Basic Information
VIS ID
TVIS20004415
Fusion event
HPV-CASC21 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
2894
Integrated sequence
AAATACTAACACATTATGAAAATGATAGTACAGACCTACGTGACCATATAGACTATTGGAAACACATGCGCCTAGAATGTGCTATTTATTACAAGGCCAG| |AGAAATGGGATTTAAACATATTAACCACCAAGTGGTGCCAACACTGGCTGTATCAAAGAATAAAGCATTACAAGCAATTGAACTGCAACTAACGTTAGAA
Host Sequence
Chromosome
chr8
Cytoband
q24.21
Reference genome
GRCh37.p5
Start
128266756/127254511 (Hg38)
End
128266756/127254511 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA8C ; FRA8E
Target gene
CASC21
Nearest miRNA
hsa-mir-12123/Upstream/2432453; hsa-mir-10400/Downstream/541451;
Nearest TSS
ENST00000518652/Upstream/9874; ENST00000642795/Downstream/38301;
Nearest CpG islands
None/Target, chr8-CpG: 109/Upstream/695986, chr8-CpG: 29/Downstream/61131
Upstream sequence
AAATCCAACTTGAAGCACAGTTTATTTAACATTTTAGATAGTTTATAAAGTATTAACAAATTAAGCTGGGTGTGGTGGCTCACCCCTGTAATCCCAGCAT
Downstream sequence
GCCGGGTGTGGTGGCACAGGCCTGTAATGCCAGCTTCTTGGGAGGGTGAGGCAGGAGAATCACTTGAACCTGGAAGGCAGAGGCTGCAGGGAGCGGGGAT
Target sequence
TTTGGGAGAATGAGGTGGGTGGATCACGTGGAGTCAGGAGTTCGAGACCAGCCTCGCCAACATGGTGAAACCCTGTCTCTATTAAAAATATAAAAATTA
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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