Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005102
Fusion event
HBV-SYT1 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
1826
Orient
+
Integrated sequence
GGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAACTTTTTC| |ACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCGTATAAAGAATT
Host Sequence
Chromosome
chr12
Cytoband
q21.2
Reference genome
Start
End
79543813/79150033 (Hg38)
Orient
-
Location type
Intron
Target gene
miRNAs that regulate target gene
hsa-mir-34a-5p ; hsa-mir-335-5p ; hsa-mir-8064 ; hsa-mir-8485 ; hsa-let-7a-5p ; hsa-let-7b-5p ; hsa-let-7c-5p ; hsa-let-7d-5p ; hsa-let-7e-5p ; hsa-let-7f-5p ; hsa-let-7g-5p ; hsa-let-7i-5p ; hsa-mir-202-3p ; hsa-mir-4458 ; hsa-mir-4500 ; hsa-mir-4678 ; hsa-mir-4699-3p ; hsa-mir-5683 ; hsa-mir-711 ; hsa-mir-7162-3p ; hsa-mir-98-5p
Nearest miRNA
hsa-let-7i/Upstream/9565210; hsa-mir-1178/Downstream/269224;
Nearest CpG islands
Nearest cancer related gene
SYT1(OG, No orient, 0)
Upstream sequence
gaaataagtAAATGAGGGTGAATGAATGAAAGGTCTGAAACGGTGTTTTGTTATGTAACCCAGATTAGACTAGTTTTGAATTttttatttttaatttata
Downstream sequence
aatagtaattgtatatgttgatggggtccagtgagatgttttgatatttgtatacaacatggtataattaaatcaagtaattaacatatccatcagttca
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).