Basic Information
VIS ID
TVIS20003775
Fusion event
HPV-LOC107986410 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
3692
End
3718
Orient
-
Integrated sequence
TGCAGTGTCGTCTACATGGCATTGGAC
Host Sequence
Chromosome
chr5
Cytoband
p13.3
Reference genome
GRCh37/hg19
Start
29041014/29040907 (Hg38)
End
29041014/29040907 (Hg38)
Location type
Intronic
Fragile sites / regions
FRA5A
Target gene
LOC107986410
Nearest miRNA
hsa-mir-10397/Upstream/11884915; hsa-mir-103a-1/Downstream/2895195;
Nearest TSS
ENST00000502646/Upstream/231658; ENST00000602801/Downstream/102596;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/112377, chr5-CpG: 37/Downstream/2152938
Upstream sequence
AATTAGTTGATTCCAATATGTCTTGAGCCAGAAGTGTTTACAGCTTAGACCATAAAGGTATAGTCTATACACTGACGGCCAAGCCCTCATTAATTCATACAGTAGAATTCAGAAAGGGTTATGTAGTAGTTAATTTGAAGAACATTGAACAAAGTAAGAACTCGGAACTTCAGGTAGTAGAGAGAATCTTGGCTCAAGTCTGTCTGACAATAAGTCTAGTGGAACTGTGGACCTCTCCTGTTTTTATTTT
Junction sequence
AATTAGTTGATTCCAATATGTCTTGAGCCAGAAGTGTTTACAGCTTAGACCATAAAGGTATAGTCTATACACTGACGGCCAAGCCCTCATTAATTCATACAGTAGAATTCAGAAAGGGTTATGTAGTAGTTAATTTGAAGAACATTGAACAAAGTAAGAACTCGGAACTTCAGGTAGTAGAGAGAATCTTGGCTCAAGTCTGTCTGACAATAAGTCTAGTGGAACTGTGGACCTCTCCTGTTTTTATTTTCCAAT
* 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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