Basic Information
VIS ID
TVIS20004586
Fusion event
HPV-LINC01830 integration
Validated
Yes
Detection method
FISH, WGS, RNA-seq, qPCR
Data source
Curated
Sample type
Cell line
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
Region type
LCR
Start
7259
End
7359
Integrated sequence
TAATAAACACGTGTGTATGTGTTTTTAAATGCTTGTGTAACTATTGTGTCATGCAACATAAATAAACTTATTGTTTCAACACCTACTAATTGTGTTGTGGT
Host Sequence
Chromosome
chr2
Cytoband
p24.1
Reference genome
GRCh37/hg19
Start
22639132/22416230 (Hg38)
End
22639102/22416260 (Hg38)
Location type
Intronic
Target gene
LINC01830
Nearest miRNA
hsa-mir-3125/Upstream/3067725; hsa-mir-10b/Downstream/2912380;
Nearest TSS
ENST00000437798/Upstream/38636; ENST00000433429/Downstream/114845;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/1372141, chr2-CpG: 256/Downstream/968598
Upstream sequence
ATTTCTATCACTGATGGGCATTTGGGTTGAT
Target sequence
tcaacccaaatgcccatcagtgatagaaat
Junction sequence
ATTTCTATCACTGATGGGCATTTGGGTTGATAATAAACACGTGTGTATGTGTTTTTAAATGCTTGTGTAACTATTGTGTGATGCAACATAAATAAACTTA
* 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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