Basic Information
VIS ID
TVIS20003741
Fusion event
HPV-PCDH20 integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Tumor
Disease
Not given
Quality evaluation
Perfect
Reported year
2015
PubMed ID
25581428
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
NC_001526.2
Start
870
End
889
Orient
-
Integrated sequence
GATCCTGCAGGTACCAATGG
Host Sequence
Chromosome
chr13
Cytoband
q21.2
Reference genome
GRCh37/hg19
Start
61710697/61136563 (Hg38)
End
61710697/61136563 (Hg38)
Location type
Intronic
Fragile sites / regions
FRA13B
Target gene
PCDH20
Nearest miRNA
hsa-mir-1297/Upstream/5962015; hsa-mir-1267/Downstream/63235;
Nearest TSS
ENST00000623511/Upstream/219521; ENST00000455977/Downstream/278959;
Nearest CpG islands
None/Target, chr13-CpG: 551/Upstream/738652, chr13-CpG: 36/Downstream/2675023
Downstream sequence
GTGGGTCCAATAAATCAGTTTTTGGCTTATAAATCTGTACAGAAGAAATTAGGGGAAAGGATCA
Junction sequence
TAACTTTCTGGGTCGCTCCTGTGGGTCCAATAAATCAGTTTTTGGCTTATAAATCTGTACAGAAGAAATTAGGGGAAAGGATCA
* 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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