Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005255
Fusion event
HBV-ZSWIM9 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
1823
Orient
+
Integrated sequence
TAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAACTTT| |TTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCGTATAAAGA
Host Sequence
Chromosome
chr19
Cytoband
q13.33
Reference genome
Start
End
48687645/48184388 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-6881-3p ; hsa-mir-6780a-3p ; hsa-mir-7111-3p ; hsa-mir-6845-3p ; hsa-mir-1976 ; hsa-mir-3653-5p ; hsa-mir-3667-3p ; hsa-mir-6893-3p ; hsa-mir-370-3p ; hsa-mir-6769b-3p ; hsa-mir-4723-3p ; hsa-mir-3183 ; hsa-mir-5088-3p ; hsa-mir-1247-5p ; hsa-mir-1238-3p ; hsa-mir-670-3p ; hsa-mir-3679-3p ; hsa-mir-6891-3p ; hsa-mir-6072 ; hsa-mir-361-3p ; hsa-mir-208b-5p ; hsa-mir-208a-5p
Nearest miRNA
hsa-mir-10395/Upstream/957367; hsa-let-7e/Downstream/825518;
Nearest CpG islands
None/Target, chr19-CpG: 112/Upstream/1560, chr19-CpG: 108/Downstream/10255
Upstream sequence
gccagtgcaaaggcccagaggcacgagcaagcttgtgttggaggaacagtgaggaTGGCTGCTGCTCCATAAGGAATCTCTGCGGCTTTAATCCAACTTC
Downstream sequence
AAGTTTGGGGTGAACTTGAAGTTTAAAGAGGAAAGAAAGATGAGAAAGTAGGGGAAGAACTGGTTTCTCCTCCTGGCTGTGCCTTTGTCTCCCTTGTGTG
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).