Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005263
Fusion event
HBV-SLC8A1 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
1916
Orient
-
Integrated sequence
CAACTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCGT| |ATAAAGAATTTGGAGCTTCTGTGGAGTTACTCTCTTTTTTGCCTTCTGACTTCTTTCCTTCTATTCGAGATCTCCTCGACACCGCCTCTGCTCTGTATCG
Host Sequence
Chromosome
chr2
Cytoband
p22.1
Reference genome
Start
End
40610322/40383182 (Hg38)
Orient
-
Location type
Intron
Target gene
miRNAs that regulate target gene
hsa-mir-1-3p ; hsa-mir-557 ; hsa-mir-507 ; hsa-mir-1273e ; hsa-mir-3924 ; hsa-mir-590-3p ; hsa-mir-190a-3p ; hsa-mir-5011-5p ; hsa-mir-513c-3p ; hsa-mir-513a-3p ; hsa-mir-3606-3p ; hsa-mir-410-3p ; hsa-mir-4699-3p ; hsa-mir-4683 ; hsa-mir-4784 ; hsa-mir-3150b-3p ; hsa-mir-494-3p ; hsa-mir-199b-5p ; hsa-mir-199a-5p ; hsa-mir-1825 ; hsa-mir-6847-5p ; hsa-mir-512-3p ; hsa-mir-6888-5p ; hsa-mir-5693 ; hsa-mir-8057 ; hsa-mir-4423-3p ; hsa-mir-760 ; hsa-mir-6822-3p ; hsa-mir-3135a ; hsa-mir-4766-5p ; hsa-mir-146a-3p ; hsa-mir-3622a-5p ; hsa-mir-5582-5p ; hsa-mir-4775 ; hsa-mir-4668-3p ; hsa-mir-1305 ; hsa-mir-599 ; hsa-mir-3978 ; hsa-mir-3161 ; hsa-mir-6124 ; hsa-mir-4282 ; hsa-mir-3148 ; hsa-mir-501-5p ; hsa-mir-500a-5p ; hsa-mir-185-5p
Nearest miRNA
hsa-mir-1301/Upstream/4911696; hsa-mir-10b/Downstream/6994493;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/603859, chr2-CpG: 16/Downstream/68155
Upstream sequence
TATCCCTGCTTTGATTTTGTTTTTTAATGATACGTTCTGTTTTGACACATCCTTGTATTCAAAATTGGCAAATTAAAGATTACAGACACGTTGTAGATAA
Downstream sequence
TAAACATAAATCATGGAGCAAAGTTTCATGAATTTTTCACATTTTTTTGAAATTTGGAGAGGCTATTGTTTGTATATCTCACTTGTCACTTAGTAACTTT
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).