Basic Information
VIS ID
TVIS20003926
Fusion event
HPV-chr1:p36.21 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
754
Host Sequence
Chromosome
chr1
Cytoband
p36.21
Reference genome
GRCh37/hg19
Start
16138564/15812069 (Hg38)
End
16138564/15812069 (Hg38)
Location type
Intergenic
Fragile sites / regions
FRA1A
Nearest miRNA
hsa-mir-12136/Upstream/3233046; hsa-mir-101-1/Downstream/1046880;
Nearest TSS
ENST00000473358/Upstream/2721; ENST00000471538/Downstream/35795;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/52702, chr1-CpG: 152/Downstream/22696
Nearby gene
FLJ37453(+22145) ;
Upstream sequence
ggggtaatatattttaatttccttTGGCACATTCTCCCAAAGTGGTGCCTTGGGAGACATCAGAGAACTTTCAACAAGTTTTAAAAATAATGCATCACTA
Downstream sequence
TGTTGGTCACTAAGACTGTGAGGCAAATATGTAAGAGGGAGCAGTGGGAATGGAATACAATGTCGTGAGAtttatttatttagagacagagtcttcgcac
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