Basic Information
VIS ID
TVIS20003890
Fusion event
HPV-chr9:q34.11 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
407
Host Sequence
Chromosome
chr9
Cytoband
q34.11
Reference genome
GRCh37/hg19
Start
131856423/129094144 (Hg38)
End
131856423/129094144 (Hg38)
Location type
Intergenic
Nearest miRNA
hsa-let-7a-1/Upstream/701430; hsa-mir-12126/Downstream/775461;
Nearest TSS
ENST00000422679/Upstream/9545; ENST00000434250/Downstream/3710;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/12675, chr9-CpG: 135/Downstream/16201
Nearby gene
CRAT(+649) ;
Upstream sequence
CTGTAAAAATACTTTGAATACTCTGTTATCTTAAATTTTATTTGTGTATTTTTATGAGATATTGATAAAAAATACAACTTTTTTTTTTTTTTAATCACAC
Downstream sequence
gtagtttgtgagatggctgtgatcctgtcggtaaggaacatttaaccaggaactgatttggttggttttcttgtcgctccctcattctttgagctctttc
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