Basic Information
VIS ID
TVIS20003888
Fusion event
HPV-chr5:p14.1 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
684
Host Sequence
Chromosome
chr5
Cytoband
p14.1
Reference genome
GRCh37/hg19
Start
26129128/26129019 (Hg38)
End
26129128/26129019 (Hg38)
Location type
Intergenic
Fragile sites / regions
FRA5E
Nearest miRNA
hsa-mir-10397/Upstream/8973027; hsa-mir-103a-1/Downstream/5807083;
Nearest TSS
ENST00000502646/Upstream/683094; ENST00000514255/Downstream/270800;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/219477, chr5-CpG: 28/Downstream/540420
Nearby gene
CDH9(+751580) ;
Upstream sequence
GCTGTAACAACATTCTGAGTTAAAGAGTTAAAGTAATTTGGTTTAAAATGTGTACAGGATGAAGAGGGATGGCCAGAAAATACTTTGATCCTTGATGCTG
Downstream sequence
cttcctcataccccaggatttttcaggctcttcttgtattttcttatcctggctgtgtcacttttctagtggtaaatggtgtttaaaatccaacatcttg
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