Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005377
Fusion event
HBV-SFMBT2 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
1992
Orient
-
Integrated sequence
TTTGGGGCATGGACATTGACCCGTATAAAGAATTTGGAGCTTCTGTGGAGTTACTCTCTTTTTTGCCTTCTGACTTCTTTCCTTCTATTCGAGATCTCCT| |CGACACCGCCTCTGCTCTGTATCGGGAGGCCTTAGAGTCTCCGGAACATTGTTCACCTCACCATACAGCACTCAGGCAAGCTATTCTGTGTTGGGGTGAG
Host Sequence
Chromosome
chr10
Cytoband
p14
Reference genome
Start
End
7312353/7270391 (Hg38)
Orient
-
Location type
Intron
Target gene
miRNAs that regulate target gene
hsa-mir-4743-3p ; hsa-mir-6888-3p ; hsa-mir-539-5p ; hsa-mir-7843-3p ; hsa-mir-4786-3p ; hsa-mir-6859-5p ; hsa-mir-3916 ; hsa-mir-3125 ; hsa-mir-6856-5p ; hsa-mir-6758-5p ; hsa-mir-5197-3p ; hsa-mir-7161-5p ; hsa-mir-548u ; hsa-mir-1178-3p ; hsa-mir-3972 ; hsa-mir-3194-5p ; hsa-mir-1202 ; hsa-mir-4722-5p ; hsa-mir-4524a-3p ; hsa-mir-4530 ; hsa-mir-4768-3p ; hsa-mir-4302 ; hsa-mir-761 ; hsa-mir-3619-5p ; hsa-mir-214-3p ; hsa-mir-648 ; hsa-mir-6165 ; hsa-mir-6868-3p ; hsa-mir-4263 ; hsa-mir-6499-3p ; hsa-mir-423-3p ; hsa-mir-631 ; hsa-mir-3661 ; hsa-mir-17-3p ; hsa-mir-598-5p ; hsa-mir-1248 ; hsa-mir-6893-3p ; hsa-mir-1237-3p ; hsa-mir-8079 ; hsa-mir-370-3p ; hsa-mir-1245a ; hsa-mir-4652-3p ; hsa-mir-616-3p ; hsa-mir-215-3p ; hsa-mir-6773-3p ; hsa-mir-4282 ; hsa-mir-1247-3p ; hsa-mir-1827 ; hsa-mir-185-5p ; hsa-mir-34b-3p ; hsa-mir-3614-5p ; hsa-mir-4306 ; hsa-mir-4644 ; hsa-mir-4649-3p ; hsa-mir-6500-3p ; hsa-mir-665 ; hsa-mir-6731-5p ; hsa-mir-6746-5p ; hsa-mir-6808-5p ; hsa-mir-6893-5p ; hsa-mir-7160-5p ; hsa-mir-8085 ; hsa-mir-940
Nearest miRNA
hsa-mir-3155a/Upstream/1118114; hsa-mir-107/Downstream/4860369;
Nearest CpG islands
None/Target, chr10-CpG: 68/Upstream/98250, chr10-CpG: 21/Downstream/97205
Upstream sequence
aggggagtgtggtcctgccgacaccctgatttcacacactagtctccagaagcatgagagaacaaatttctgtcattctaagtcatccagtccatgggaa
Downstream sequence
tttgtgacagtagcctttgcaaactaaGAAAATGATGTTCTCACACCCTCCAAATTAAACGTGTAGATTCTCACTCATTACAAAATATAGTTAAGAAACC
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).