925471421147514621465Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3AL2
Q925471421147511522ChainID=PRO_0000072631;Note=DNA topoisomerase 2-binding protein 1
Q925471421147513891486DomainNote=BRCT 8;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00033
Q925471421147514281433HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3AL2
Q925471421147514531458HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3AL2
Q925471421147514671474HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3AL2


check button 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 featureDescription of feature
Q92547247307260262Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OLC
Q92547247307282284Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OLC
Q9254724730711522ChainID=PRO_0000072631;Note=DNA topoisomerase 2-binding protein 1
Q92547247307195284DomainNote=BRCT 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00033
Q92547247307249256HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OLC
Q92547247307264273HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OLC
Q92547247307279281HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OLC
Q92547247307298298Modified residueNote=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163
Q92547247307301301Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:17525332;Dbxref=PMID:17525332
Q925471421147514351439Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3AL2
Q925471421147514621465Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3AL2
Q925471421147511522ChainID=PRO_0000072631;Note=DNA topoisomerase 2-binding protein 1
Q925471421147513891486DomainNote=BRCT 8;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00033
Q925471421147514281433HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3AL2
Q925471421147514531458HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3AL2
Q925471421147514671474HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3AL2


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SNVs in the skipped exons for TOPBP1

check button - Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.
lollipop

check button - Differential PSIs between mutated versus non-mutated samples.
TOPBP1_LUSC_exon_skip_388639_psi_boxplot.png
boxplot
TOPBP1_STAD_exon_skip_388639_psi_boxplot.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
LIHCTCGA-DD-A39Y-01exon_skip_388636
133327379133327540133327489133327489Frame_Shift_DelA-p.S1439fs
STADTCGA-BR-4361-01exon_skip_388639
133335658133335769133335731133335731Frame_Shift_DelT-p.K1266fs
UCECTCGA-D1-A174-01exon_skip_388639
133335658133335769133335731133335731Frame_Shift_DelT-p.K1266fs
LIHCTCGA-G3-A3CJ-01exon_skip_388640
133337057133337277133337094133337094Frame_Shift_DelA-p.F1185fs
LIHCTCGA-DD-A1EG-01exon_skip_388640
133337057133337277133337167133337167Frame_Shift_DelA-p.L1161fs
LIHCTCGA-DD-A1EG-01exon_skip_388640
133337057133337277133337230133337230Frame_Shift_DelT-p.N1140fs
LIHCTCGA-G3-A3CJ-01exon_skip_388640
133337057133337277133337230133337230Frame_Shift_DelT-p.N1140fs
LIHCTCGA-DD-A3A0-01exon_skip_388640
133337057133337277133337234133337234Frame_Shift_DelG-p.Q1139fs
LIHCTCGA-DD-A3A0-01exon_skip_388648
133371307133371391133371359133371359Frame_Shift_DelT-p.N346fs
LIHCTCGA-DD-A3A0-01exon_skip_388649
133371307133371458133371359133371359Frame_Shift_DelT-p.N346fs
LIHCTCGA-DD-A3A0-01exon_skip_388650
133371307133371473133371359133371359Frame_Shift_DelT-p.N346fs
LIHCTCGA-G3-A3CJ-01exon_skip_388648
133371307133371391133371359133371359Frame_Shift_DelT-p.N346fs
LIHCTCGA-G3-A3CJ-01exon_skip_388649
133371307133371458133371359133371359Frame_Shift_DelT-p.N346fs
LIHCTCGA-G3-A3CJ-01exon_skip_388650
133371307133371473133371359133371359Frame_Shift_DelT-p.N346fs
COADTCGA-A6-5665-01exon_skip_388653
exon_skip_388654
133372189133372368133372307133372307Frame_Shift_DelA-p.D269fs
COADTCGA-AA-3713-01exon_skip_388659
133379888133379978133379900133379900Frame_Shift_DelA-p.K25fs
ESCATCGA-L5-A43J-01exon_skip_388659
133379888133379978133379900133379900Frame_Shift_DelA-p.F24fs
ESCATCGA-L5-A43J-01exon_skip_388659
133379888133379978133379900133379900Frame_Shift_DelA-p.K25fs
LIHCTCGA-DD-A1EG-01exon_skip_388659
133379888133379978133379900133379900Frame_Shift_DelA-p.F24fs
UCECTCGA-BS-A0UF-01exon_skip_388637
133331233133331396133331328133331328Nonsense_MutationGAp.R1314*
READTCGA-EI-6512-01exon_skip_388639
133335658133335769133335718133335718Nonsense_MutationGAp.Q1271X
LUSCTCGA-60-2713-01exon_skip_388639
133335658133335769133335770133335770Splice_SiteCGp.I1254_splice
UCECTCGA-AP-A054-01exon_skip_388650
133371307133371473133371475133371475Splice_SiteTCe7-2

