Basic Information
VIS ID
TVIS20004287
Fusion event
HPV-chr5:p15.33 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
E7-E1
Start
861
Integrated sequence
GTGCGTACAAAGCACACACGTAGACATTCGTACTTTGGAAGACCTGTTAATGGGCACACTAGGAATTGTGTGCCCCATCTGTTCTCAGAAACCATAATCT| |ACCATGGCTGATCCTGCAGGTACCAATGGGGAAGAGGGTACGGGATGTAATGGATGGTTTTATGTAGAGGCTGTAGTGGAAAAAAAAACAGGGGATGCTA
Host Sequence
Chromosome
chr5
Cytoband
p15.33
Reference genome
GRCh37/hg19
Start
3875126/3875012 (Hg38)
End
3875126/3875012 (Hg38)
Nearest miRNA
hsa-mir-4277/Upstream/2166144; hsa-mir-10397/Downstream/2952841;
Nearest TSS
ENST00000502646/Upstream/274824; ENST00000503415/Downstream/138637;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/20330, chr5-CpG: 17/Downstream/87160
Junction sequence
ATGGGTAACATTCTCCAGGCGGCAGACAAGGCAAAGGCCATTGGTCT---[TG]---TACCTGGCTGATCCTGCAGGTACCAATGGGGAAGAGGGTACGGGATGTAATG
* 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