Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10004724
Fusion event
HBV-NRXN1 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
1417
Orient
-
Integrated sequence
AAACTTATCGGGACTGACAACTCTGTTGTCCTCTCTCGGAAATACACCTCCTTCCCATGGCTGCTCGGGTGTGCTGCCAACTGGATCCTGCGCGGGACGT| |CCTTTGTCTACGTCCCGTCGGCGCTGAATCCCGCGGACGACCCGTCTCGGGGCCGTTTGGGGCTCTACCGTCCCCTTCTTCATCTGCCGTTCCGGCCGAC
Host Sequence
Chromosome
chr2
Cytoband
p16.3
Reference genome
Start
End
50288939/50061801 (Hg38)
Orient
+
Location type
Intron
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-196a-5p ; hsa-mir-16-5p ; hsa-mir-616-5p ; hsa-mir-498 ; hsa-mir-1537-5p ; hsa-mir-302a-5p ; hsa-mir-3607-3p ; hsa-mir-548as-3p ; hsa-mir-548z ; hsa-mir-548h-3p ; hsa-mir-548d-3p ; hsa-mir-548bb-3p ; hsa-mir-548ac ; hsa-mir-574-5p ; hsa-mir-4752 ; hsa-mir-6867-5p ; hsa-mir-8056 ; hsa-mir-3691-5p ; hsa-mir-376c-5p ; hsa-mir-376b-5p ; hsa-mir-7114-5p ; hsa-mir-6818-5p ; hsa-mir-4320
Nearest miRNA
hsa-mir-1301/Upstream/1002143; hsa-mir-10b/Downstream/634371;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/1306055, chr2-CpG: 74/Downstream/285102
Upstream sequence
TAGTTAAAAGATAACAATTTAGTCTCACACTTTTCCCATGATAAAAGCAAGATAGGATTTTCCTTTGATTTCTTTTTCCTCCAGTTAATTTTGTGTGGTT
Downstream sequence
TGATCTGTTGGTACCTTCACTGAAAATGTCAGTGACAACATACATGCCTCTGCCGAAGTAATTTTCAAGCAATGAAACTGCATGTAAAATTTGGTTTTAT
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).