Basic Information
VIS ID
TVIS20004240
Fusion event
HPV-LOC100506023 integration
Validated
Yes
Detection method
WGS, RNA-seq, Whole-Exome sequencing, PCR
Data source
Curated
Sample type
Tumor
Disease
Head and neck squamous cell carcinoma (HNSCC)
Quality evaluation
Perfect
Reported year
2014
PubMed ID
25313082
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
AY686584
Gene
E1
Start
2143
Integrated sequence
AAAAGTAATTCACAGGCAAAAATTGTAAAGGATTGTGCAACAATGTGTAGACATTATAAACGAGCAGAAAAAAAACAAATGAGTATGAGTCAATGGATAA| |AATATAGATGTGATAGGGTAGATGATGGAGGTGATTGGAAGCAAATTGTTATGTTTTTAAGGTATCAAGGTGTAGAGTTTATGTCATTTTTAACTGCATT
Host Sequence
Chromosome
chr1
Cytoband
q25.1
Reference genome
GRCh37/hg19
Start
173239973/173270834 (Hg38)
End
173239973/173270834 (Hg38)
Location type
Intronic
Fragile sites / regions
FRA1G
Target gene
LOC100506023
Nearest miRNA
hsa-mir-101-1/Upstream/1126190; hsa-mir-1182/Downstream/2697536;
Nearest TSS
ENST00000473358/Upstream/63521; ENST00000460950/Downstream/171263;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/737429, chr1-CpG: 100/Downstream/206005
Junction sequence
CTATAGTACATTTTTTAATGAGGTGGCAC---TTTATCCATTGACTCATACTCATTTGTTTTTTTTCTGCTCGTTTATAATGTCTACACATTGTTGCACAATCC
* Color:  Human Sequence / Virus Sequence / Overlapped sequence / Unknown sequence
Reference
Parfenov, M., et al. Characterization of HPV and host genome interactions in primary head and neck cancers. Proc Natl Acad Sci U S A,2014,111(43): 15544-15549.
Curate