Basic Information
VIS ID
TVIS20003789
Fusion event
HPV-chr5 integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Tumor
Disease
Squamous-cell carcinoma (SCC)
Quality evaluation
Perfect
Reported year
2015
PubMed ID
25581428
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
NC_001526.2
Start
2701
End
2746
Orient
-
Integrated sequence
CTCAAGGACGTGGTCCAGATTAAGTTTGCACGAGGACGAGGACAAG
Host Sequence
Chromosome
chr5
Cytoband
q34
Reference genome
GRCh37/hg19
Start
164994449/165567444 (Hg38)
End
164994449/165567444 (Hg38)
Nearest miRNA
hsa-mir-10397/Upstream/5081994; hsa-mir-103a-1/Downstream/2598401;
Nearest TSS
ENST00000502646/Upstream/218414; ENST00000520075/Downstream/561054;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/2061504, chr5-CpG: 17/Downstream/1411035
Downstream sequence
GGCACTAATAGATCCATCAGATCCATATTGTACATTTC
Junction sequence
TCTCAAGGACGTGGTCCAGATTAAGTTTGCACGAGGACGAGGACAAGGCACTAATAGATCCATCAGATCCATATTGTACATTTC
* Color:  Human Sequence / Virus Sequence / Overlapped sequence / Unknown sequence
Reference
Hu, Z., et al. Genome-wide profiling of HPV integration in cervical cancer identifies clustered genomic hot spots and a potential microhomology-mediated integration mechanism. Nat Genet,2015, 47(2): 158-163.
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