Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005389
Fusion event
HBV-HDAC4 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
1569
Orient
+
Integrated sequence
CCGTTTGGGGCTCTACCGTCCCCTTCTTCATCTGCCGTTCCGGCCGACCACGGGGCGCACCTCTCTTTACGCGGTCTCCCCGTCTGTGCCTTCTCATCTG| |CCGGACCGTGTGCACTTCGCTTCACCTCTGCACGTCGCATGGAGACCACCGTGAACGCCCACCAGGTCTTGCCCAAGGTCTTACATAAGAGGACTCTTGG
Host Sequence
Chromosome
chr2
Cytoband
q37.3
Reference genome
End
239979162/239057466 (Hg38)
Orient
-
Location type
Intron
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-29b-3p ; hsa-mir-140-5p ; hsa-mir-1-3p ; hsa-mir-22-3p ; hsa-mir-30c-5p ; hsa-mir-302b-3p ; hsa-mir-9-5p ; hsa-mir-206 ; hsa-mir-3149 ; hsa-mir-587 ; hsa-mir-4686 ; hsa-mir-513c-3p ; hsa-mir-513a-3p ; hsa-mir-3606-3p ; hsa-mir-4282 ; hsa-mir-19b-3p ; hsa-mir-19a-3p ; hsa-mir-381-3p ; hsa-mir-125a-5p ; hsa-mir-675-5p
Nearest miRNA
hsa-mir-10b/Upstream/1546478; hsa-mir-149/Downstream/11351;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/4438, chr2-CpG: 22/Downstream/9288
Upstream sequence
TATGATGAAACAACCAGAGATTTATGAACGTGACATGGAAGATGTGAGACCCAAGCCAGGGGCAAAAAAACCCAGGaatgcacacctaggtacatcagag
Downstream sequence
taaaactgcagaacatcaaaaacaaaaagaaaattctaaaagctgctagagaaaacagaatcttcaaagaggtagccattagccacacaccaactcctta
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).