Basic Information
VIS ID
TVIS20003760
Fusion event
HPV-LOC105379109 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
1665
End
1717
Orient
-
Integrated sequence
CATGTTCATGGGGAATGGTTGTGTTACTATTAGTAAGATATAAATGTGGAAAA
Host Sequence
Chromosome
chr5
Cytoband
q21.2
Reference genome
GRCh37/hg19
Start
104069741/104734040 (Hg38)
End
104069741/104734040 (Hg38)
Location type
Intronic
Fragile sites / regions
FRA5F
Target gene
LOC105379109
Nearest miRNA
hsa-mir-10397/Upstream/3917475; hsa-mir-103a-1/Downstream/5779789;
Nearest TSS
ENST00000502646/Upstream/654129; ENST00000523745/Downstream/5501;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/1474191, chr5-CpG: 253/Downstream/2935389
Upstream sequence
TTGTGTTGTGCAGAGTTCCTGACTATTGTACAGTTTAGACAGAAAAATTTTAAAGGCTCATTTGTTTCTCTATTTT
Junction sequence
TTGTGTTGTGCAGAGTTCCTGACTATTGTACAGTTTAGACAGAAAAATTTTAAAGGCTCATTTGTTTCTCTATTTTTTCCACATTTATATCTCACTAATAGTAACACAACCATTCCACATGAACATGCT
* 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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