Basic Information
VIS ID
TVIS20004414
Fusion event
HPV-LAMTOR4 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
1124
Integrated sequence
ATGATAATGATTATTTAACACAGGCAGAAACAGAGACAGCACATGCGTTGTTTACTGCACAGGAAGCAAAACAACATAGAGATGCAGTACAGGTTCTAAA| |ACGAAAGTATTTGGTAGTCCACTTAGTGATATTAGTGGATGTGTAGACAATAATATTAGTCCTAGATTAAAAGCTATATGTATAGAAAAACAAAGTAGAG
Host Sequence
Chromosome
chr7
Cytoband
q21.1
Reference genome
GRCh37.p5
Start
99750064/100152441 (Hg38)
End
99750064/100152441 (Hg38)
Orient
-
Location type
Intron2
Fragile sites / regions
FRA7F
Target gene
LAMTOR4
miRNAs that regulate target gene
hsa-mir-16-5p ; hsa-mir-766-3p ; hsa-mir-424-5p ; hsa-mir-331-3p
Nearest miRNA
hsa-mir-10525/Upstream/58367; hsa-mir-10399/Downstream/4164;
Nearest TSS
ENST00000635602/Upstream/3082; ENST00000488338/Downstream/239;
Nearest CpG islands
None/Target, chr7-CpG: 39/Upstream/3421, chr7-CpG: 81/Downstream/5752
Upstream sequence
CTACAAAAAATTAGCCTGGCATGGAAGCACATGCATGTAATCCCAGCTTCTTGGGAGGTTGAGGCAGGAGAATTGCTTGAACCCAGGAGGCAGAGGTTGC
Downstream sequence
GATTGGGAAGGAGGTGGATAAGGATAAGGTGAAATTTGATGGCCCAACTTTAGACATTGAGTTTGATATAAAATAGCAGTTAATATATATTGCTAGTTCA
Target sequence
AGTGAGCCAAGATTGCACCACTGTACTCCAGCCTGGGTGATAGAGTGAGACTCTGTCTCAAAAAACAAACAAACAAACAGGAAATCAAAAAAAGAAGTG
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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