Basic Information
VIS ID
TVIS10005320
Fusion event
HBV-PRKN integration
Validated
No
Detection method
PCR and Ultra-deep sequencing
Data source
Curated
Sample type
Nontumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
29861854
Virus Sequence
Virus name
HBV
Reference genome
AP011098
Start
1818
Orient
+
Integrated sequence
TTGTTTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCA| |ACTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCGTAT
Host Sequence
Chromosome
chr6
Cytoband
q26
Reference genome
GRCh37/hg19
Start
162647385/162226353 (Hg38)
End
162647385/162226353 (Hg38)
Orient
-
Location type
Intron
Fragile sites / regions
FRA6E
Target gene
PRKN
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-26b-5p ; hsa-mir-3187-3p ; hsa-mir-1303 ; hsa-mir-4435 ; hsa-mir-588 ; hsa-mir-4701-5p ; hsa-mir-548s ; hsa-mir-193b-5p ; hsa-mir-4755-3p ; hsa-mir-483-5p ; hsa-mir-19a-3p ; hsa-mir-19b-3p ; hsa-mir-181a-5p
Nearest miRNA
hsa-mir-10398/Upstream/3461600; hsa-mir-1913/Downstream/4283001;
Nearest TSS
ENST00000381078/Upstream/656933; ENST00000544266/Downstream/36415;
Nearest CpG islands
None/Target, chr6-CpG: 120/Upstream/579696, chr6-CpG: 75/Downstream/500991
Nearest cancer related gene
PRKN(TSG, No orient, 0)
Upstream sequence
tccatatagtgtgtgtacattttctggttatttatacaagagggtgctgtggtttgaatgtgtcctccaaatttcatgcgttggaaacttaatcctcaaa
Downstream sequence
TGTGGATAGGGGCCCTAGGGCTCCTCCTTCCACAATGGCACTGTAATGGGAAAGGCCCACAACAAGCATGAAACCAGTCCTCACGAGCAGAGCCATGTGG
Reference
Tu, T., et al. Hepatitis B Virus DNA Integration Occurs Early in the Viral Life Cycle in an In Vitro Infection Model via Sodium Taurocholate Cotransporting Polypeptide-Dependent Uptake of Enveloped Virus Particles. J Virol ,2018,92(11).
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