Basic Information
VIS ID
TVIS20004008
Fusion event
HPV-chr11:q13.3 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
E6
Start
549
Host Sequence
Chromosome
chr11
Cytoband
q13.3
Reference genome
GRCh37/hg19
Start
68950302/69182834 (Hg38)
End
68950302/69182834 (Hg38)
Location type
Intergenic
Fragile sites / regions
FRA11H ; FRA11A
Nearest miRNA
hsa-mir-10392/Upstream/99576; hsa-let-7a-2/Downstream/1101121;
Nearest TSS
ENST00000527297/Upstream/11270; ENST00000540760/Downstream/111304;
Nearest CpG islands
None/Target, chr11-CpG: 30/Upstream/25345, chr11-CpG: 26/Downstream/194225
Nearby gene
MYEOV(-111319) ;
Upstream sequence
ctccacgcacacacacacgatgcacacacatgcacaaacaTGCCTTTGCTTGTTTCCAACCATCCAAAAAAACGTAACTTTCTAAAACCAGGGAACTGAA
Downstream sequence
ATGCACCTTTAGCCCGATTTCTGGGAATGCCGTCTTCCTCTTAAAGCAGCAGCTGACGCAGGCTGATGCCAGCGCGGATTCTGCTGTGCTGGAAGCAAGC
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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