Basic Information
VIS ID
TVIS20004416
Fusion event
HPV-LHFPL3 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
2908
Integrated sequence
TATGAAAATGATAGTACAGACCTACGTGACCATATAGACTATTGGAAACACATGCGCCTAGAATGTGCTATTTATTACAAGGCCAGAGAAATGGGATTTA| |AACATATTAACCACCAAGTGGTGCCAACACTGGCTGTATCAAAGAATAAAGCATTACAAGCAATTGAACTGCAACTAACGTTAGAAACAATATATAACTC
Host Sequence
Chromosome
chr7
Cytoband
q22.2
Reference genome
GRCh37.p5
Start
104159073/104518626 (Hg38)
End
104159073/104518626 (Hg38)
Orient
-
Location type
Intron1
Fragile sites / regions
FRA7F
Target gene
LHFPL3
miRNAs that regulate target gene
hsa-mir-4709-3p ; hsa-mir-578 ; hsa-mir-526b-5p ; hsa-mir-4635 ; hsa-mir-8067 ; hsa-mir-6508-5p ; hsa-mir-513c-3p ; hsa-mir-513a-3p ; hsa-mir-3606-3p ; hsa-mir-1269b ; hsa-mir-1269a ; hsa-mir-4497 ; hsa-mir-6780b-5p ; hsa-mir-4725-3p ; hsa-mir-5196-5p ; hsa-mir-4271 ; hsa-mir-4747-5p ; hsa-mir-6787-5p ; hsa-mir-663a ; hsa-mir-1908-5p ; hsa-mir-4515 ; hsa-mir-1288-3p ; hsa-mir-4740-5p ; hsa-mir-3202 ; hsa-mir-4749-5p ; hsa-mir-3195 ; hsa-mir-4706 ; hsa-mir-3179 ; hsa-mir-525-3p ; hsa-mir-524-3p ; hsa-mir-342-3p ; hsa-mir-6793-3p ; hsa-mir-574-3p ; hsa-mir-8485 ; hsa-mir-3939 ; hsa-mir-361-3p
Nearest miRNA
hsa-mir-10525/Upstream/2047095; hsa-mir-10399/Downstream/10134719;
Nearest TSS
ENST00000635602/Upstream/189926; ENST00000415513/Downstream/422437;
Nearest CpG islands
None/Target, chr7-CpG: 39/Upstream/189115, chr7-CpG: 45/Downstream/465264
Upstream sequence
AAATCTTTGACTAAGAGGTTGTACCTTGTTTTTTAAATAAATGATAATGGATGTCCAATCTCTATGGTGTTTAAATTCTACTACTGGACACATTTAAAAG
Downstream sequence
TACAAAAATTAGCCAGGCATAGTGGCAGGCACCTGCAATCTCAGCTATTCAGGAAGCTGAGGCAGGAGAATCACTTGAACATGGGAGGTGGAGGTTGCAG
Target sequence
TGCAATGCCACTTTGGGAGGCTGAGGCAGGCAGGTCACCTGAGGTCAGGAGTTAGAGGCCAGCCTGGCCAACATGGCGAAACCCTGTCTCCATTAAAAA
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.
Curate