Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10000111
Fusion event
HBV-RBMS3 integration
Validated
Yes
Detection method
invPCR
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Perfect
Reported year
2018
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
End
1813
Integrated sequence
AGACTGTTTGTTTAAAGACTGGGAGGAGTTGGGGGAGGAGATTAGATTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGCGCACCAGCA| |CCATGCAACTTTTTCACCTCTGCCTAATCATCTCTTGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATCGA
Host Sequence
Chromosome
chr3
Cytoband
p24.1
Reference genome
Start
End
29694365 (Hg38)
Orient
-
Location type
Intronic
Target gene
miRNAs that regulate target gene
hsa-mir-30a-5p ; hsa-mir-16-5p ; hsa-mir-578 ; hsa-mir-526b-5p ; hsa-mir-3190-3p ; hsa-mir-6077 ; hsa-mir-7-5p ; hsa-mir-4282 ; hsa-mir-3674 ; hsa-mir-1238-3p ; hsa-mir-670-3p ; hsa-mir-5706 ; hsa-mir-4782-5p ; hsa-mir-516b-5p ; hsa-mir-1299 ; hsa-mir-6881-3p ; hsa-mir-6780a-3p ; hsa-mir-7111-3p ; hsa-mir-4703-3p ; hsa-mir-5093 ; hsa-mir-3182 ; hsa-mir-6128 ; hsa-mir-875-3p ; hsa-mir-877-3p ; hsa-mir-1324
Nearest miRNA
hsa-mir-12127/Upstream/4029426; hsa-let-7g/Downstream/1467339;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/1117886, chr3-CpG: 88/Downstream/912130
Nearest cancer related gene
RBMS3(TSG, No orient, 0)
Downstream sequence
AGCAGAGAAATTTGTTATATAGACAAAGGC
Junction sequence
TGTAGGCATAAATTGGTCTGCGCACCAGCAAGCAGAGAAATTTGTTATATAGACAAAGGC
* Color:
Human Sequence
/
Virus Sequence
/
Overlapped sequence
/
Unknown sequence
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).