Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005486
Fusion event
HBV-ROBO1 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
1819
Orient
+
Integrated sequence
TGTTTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAA| |CTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCGTATA
Host Sequence
Chromosome
chr3
Cytoband
p12.3
Reference genome
Start
End
79612411/79563261 (Hg38)
Orient
-
Location type
Intron
Target gene
miRNAs that regulate target gene
hsa-mir-217 ; hsa-mir-218-5p ; hsa-mir-423-3p ; hsa-mir-25-3p ; hsa-mir-6835-3p ; hsa-mir-146a-5p ; hsa-mir-377-3p ; hsa-mir-1185-2-3p ; hsa-mir-876-3p ; hsa-mir-3591-5p ; hsa-mir-921 ; hsa-mir-3606-5p ; hsa-mir-524-5p ; hsa-mir-520d-5p ; hsa-mir-636 ; hsa-mir-3140-3p ; hsa-mir-4445-5p ; hsa-mir-508-3p ; hsa-mir-8062 ; hsa-mir-8079 ; hsa-mir-1245a ; hsa-mir-561-3p ; hsa-mir-548at-5p ; hsa-mir-548ay-3p ; hsa-mir-548at-3p ; hsa-mir-548as-3p ; hsa-mir-548t-3p ; hsa-mir-548ap-3p ; hsa-mir-548aa ; hsa-mir-299-5p ; hsa-mir-5590-3p ; hsa-mir-142-5p ; hsa-mir-4782-3p ; hsa-mir-6766-3p ; hsa-mir-219a-5p ; hsa-mir-6885-3p ; hsa-mir-1273e ; hsa-mir-4327 ; hsa-mir-1287-5p ; hsa-mir-3135b ; hsa-mir-330-3p ; hsa-mir-29a-3p ; hsa-mir-218-2-3p
Nearest miRNA
hsa-let-7g/Upstream/55292; hsa-mir-12124/Downstream/5822449;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/543845, chr3-CpG: 29/Downstream/203227
Nearest cancer related gene
ROBO1(TSG, No orient, 0)
Upstream sequence
CCAGATtgtgtctcaatgccttcatttgtgaaatgctgatagcaataatacctacaccaatagattgttgtcaaaatataattctggaatacacttaaat
Downstream sequence
AAGTTTCATGAAATGATGCAGATAATTAAATCATGTCTTCTAAAGACATAAACTTCAACTACAAATGATAAGATGTAATCAGAAACACCCCATAAAAGCG
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).