Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10004803
Fusion event
HBV-THRB 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
2156
Orient
+
Integrated sequence
ACAGCACTCAGGCAAGCTATTCTGTGTTGGGGTGAGTTGATGAATCTGGCCACCTGGGTGGGAAGTAATTTGGAAGACCCAGCATCCAGGGAATTAGTAG| |TCAGCTATGTCAATGTTAATATGGGCCTAAAAATCAGACAACTATTGTGGTTTCACATTTCCTGTCTTACTTTTGGAAGAGAAACTGTTCTTGAGTATTT
Host Sequence
Chromosome
chr3
Cytoband
p24.2
Reference genome
Start
End
24499357/24457866 (Hg38)
Orient
-
Location type
Intron
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-27a-3p ; hsa-mir-204-5p ; hsa-mir-155-5p ; hsa-mir-425-5p ; hsa-mir-452-5p ; hsa-mir-4677-3p ; hsa-mir-4679 ; hsa-mir-3161 ; hsa-mir-3689f ; hsa-mir-3689e ; hsa-mir-3689b-5p ; hsa-mir-3689a-5p ; hsa-mir-3926 ; hsa-mir-4778-5p ; hsa-mir-4753-5p ; hsa-mir-6794-3p ; hsa-mir-3152-5p ; hsa-mir-6836-3p ; hsa-mir-15b-3p ; hsa-mir-4264 ; hsa-mir-4797-3p ; hsa-mir-6809-3p ; hsa-mir-4753-3p ; hsa-mir-4436b-5p ; hsa-mir-6509-3p ; hsa-mir-1236-3p ; hsa-mir-6515-3p ; hsa-mir-101-3p ; hsa-mir-200a-3p ; hsa-mir-1238-5p ; hsa-mir-129-5p ; hsa-mir-3659 ; hsa-mir-4658 ; hsa-mir-4758-5p ; hsa-mir-574-5p ; hsa-mir-6790-5p ; hsa-mir-8055 ; hsa-mir-8081 ; hsa-mir-1537-5p ; hsa-mir-320a ; hsa-mir-320b ; hsa-mir-320c ; hsa-mir-320d ; hsa-mir-3607-3p ; hsa-mir-4429 ; hsa-mir-4633-3p ; hsa-mir-4793-5p ; hsa-mir-5002-5p ; hsa-mir-5196-3p ; hsa-mir-6500-5p ; hsa-mir-6870-3p ; hsa-mir-6874-5p ; hsa-mir-9-3p
Nearest miRNA
hsa-mir-12127/Upstream/4320225; hsa-let-7g/Downstream/1207007;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/511336, chr3-CpG: 135/Downstream/36487
Nearest cancer related gene
THRB(TSG, No orient, 0)
Upstream sequence
TTTAAAACTGAGTCTGAGAATTATTGCCATGTCTGCAGGCCAGAGATAAAGCAGGGAACGTGGCGACGGACTACAGGCCTTTCAGTAAACTCTGCAGTAC
Downstream sequence
gttaggcgcatttgaaggctataggagctcttcagagtcatgatggtagtaattactcagtaactgctttagtgATTTAAAGcagagcttctcaaacatg
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).