Basic Information
VIS ID
TVIS20004400
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
E1
Start
2253
Integrated sequence
GATAGGGTAGATGATGGAGGTGATTGGAAGCAAATTGTTATGTTTTTAAGGTATCAAGGTGTAGAGTTTATGTCATTTTTAACTGCATTAAAAAGATTTT| |TGCAAGGCATACCTAAAAAAAATTGCATATTACTATATGGTGCAGCTAACACAGGTAAATCATTATTTGGTATGAGTTTAATGAAATTTCTGCAAGGGTC
Host Sequence
Chromosome
chr17
Cytoband
q21.2
Reference genome
GRCh37.p5
Start
39827047/41670795 (Hg38)
End
39827047/41670795 (Hg38)
Orient
-
Location type
Intergenic
Nearest miRNA
hsa-mir-1180/Upstream/153578; hsa-mir-10226/Downstream/823978;
Nearest TSS
ENST00000595228/Upstream/45953; ENST00000586699/Downstream/18090;
Nearest CpG islands
None/Target, chr17-CpG: 26/Upstream/4612, chr17-CpG: 99/Downstream/17786
Upstream sequence
GAGTAGCCTGAACAGAGATGTTTCTGGTTCACTGAGCTGCTGTGATTCTAACACCCCCTCTGGGGAGAGATCTGGAAATATAAACCCATGAGAGCTGAAC
Downstream sequence
CTCACTGCAGCCTCGACCTCCCAGGCTCAGGGGATCCTCCCACCTCAGCCTCCCAAGTATCTGGGACCACAGGCATGTGCCACCATATCCAGTGTATTAG
Target sequence
TGAACTAACGTGCAACTTTAGGAATCTTTTTTTTTTTTTTTTGAGACAGAGTCTCCCTCTGTCACCAGGCTGGAGTGCAGTGAGAGAGCACAATCACAG
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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