Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005342
Fusion event
HBV-IQSEC3 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
3170
Orient
+
Integrated sequence
TGGGGTGGAGCCCTCAGGCTCAGGGCATATTGACAACAGTGCCAGCAGCGCCTCCTCCTGCCTCCACCAATCGGCAGTCAGGAAGACAGCCTACTCCCAT| |CTCTCCACCTCTAAGAGACAGTCATCCTCAGGCCATGCAGTGGAA
Host Sequence
Chromosome
chr12
Cytoband
p13.33
Reference genome
Start
End
95741/95741 (Hg38)
Orient
+
Location type
Intronic
Target gene
miRNAs that regulate target gene
hsa-mir-6780a-5p ; hsa-mir-6779-5p ; hsa-mir-3689c ; hsa-mir-3689b-3p ; hsa-mir-3689a-3p ; hsa-mir-30b-3p ; hsa-mir-1273h-5p ; hsa-mir-625-5p ; hsa-mir-6780b-5p ; hsa-mir-4725-3p ; hsa-mir-4271 ; hsa-mir-6883-5p ; hsa-mir-6799-5p ; hsa-mir-6785-5p ; hsa-mir-4728-5p ; hsa-mir-149-3p ; hsa-mir-7106-5p ; hsa-mir-5196-5p ; hsa-mir-4747-5p ; hsa-mir-6775-3p ; hsa-mir-1291 ; hsa-mir-765 ; hsa-mir-4533 ; hsa-mir-5008-5p ; hsa-mir-3192-5p ; hsa-mir-4292 ; hsa-mir-6791-5p ; hsa-mir-6794-5p ; hsa-mir-4716-3p ; hsa-mir-4779 ; hsa-mir-8080 ; hsa-mir-8485 ; hsa-mir-548ad-3p
Nearest miRNA
hsa-let-7i/Downstream/1564574;
Nearest CpG islands
None/Target, chr12-CpG: 104/Upstream/17297, chr12-CpG: 40/Downstream/8856
Upstream sequence
agggttagggttagggttagggttagggttagggttagggttagggttagggttagggttagggttagggttagggttagggttagggttagggttagNN
Downstream sequence
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
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).