Virus Integration Site Database Data Release 2.0

Details for VISDB ID: TVIS20065154

Genomic Region Visualization (IGV)

Basic Information ▶
VISDB IDTVIS20065154
Fusion NameHPV-NUP98 integration
ValidatedNo
Curated WayCurated
MethodHigh-throughput Viral Integration Detection method
Wet AssayYes
Sample ID-
Sample NameS024
Sample TypeTumor
Age57 = 59; >57 = 50
Gender-
Disease Information ▶
Disease NameOropharyngeal squamous cell carcinoma
Disease AbbreviationOPSCC
CancerYes
Literature ▶
PubMed ID38279874
JournalClinical and Translational Medicine
Published Year2024
Human Genome ▶
Human Genome Version DescriptionGRCh37/hg19
Human Genome RefSeq AccessionGCF_000001405.13
Human Chromosomechr11
Cytogenetic Bandp15.4
Human Strand-
Human Integration Location Typeintronic
Hg19 Start3703399
Hg19 End3703399
Hg38 Start3682169
Hg38 End3682169
Junction SequenceTAAAAGCCATTTTTGGTTGCAGCCATTATATGATGCCAAAATAGCTATGTTAGATGATGCTACATCGCCATGTTGGGCATATATAGACCAATATTTAAGAAATGCACTAGATGGAAATCCTATTTCATTAGATGTAAAGCCTAAAAATACAGAAAAGTTAGCCAGGCATGGTGGCGGGCACCTGTAATCCCAGCTACTCGGGAGGCTGAG
Target Gene ▶
Target GeneNUP98
Nearby Gene-
Distance-
Virus Information ▶
Virus NameHuman Papillomavirus
Virus Subtype NameHPV35
Virus Genome AccessionHQ537713
TaxonomyID10566
Virus AbbreviationHPV
Virus GenomeHuman papillomavirus type 35 isolate Z049, complete genome
Virus Genome Length7883 bp
Virus Breakpoint12475
Virus Breakpoint2-
Virus Gene NameHpV35gp3_E1
Virus Region Type-
Integrated Virus Sequence-
ViMIC ID-
Predicted VIS Effect ▶
Gene IdENSG00000110713.19
Gene NameNUP98
TranscriptTranscript 1: ENST00000915300.1, Transcript 2: ENST00000915301.1, Transcript 3: ENST00000915302.1, Transcript 4: ENST00000915303.1, Transcript 5: ENST00000359171.8, Transcript 6: ENST00000915305.1, Transcript 7: ENST00000915304.1, Transcript 8: ENST00000851289.1, Transcript 9: ENST00000915312.1, Transcript 10: ENST00000915311.1, Transcript 11: ENST00000915308.1, Transcript 12: ENST00000915309.1, Transcript 13: ENST00000324932.12, Transcript 14: ENST00000915299.1, Transcript 15: ENST00000915310.1, Transcript 16: ENST00000915307.1, Transcript 17: ENST00000943236.1, Transcript 18: ENST00000915306.1, Transcript 19: ENST00000943237.1, Transcript 20: ENST00000529379.2, Transcript 21: ENST00000700595.1, Transcript 22: ENST00000700596.1, Transcript 23: ENST00000700597.1, Transcript 24: ENST00000700598.1, Transcript 25: ENST00000527104.6, Transcript 26: ENST00000355260.8, Transcript 27: ENST00000700599.1, Transcript 28: ENST00000700600.1, Transcript 29: ENST00000529063.2, Transcript 30: ENST00000650171.1, Transcript 31: ENST00000700601.1, Transcript 32: ENST00000469881.2, Transcript 33: ENST00000700602.1, Transcript 34: ENST00000943238.1, Transcript 35: ENST00000851290.1, Transcript 36: ENST00000429801.5, Transcript 37: ENST00000915314.1, Transcript 38: ENST00000915313.1, Transcript 39: ENST00000700603.1, Transcript 40: ENST00000524563.1
Transcript 1 Regionintron
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Transcript 32 Regionpromoter
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SpliceAI Score
Delta ScoresAcceptor Gain: 0.050 | Acceptor Loss: 0.010 | Donor Gain: 0.030 | Donor Loss: 0.010
Delta Score Max0.050
Delta Position at Max-136
Delta Score FlagLOW
GeneNUP98
AlphaGenome Analysis
Windowchr11:3616633-3747705
RNA-seq Change (±2kb)Mean: -0.0004728824133053422 | Peak: 4.1075439453125
ATAC Change (±2kb)Mean: -0.0013139506336301565 | Peak: 1.7887954711914062
InterpretationRNA-seq: minimal change -0.6% | Splice sites: no signal in region (REF≈0, ALT≈0) | ATAC: minimal change -5.3%
Visualization
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