Basic Information
VIS ID
TVIS20004612
Fusion event
HPV-PTCSC2 integration
Validated
Yes
Detection method
FISH, WGS, RNA-seq, qPCR
Data source
Curated
Sample type
Tumor
Disease
Cervical carcinoma (CC)
Quality evaluation
Perfect
Reported year
2014
PubMed ID
24201445
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
NC_001526.2
Gene
E1
Start
1755
End
1824
Integrated sequence
TATGTGTGTCTCCAATGTGTATGATGATAGAGCCTCCAAAATTGCGTAGTACAGCAGCAGCATTATATTG
Host Sequence
Chromosome
chr9
Cytoband
q22.33
Reference genome
GRCh37/hg19
Start
100575623/97813316 (Hg38)
End
100575598/97813341 (Hg38)
Location type
Intronic
Target gene
PTCSC2
Nearest miRNA
hsa-let-7a-1/Upstream/449635; hsa-mir-12126/Downstream/415808;
Nearest TSS
ENST00000422679/Upstream/3308; ENST00000375123/Downstream/39913;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/9419, chr9-CpG: 66/Downstream/35073
Downstream sequence
TTCACATCTACTAGAAAAGGTAAAAT
Target sequence
ttttaccttttctagtagatgtgaa
Junction sequence
TTATGTGTGTCTCCAATGTGTATGATGATAGAGCCTCCAAAATTGCGTAGTACAGCAGCAGCATTATATTCACATCTACTAGAAAAGGTAAAAT
* Color:  Human Sequence / Virus Sequence / Overlapped sequence / Unknown sequence
Reference
Akagi, K., et al.Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability. Genome Res ,2014,24(2): 185-199.
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