Basic Information
VIS ID
TVIS20003963
Fusion event
HPV-chr9:p24.1 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
E1
Start
730
Host Sequence
Chromosome
chr9
Cytoband
p24.1
Reference genome
GRCh37/hg19
Start
5579823/5579823 (Hg38)
End
5579823/5579823 (Hg38)
Location type
Intergenic
Nearest miRNA
hsa-mir-101-2/Upstream/729448; hsa-let-7a-1/Downstream/428003;
Nearest TSS
ENST00000422679/Upstream/69253; ENST00000443792/Downstream/4667;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/129194, chr9-CpG: 107/Downstream/48747
Nearby gene
RIC1(-49295) ;
Upstream sequence
ATGGAAAATCTGTTTTATTGCATAGAAGTTAAGTGCCTTAAAATACTTTTTACTTTACAAATTCAATCTGATTCTAAATAAATTGGTTGGAAACATCAGC
Downstream sequence
TTCACTCACAGGCCAGCCAACCTCCCCCAGCCCACCCCGGCATCCGCCCTTGTGGTTTCACACAGGCCTTCCTCACAGGCCAGTGTCCTAATGGGAGACT
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.
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