Virus Integration Site Database Data Release 2.0

Details for VISDB ID: TVIS20055578

Genomic Region Visualization (IGV)

Basic Information ▶
VISDB IDTVIS20055578
Fusion NameHPV-LIMS1 integration
ValidatedNo
Curated WayCurated
MethodHigh-throughput Viral Integration Detection method
Wet AssayYes
Sample ID-
Sample NameS110
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 Chromosomechr2
Cytogenetic Bandq12.3
Human Strand+
Human Integration Location Typeintronic
Hg19 Start109275937
Hg19 End109275937
Hg38 Start108659481
Hg38 End108659481
Junction SequenceGTCCACTCTAGGTTTATGGAGAGGAAAATTCATTATAATCTGACATTATTTGGCTATGACCATGTAATGGATGGTTTTATGTAGAGGCTGTAGTGGAAAAAAAAACAGGGGATGCTATATCAGATGACGAGAACGAAAA
Target Gene ▶
Target GeneLIMS1
Nearby Gene-
Distance-
Virus Information ▶
Virus NameHuman Papillomavirus
Virus Subtype NameHPV16
Virus Genome AccessionAF534061
TaxonomyID10566
Virus AbbreviationHPV
Virus GenomeHuman papillomavirus type 16 East Asian type, complete genome
Virus Genome Length7905 bp
Virus Breakpoint1905
Virus Breakpoint2-
Virus Gene NameHpV16gp3_E1
Virus Region Type-
Integrated Virus Sequence-
ViMIC ID-
Predicted VIS Effect ▶
Gene IdENSG00000169756.18
Gene NameLIMS1
TranscriptTranscript 1: ENST00000695516.1, Transcript 2: ENST00000939438.1, Transcript 3: ENST00000968507.1, Transcript 4: ENST00000695517.1, Transcript 5: ENST00000968506.1, Transcript 6: ENST00000544547.6, Transcript 7: ENST00000695518.1, Transcript 8: ENST00000695519.1, Transcript 9: ENST00000332345.10, Transcript 10: ENST00000695520.1, Transcript 11: ENST00000393310.5, Transcript 12: ENST00000695521.1, Transcript 13: ENST00000410093.5, Transcript 14: ENST00000449684.6, Transcript 15: ENST00000409441.5, Transcript 16: ENST00000422797.5, Transcript 17: ENST00000338045.7, Transcript 18: ENST00000474038.1, Transcript 19: ENST00000462817.5, Transcript 20: ENST00000496653.4, Transcript 21: ENST00000695522.1, Transcript 22: ENST00000414829.2, Transcript 23: ENST00000434274.2, Transcript 24: ENST00000695523.1
Transcript 1 Regionintron
Transcript 1 Impactintronic_insertion
Transcript 2 Regionintron
Transcript 2 Impactintronic_insertion
Transcript 3 Regionintron
Transcript 3 Impactintronic_insertion
Transcript 4 Regionintron
Transcript 4 Impactintronic_insertion
Transcript 5 Regionintron
Transcript 5 Impactintronic_insertion
Transcript 6 Regionintron
Transcript 6 Impactintronic_insertion
Transcript 7 Regionintron
Transcript 7 Impactintronic_insertion
Transcript 8 Regionintron
Transcript 8 Impactintronic_insertion
Transcript 9 Regionintron
Transcript 9 Impactintronic_insertion
Transcript 10 Regionintron
Transcript 10 Impactintronic_insertion
Transcript 11 Regionintron
Transcript 11 Impactintronic_insertion
Transcript 12 Regionintron
Transcript 12 Impactintronic_insertion
Transcript 13 Regionintron
Transcript 13 Impactintronic_insertion
Transcript 14 Regionintron
Transcript 14 Impactintronic_insertion
Transcript 15 Regionintron
Transcript 15 Impactintronic_insertion
Transcript 16 Regionintron
Transcript 16 Impactintronic_insertion
Transcript 17 Regionintron
Transcript 17 Impactintronic_insertion
Transcript 18 Regionintron
Transcript 18 Impactintronic_insertion
Transcript 19 Regionintron
Transcript 19 Impactintronic_insertion
Transcript 20 Regionintron
Transcript 20 Impactintronic_insertion
Transcript 21 Regionintron
Transcript 21 Impactintronic_insertion
Transcript 22 Regionintron
Transcript 22 Impactintronic_insertion
Transcript 23 Regionintron
Transcript 23 Impactintronic_insertion
Transcript 24 Regionpromoter
Transcript 24 Impactpromoter_insertion
SpliceAI Score
Delta ScoresAcceptor Gain: 0.020 | Acceptor Loss: 0.010 | Donor Gain: 0.000 | Donor Loss: 0.030
Delta Score Max0.030
Delta Position at Max-25
Delta Score FlagLOW
GeneLIMS1
AlphaGenome Analysis
Windowchr2:108593945-108725017
RNA-seq Change (±2kb)Mean: -0.002672439906746149 | Peak: 7.39801025390625
ATAC Change (±2kb)Mean: -0.000504279974848032 | Peak: 2.1837158203125
InterpretationRNA-seq: minimal change -4.8% | Splice sites: no signal in region (REF≈0, ALT≈0) | ATAC: minimal change -1.1%
Visualization
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