Basic Information
VIS ID
TVIS20004040
Fusion event
HPV-LOC105378833 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
E7
Start
2889
Host Sequence
Chromosome
chr1
Cytoband
p22.3
Reference genome
GRCh37/hg19
Start
87889221/87423538 (Hg38)
End
87889221/87423538 (Hg38)
Location type
Intronic
Fragile sites / regions
FRA1D
Target gene
LOC105378833
Nearest miRNA
hsa-mir-101-1/Upstream/1065851; hsa-mir-11399/Downstream/6423294;
Nearest TSS
ENST00000473358/Upstream/51883; ENST00000436111/Downstream/482176;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/87989, chr1-CpG: 63/Downstream/1039062
Nearby gene
PKN2(-1260700) ;
Upstream sequence
ggtGACAGAGTGAGATTCCATCTCAAGAAAAAAAAAAAAAGTAGggccaggcgcggtggctcacgcatgtaatcccagcactttgggaggccaaggcggg
Downstream sequence
tggatcacgaggtcaagagatggagaccatcctggccaacttgatgaaaccccgtctctactaaaaatacaaaaattagccaggcgtggtggcgggcgcc
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