Basic Information
VIS ID
TVIS20004413
Fusion event
HPV-chr17:q21.2 integration
Validated
Yes
Detection method
DIPS-PCR
Data source
Curated
Sample type
Tumor
Disease
Oropharyngeal squamous cell carcinoma (OSCC)
Quality evaluation
Normal
Reported year
2014
PubMed ID
24586376
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
NC_001526.1
Gene
E2
Start
2875
Integrated sequence
TTAAATGTGTGTCAGGACAAAATACTAACACATTATGAAAATGATAGTACAGACCTACGTGACCATATAGACTATTGGAAACACATGCGCCTAGAATGTG| |CTATTTATTACAAGGCCAGAGAAATGGGATTTAAACATATTAACCACCAAGTGGTGCCAACACTGGCTGTATCAAAGAATAAAGCATTACAAGCAATTGA
Host Sequence
Chromosome
chr17
Cytoband
q21.2
Reference genome
GRCh37.p5
Start
39678949/41522697 (Hg38)
End
39678949/41522697 (Hg38)
Orient
+
Location type
Intergenic
Nearest miRNA
hsa-mir-1180/Upstream/5480; hsa-mir-10226/Downstream/972076;
Nearest TSS
ENST00000595228/Upstream/168; ENST00000586699/Downstream/2054;
Nearest CpG islands
None/Target, chr17-CpG: 26/Upstream/658848, chr17-CpG: 83/Downstream/4959
Nearby gene
MIR6510(-773) ; KRT19(+920) ;
Nearest cancer related gene
KRT19(TSG, +920) ;
Upstream sequence
GAAGAAGTGGGACTTCTTTTGGGGCCTCTTCCTTACCTTGAATTGGCCTCAGTTCTTGGCAGCTGAGATGTAAACCACAGGAGCAGGGCCATACCTACCC
Downstream sequence
TCACTGCTGGGTCCCATTCTGGGCTCTGGGCCCAGGTATGGGCTGGTGGGCGTTAAAGGGCTTATGCAGGGCTGCCCCAAAAATGGGTGAATGTGTTAGT
Target sequence
AAGGGCAGAGTTGTACCAGGAAGCTGGGACTTCGTTCTTTTGCTGGCCCAGGGCAGGCCCCAGGCAAGCCAGGGTTGGGGTCTCTGTGGGAGGTCTGGG
Reference
Olthof, N. C., et al.Comprehensive analysis of HPV16 integration in OSCC reveals no significant impact of physical status on viral oncogene and virally disrupted human gene expression.2014, PLoS One 9(2): e88718.
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