Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10004824
Fusion event
HBV-TMED5 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
1814
Orient
+
Integrated sequence
CTGTTTGTTTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCA| |TGCAACTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCC
Host Sequence
Chromosome
chr1
Cytoband
p22.1
Reference genome
Start
End
93640119/93174562 (Hg38)
Orient
-
Location type
Intron
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-375 ; hsa-mir-30a-5p ; hsa-mir-26b-5p ; hsa-let-7b-5p ; hsa-mir-652-3p ; hsa-mir-301a-3p ; hsa-mir-30b-5p ; hsa-mir-101-3p ; hsa-mir-587 ; hsa-mir-6083 ; hsa-mir-6509-5p ; hsa-mir-331-5p ; hsa-mir-1258 ; hsa-mir-194-5p ; hsa-mir-4650-3p ; hsa-mir-5702 ; hsa-mir-4289 ; hsa-mir-4328 ; hsa-mir-4756-3p ; hsa-mir-3919 ; hsa-mir-664a-3p ; hsa-mir-1244 ; hsa-mir-802 ; hsa-mir-6831-5p ; hsa-mir-3927-3p ; hsa-mir-10b-5p ; hsa-mir-10a-5p ; hsa-mir-504-5p ; hsa-mir-4700-3p ; hsa-mir-4760-3p ; hsa-mir-34b-3p ; hsa-mir-6891-5p ; hsa-mir-3173-3p ; hsa-mir-4428 ; hsa-mir-144-3p ; hsa-let-7e-5p ; hsa-let-7f-5p ; hsa-let-7d-5p ; hsa-let-7g-5p ; hsa-let-7c-5p ; hsa-let-7i-5p ; hsa-mir-4500 ; hsa-mir-4458 ; hsa-let-7a-5p ; hsa-mir-98-5p ; hsa-mir-3681-3p ; hsa-mir-27b-3p ; hsa-mir-128-3p ; hsa-mir-216a-3p ; hsa-mir-27a-3p ; hsa-mir-3129-5p ; hsa-mir-199a-3p ; hsa-mir-199b-3p ; hsa-mir-5582-5p ; hsa-mir-124-3p ; hsa-mir-548an ; hsa-mir-4768-3p
Nearest miRNA
hsa-mir-101-1/Upstream/6816875; hsa-mir-11399/Downstream/672270;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/95087, chr1-CpG: 77/Downstream/5553
Upstream sequence
gtgagaccccatatctCTCttttttttaacttttattttaggcttggggatacatgtgaaggttacataggtaaacgtgttaaaaaccacaattattttt
Downstream sequence
gcaccaacttagtatttcatcacccagatataaagcccagtacccaatagttaacttttctgtgcctctctgtccttccaccctccctcctcaagtaaat
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).