Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10006126
Fusion event
HBV-PXDN integration
Validated
No
Detection method
PCR and Ultra-deep sequencing
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Start
142
Orient
-
Integrated sequence
GGGCCTATATTTTCCTGCTGGTGGCTCCAGTTCCGGAACAGTAAACCCTGTTCCGACTACTGCCTCACCCATATCGTCAATCTTCTCGAGGACTGGGGAC| |CCTGCACAGAACATGGAGAGCACAACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAGAATCCTCACAATACCAC
Host Sequence
Chromosome
chr2
Cytoband
p25.3
Reference genome
Start
End
1681521/1677749 (Hg38)
Orient
+
Location type
Intron
Target gene
miRNAs that regulate target gene
hsa-let-7b-5p ; hsa-mir-29a-3p ; hsa-mir-9-5p ; hsa-mir-1-3p ; hsa-mir-192-5p ; hsa-mir-98-5p ; hsa-mir-324-5p ; hsa-mir-6749-3p ; hsa-mir-4279 ; hsa-mir-188-3p ; hsa-mir-532-3p ; hsa-mir-589-3p ; hsa-mir-4773 ; hsa-mir-4670-3p ; hsa-mir-342-3p ; hsa-mir-521 ; hsa-mir-3912-3p ; hsa-mir-377-3p ; hsa-mir-623 ; hsa-mir-4268 ; hsa-mir-3670 ; hsa-mir-4685-3p ; hsa-mir-4287 ; hsa-mir-660-3p ; hsa-mir-5193 ; hsa-mir-6780b-3p ; hsa-mir-4780
Nearest miRNA
hsa-mir-10b/Downstream/4296913;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/11318, chr2-CpG: 190/Downstream/65312
Upstream sequence
TCCTCGAGGGCTGACGGCTCCCAGGCTCCCGTCCCTGGTGGCTGCTCCGGAGCTCCAGGCCCGCACAGGGAGCGGCCTTCTCTAAGGCTCCCCTCAGCAG
Downstream sequence
CCATGAGGGAACCACACCAAGGGCAGGCCTAGGCTTCCATCTCTGCCTCGTCACCTCAGTGTGCGAATCTGTCTCCATGTACATTCTGTGAGCATCACGA
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).