Basic Information
VIS ID
TVIS20004278
Fusion event
HPV-LOC101928856 integration
Validated
Yes
Detection method
WGS, RNA-seq, Whole-Exome sequencing, PCR
Data source
Curated
Sample type
Tumor
Disease
Head and neck squamous cell carcinoma (HNSCC)
Quality evaluation
Perfect
Reported year
2014
PubMed ID
25313082
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
AY686584
Gene
E1
Start
1716
Integrated sequence
AAAAACACTATTACAACAATATTGTTTATATTTACACATTCAAAGTTTAGCATGTTCATGGGGAATGGTTGTGTTACTATTAGTAAGATATAAATGTGGA| |AAAAATAGAGAAACAATTGAAAAATTGCTGTCTAAACTATTATGTGTGTCTCCAATGTGTATGATGATAGAGCCTCCAAAATTGCGTAGTACAGCAGCAG
Host Sequence
Chromosome
chr3
Cytoband
q26.33
Reference genome
GRCh37/hg19
Start
180310599/180592811 (Hg38)
End
180310599/180592811 (Hg38)
Location type
Intronic
Target gene
LOC101928856
Nearest miRNA
hsa-let-7g/Upstream/4077660; hsa-mir-1224/Downstream/3293989;
Nearest TSS
ENST00000440867/Upstream/178599; ENST00000491380/Downstream/9124;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/555354, chr3-CpG: 55/Downstream/9224
Junction sequence
GCAATCTCTGCCTCCTGGGTTCAAGC---GAAAAAATAGAGAAACAATTGAAAAATTGCTGTCTAAACTATTATGTGTGTCTCCAATGTGTATGATGATAGAGC
* Color:  Human Sequence / Virus Sequence / Overlapped sequence / Unknown sequence
Reference
Parfenov, M., et al. Characterization of HPV and host genome interactions in primary head and neck cancers. Proc Natl Acad Sci U S A,2014,111(43): 15544-15549.
Curate