Basic Information
VIS ID
TVIS20003966
Fusion event
HPV-chr13:q22.1 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
1929
Host Sequence
Chromosome
chr13
Cytoband
q22.1
Reference genome
GRCh37/hg19
Start
73871219/73297082 (Hg38)
End
73871219/73297082 (Hg38)
Location type
Intergenic
Fragile sites / regions
FRA13B
Nearest miRNA
hsa-mir-1297/Upstream/7078758; hsa-mir-1267/Downstream/4400930;
Nearest TSS
ENST00000623511/Upstream/222067; ENST00000430033/Downstream/249759;
Nearest CpG islands
None/Target, chr13-CpG: 551/Upstream/236850, chr13-CpG: 31/Downstream/836890
Nearby gene
KLF12(+388929) ;
Upstream sequence
TCCAGCATTCTATGATGTACAAGTCACTCTATATCCCTCATCTTCAGTCACTAAATACCTCTATAAAATGTGCCAGGCAGCACCCTGCAAAGTAATTCAC
Downstream sequence
TTACCCATGTTGAGGATTGTGGGCCACAAACAGCACTTTGACAGGCACTTCTGTCTGGCGATTCTGTGTTCAGTTTGCTCAAGAACTCAGCGGTTTTGCT
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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