Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005591
Fusion event
HBV-SEMA6B 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
2471
Orient
+
Integrated sequence
AGAAGAACTCCCTCGCCTCGCAGACGAAGGTCTCAATCGCCGCGTCGCAGAAGATCTCAATCTCGGGAATCTCAATGTTAGTATCCCTTGGACTCATAAG| |GTGGGAAACTTTACTGGGCTTTATTCTTCTACTGTACCTGTCTTTAATCCTGAGTGGCAAACTCCCTCCTTTCCTAACATTCATTTACAGGAGGACATTA
Host Sequence
Chromosome
chr19
Cytoband
p13.3
Reference genome
Start
End
4558120/4558108 (Hg38)
Orient
-
Location type
Exon
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-19b-3p ; hsa-mir-7702 ; hsa-mir-4524b-3p ; hsa-mir-129-2-3p ; hsa-mir-129-1-3p ; hsa-mir-1227-5p ; hsa-mir-1229-3p ; hsa-mir-128-1-5p ; hsa-mir-128-2-5p ; hsa-mir-197-3p ; hsa-mir-3199 ; hsa-mir-3620-3p ; hsa-mir-3622b-5p ; hsa-mir-365a-5p ; hsa-mir-365b-5p ; hsa-mir-4292 ; hsa-mir-4699-3p ; hsa-mir-504-5p ; hsa-mir-6511a-3p ; hsa-mir-6511b-3p ; hsa-mir-6762-5p ; hsa-mir-6784-3p ; hsa-mir-6791-5p ; hsa-mir-6845-5p ; hsa-mir-6852-5p ; hsa-mir-6862-3p ; hsa-mir-7110-3p ; hsa-mir-8052 ; hsa-mir-92b-5p
Nearest miRNA
hsa-mir-1227/Upstream/112060; hsa-let-7e/Downstream/212562;
Nearest CpG islands
None/Target, chr19-CpG: 112/Upstream/1977, chr19-CpG: 24/Downstream/243
Upstream sequence
gctgtcccCAGCAATACCTGTCCCCAATGAACAGCGTCCTGTTGACCCGCAGGACTCGCTGGATGTTGAGGTCGTCAGCACCTTCTGCGGGGGTCAGGCG
Downstream sequence
TCCGGGCCCGCTGCCCACAAACACGGGATAGTGGTTCAGGTCTGAGTGAGGGGGTGGAGAGGGGTGTGAGCAAGGGCTGGGGGTGAAGAGAGGGTGGCCT
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).