Basic Information
VIS ID
TVIS20004405
Fusion event
HPV-HCN4 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
3351
Integrated sequence
ATATTTTGTGCAGTTTAAAGATGATGCAGAAAAATATAGTAAAAATAAAGTATGGGAAGTTCATGCGGGTGGTCAGGTAATATTATGTCCTACATCTGTG| |TTTAGCAGCAACGAAGTATCCTCTCCTGAAATTATTAGGCAGCACTTGGCCAACCACCCCGCCGCGACCCATACCAAAGCCGTCGCCTTGGGCACCGAAG
Host Sequence
Chromosome
chr15
Cytoband
q24.1
Reference genome
GRCh37.p5
Start
73615951/73323610 (Hg38)
End
73615951/73323610 (Hg38)
Orient
-
Location type
Exon8
Target gene
HCN4
miRNAs that regulate target gene
hsa-mir-133a-3p ; hsa-mir-1-3p ; hsa-mir-133b ; hsa-mir-192-5p ; hsa-mir-557 ; hsa-mir-507 ; hsa-mir-6811-5p ; hsa-mir-6511b-5p ; hsa-mir-5589-3p ; hsa-mir-329-5p ; hsa-mir-4748 ; hsa-mir-4464 ; hsa-mir-4801 ; hsa-mir-4731-3p
Nearest miRNA
hsa-mir-10393/Upstream/23631; hsa-mir-11181/Downstream/1087747;
Nearest TSS
ENST00000557528/Upstream/25311; ENST00000558742/Downstream/11650;
Nearest CpG islands
None/Target, chr15-CpG: 55/Upstream/4422, chr15-CpG: 223/Downstream/43909
Upstream sequence
GTGGGAGCCGAGGGGGAGCCACAGGCCCCGGGGGGTGGGGAGGAGCTGGATGAGGGCAGGAGTGGGCTCAGTCCAGCGGGGGCAGAGAATCCAGCCAGCT
Downstream sequence
GTTTCAGGTGCCTTGGCGTCTGCCCGGCACCGAGGTTGCCCAGCCCAGATCCTGGGGGAGGGCGGAAGATGGCAGCAGGCAGGCGAGGGTGGTGGGTGAG
Target sequence
GTTGGATGTGGAAGGAGGATGAAGACGGTGTGTCCACCTGGGACGGGCTGCTGGCGGGCGAGGCGGAGCCCAGCGCAGAAGGGATCAGGGACTGCAGCC
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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