Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005107
Fusion event
HBV-SPN 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
1866
Orient
-
Integrated sequence
TTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCA| |AGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCGTATAAAGAATTTGGAGCTTCTGTGGAGTTACTCTCTTTTTTGCCTTCTGAC
Host Sequence
Chromosome
chr16
Cytoband
p11.2
Reference genome
Start
End
29681233/29669912 (Hg38)
Orient
-
Location type
Exon
Target gene
miRNAs that regulate target gene
hsa-let-7e-5p ; hsa-let-7b-5p ; hsa-mir-4722-5p ; hsa-mir-4768-3p ; hsa-mir-5589-3p ; hsa-mir-574-5p ; hsa-mir-6867-5p ; hsa-mir-6818-5p ; hsa-mir-337-3p ; hsa-mir-6829-3p ; hsa-mir-6791-3p ; hsa-mir-4707-3p ; hsa-mir-519e-3p ; hsa-mir-515-3p ; hsa-mir-33b-3p ; hsa-mir-371a-3p ; hsa-mir-371b-3p ; hsa-mir-18a-3p ; hsa-mir-324-3p ; hsa-mir-1913 ; hsa-mir-6749-3p ; hsa-mir-7113-3p ; hsa-mir-3194-3p ; hsa-mir-510-3p ; hsa-mir-6881-3p ; hsa-mir-6780a-3p ; hsa-mir-7159-5p ; hsa-mir-877-3p ; hsa-mir-3065-5p ; hsa-mir-4666b ; hsa-mir-6750-3p ; hsa-mir-6805-3p ; hsa-mir-5691 ; hsa-mir-5001-3p ; hsa-mir-335-3p ; hsa-mir-5007-3p ; hsa-mir-4775 ; hsa-mir-664a-5p ; hsa-mir-4794 ; hsa-mir-4735-5p ; hsa-mir-1279 ; hsa-mir-6765-3p ; hsa-mir-590-3p
Nearest miRNA
hsa-mir-1225/Upstream/70647; hsa-mir-11401/Downstream/834007;
Nearest CpG islands
None/Target, chr16-CpG: 29/Upstream/5113, chr16-CpG: 21/Downstream/24965
Upstream sequence
ttgcagtgagccgagatcacgccattgcactccagcctgggcgacaagtaaaaaactccatctcaaaaaaaaaaaaGGAGATAGAGCAAGGAACAGTAAG
Downstream sequence
AAAATAGTTGGGTGCAGTGGCTATGCGGTGgcactataggaggctgaggcgggcagatcacctgaggtcaggagttggagaccagcctgggcaacataga
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).