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description
TOPBP1_133331232_133331396_133335657_133335769_133336003_133336170_TCGA-60-2713-01Sample: TCGA-60-2713-01
Cancer type: LUSC
ESID: exon_skip_388639
Skipped exon start: 133335658
Skipped exon end: 133335769
Mutation start: 133335770
Mutation end: 133335770
Mutation type: Splice_Site
Reference seq: C
Mutation seq: G
AAchange: p.I1254_splice
exon_skip_100894_LUSC_TCGA-60-2713-01.png
boxplot
exon_skip_286384_LUSC_TCGA-60-2713-01.png
boxplot
exon_skip_376191_LUSC_TCGA-60-2713-01.png
boxplot
exon_skip_388639_LUSC_TCGA-60-2713-01.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
HEC59_ENDOMETRIUM133335658133335769133335731133335731Frame_Shift_DelT-p.K1266fs
SNGM_ENDOMETRIUM133379888133379978133379900133379900Frame_Shift_DelA-p.F24fs
SW48_LARGE_INTESTINE133379888133379978133379900133379900Frame_Shift_DelA-p.F24fs
SNUC5_LARGE_INTESTINE133379888133379978133379900133379900Frame_Shift_DelA-p.F24fs
ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE133327379133327540133327488133327489Frame_Shift_Ins-Ap.S1439fs
HEC1A_ENDOMETRIUM133335658133335769133335730133335731Frame_Shift_Ins-Tp.Q1267fs
SNU175_LARGE_INTESTINE133379888133379978133379899133379900Frame_Shift_Ins-Ap.K25fs
HARA_LUNG133331233133331396133331291133331291Missense_MutationTGp.K1326T
HCC366_LUNG133335658133335769133335762133335762Missense_MutationGAp.T1256M
NCIH630_LARGE_INTESTINE133337057133337277133337087133337087Missense_MutationGCp.P1188A
SW1417_LARGE_INTESTINE133337057133337277133337171133337171Missense_MutationTCp.N1160D
GB1_CENTRAL_NERVOUS_SYSTEM133371307133371473133371344133371344Missense_MutationGTp.A351E
GB1_CENTRAL_NERVOUS_SYSTEM133371307133371391133371344133371344Missense_MutationGTp.A351E
GB1_CENTRAL_NERVOUS_SYSTEM133371307133371458133371344133371344Missense_MutationGTp.A351E
MG63_BONE133371307133371473133371449133371449Missense_MutationTCp.N316S
MG63_BONE133371307133371458133371449133371449Missense_MutationTCp.N316S
SKMEL31_SKIN133372189133372368133372215133372215Missense_MutationGCp.P299R
SKOV3_OVARY133372189133372368133372227133372227Missense_MutationTCp.N295S
AN3CA_ENDOMETRIUM133372189133372368133372321133372321Missense_MutationTCp.T264A
SCMCRM2_SOFT_TISSUE133379888133379978133379950133379950Missense_MutationGCp.P8A
SNU81_LARGE_INTESTINE133331233133331396133331328133331328Nonsense_MutationGAp.R1314*
NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE133337057133337277133337215133337215Nonsense_MutationCTp.W1145*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TOPBP1

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA 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

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for TOPBP1

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
TOPBP1C0023434Chronic Lymphocytic Leukemia1CTD_human