Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10004654
Fusion event
HBV-SOX5 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
2486
Orient
+
Integrated sequence
CCTCGCAGACGAAGGTCTCAATCGCCGCGTCGCAGAAGATCTCAATCTCGGGAATCTCAATGTTAGTATCCCTTGGACTCATAAGGTGGGAAACTTTACT| |GGGCTTTATTCTTCTACTGTACCTGTCTTTAATCCTGAGTGGCAAACTCCCTCCTTTCCTAACATTCATTTACAGGAGGACATTATTAATAGATGTCAAC
Host Sequence
Chromosome
chr12
Cytoband
p12.1
Reference genome
Start
End
24689079/24536145 (Hg38)
Orient
-
Location type
Intron
Target gene
miRNAs that regulate target gene
hsa-mir-21-5p ; hsa-mir-194-5p ; hsa-mir-335-5p ; hsa-mir-1-3p ; hsa-mir-26b-5p ; hsa-mir-96-5p ; hsa-mir-130a-3p ; hsa-mir-181a-5p ; hsa-mir-132-3p ; hsa-mir-15a-5p ; hsa-mir-16-5p ; hsa-mir-1231 ; hsa-mir-632 ; hsa-mir-4288 ; hsa-mir-548s ; hsa-mir-3926 ; hsa-mir-4766-5p ; hsa-mir-1277-5p ; hsa-mir-3924 ; hsa-mir-190a-3p ; hsa-mir-6867-5p ; hsa-mir-223-5p ; hsa-mir-511-3p ; hsa-mir-5011-5p ; hsa-mir-574-5p ; hsa-mir-5580-3p ; hsa-mir-555 ; hsa-mir-374a-3p ; hsa-mir-136-3p ; hsa-mir-4704-5p ; hsa-mir-3529-3p ; hsa-mir-6759-5p ; hsa-mir-6793-5p ; hsa-mir-6748-5p ; hsa-mir-933 ; hsa-mir-4783-5p ; hsa-mir-3607-5p
Nearest miRNA
hsa-mir-1244-3/Upstream/323650; hsa-let-7i/Downstream/1337875;
Nearest CpG islands
Upstream sequence
CACAAAAAGAAGCATTTTGTGTCACCAAATTATTATTATAGGTTACTGTTAACCCTTGGAAGATAGAGGTGAGCTCCGTAGCTCCCCACTGAGGTGACTA
Downstream sequence
TTTGTCATGAAATCATAGGCCCTACCTCAAAAGATGTTTCAGGTGAGCTTGCAATAAGGCAAACTGTCTAGTTGACCTATAGGATTCTGAAAGCTAGTTT
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).