Basic Information
VIS ID
TVIS20003973
Fusion event
HPV-LOC107985478 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
1190
Host Sequence
Chromosome
chr21
Cytoband
q22.3
Reference genome
GRCh37/hg19
Start
43084796/41664636 (Hg38)
End
43084796/41664636 (Hg38)
Location type
Intronic
Target gene
LOC107985478
Nearest miRNA
hsa-let-7c/Upstream/497007; hsa-mir-5692b/Downstream/82136;
Nearest TSS
ENST00000624081/Upstream/83317; ENST00000413718/Downstream/14545;
Nearest CpG islands
None/Target, chr21-CpG: 261/Upstream/155889, chr21-CpG: 32/Downstream/24553
Nearby gene
LINC00111(-14665) ;
Upstream sequence
TTACGGGGGAACCTGACAGTGCCCCTCAGCAGTTCTGATTCTAAAAACTGTCACACGCTGGGGGTGTCACCCGCAGAGGGAGGGGGTTCTTGTTTATCCA
Downstream sequence
GCAAGCGTGTGAGTACGGGCTTAAATCGTGACGACCACCTCTCCAGCAGCTTGACAGTCCCCCACTGGCAAACTCCTTGAATTTTCTGGAGGTCAGGTAA
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