Basic Information
VIS ID
TVIS20003846
Fusion event
HPV-chr9:q31.3 integration
Validated
No
Detection method
RNA-Seq
Data source
Curated
Sample type
Tumor
Disease
Head and neck squamous cell carcinoma (HNSCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
28928286
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
Not given
Gene
E4
Start
2863
Host Sequence
Chromosome
chr9
Cytoband
q31.3
Reference genome
GRCh37/hg19
Start
111541094/108778814 (Hg38)
End
111541094/108778814 (Hg38)
Location type
Intergenic
Fragile sites / regions
FRA9E
Nearest miRNA
hsa-let-7a-1/Upstream/2177792; hsa-mir-12126/Downstream/267415;
Nearest TSS
ENST00000422679/Upstream/75722; ENST00000333999/Downstream/78153;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/1061675, chr9-CpG: 67/Downstream/76226
Nearby gene
ACTL7B(+75774) ;
Upstream sequence
CTCTCCCCTCCCTGTCCTGCCTGGGCTGGCTGCAGGCCCACTCCTGGCTGCTCATGCAGCACTCTGCCCTGCTGTGTACCCTGTTTCCTAGCGGTTCTAG
Downstream sequence
atatctggaaggaagatattacaggcagaggaccacaatatgacaactaaggccagggaagaagaaggggtgaaacccctaggaaaatcaggacatgtaa
Reference
Koneva, L. A., et al. HPV Integration in HNSCC Correlates with Survival Outcomes, Immune Response Signatures, and Candidate Drivers. Mol Cancer Res ,2018,16(1): 90-102.
Curate