Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005623
Fusion event
HBV-SDK1 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
1821
Orient
+
Integrated sequence
TTTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAACT| |TTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCGTATAAA
Host Sequence
Chromosome
chr7
Cytoband
p22.2
Reference genome
Start
End
3660337/3620705 (Hg38)
Orient
+
Location type
Intron
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-615-3p ; hsa-mir-625-5p ; hsa-mir-6739-5p ; hsa-mir-6733-5p ; hsa-mir-3153 ; hsa-mir-3202 ; hsa-mir-6770-5p ; hsa-mir-1253 ; hsa-mir-3179 ; hsa-mir-1252-5p ; hsa-mir-3934-5p ; hsa-mir-764 ; hsa-mir-125a-3p ; hsa-mir-6794-5p ; hsa-mir-4716-3p ; hsa-mir-6876-5p ; hsa-mir-4476 ; hsa-mir-6758-5p ; hsa-mir-128-2-5p ; hsa-mir-128-1-5p ; hsa-mir-6780b-5p ; hsa-mir-4271 ; hsa-mir-4725-3p ; hsa-mir-6877-5p ; hsa-mir-5196-5p ; hsa-mir-4747-5p ; hsa-mir-4533 ; hsa-mir-6784-5p ; hsa-mir-6892-3p ; hsa-mir-6891-5p ; hsa-mir-6783-5p ; hsa-mir-3173-3p
Nearest miRNA
hsa-mir-339/Upstream/1093560; hsa-mir-10399/Downstream/1167860;
Nearest CpG islands
None/Target, chr7-CpG: 39/Upstream/318604, chr7-CpG: 21/Downstream/493308
Upstream sequence
GGAACTAGATTTGAAGTCTAATCCTGAGCATGCTAGCTGTATGACATTACACTAATTGTGATTGCCATGCTGTGTGGTATTAAACTAAATTTGATTGTCT
Downstream sequence
caatcaggagcaggcggctgagcagagctgcccccatcaaaggcatggacactccctggttctcctcggtgctctctggcAGCCCCGTCCCTTGTAGCAC
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).