Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10004840
Fusion event
HBV-ITPKB 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
1438
Orient
-
Integrated sequence
TCTGTTGTCCTCTCTCGGAAATACACCTCCTTCCCATGGCTGCTCGGGTGTGCTGCCAACTGGATCCTGCGCGGGACGTCCTTTGTCTACGTCCCGTCGG| |CGCTGAATCCCGCGGACGACCCGTCTCGGGGCCGTTTGGGGCTCTACCGTCCCCTTCTTCATCTGCCGTTCCGGCCGACCACGGGGCGCACCTCTCTTTA
Host Sequence
Chromosome
chr1
Cytoband
q42.12
Reference genome
End
226870515/226682814 (Hg38)
Orient
-
Location type
Intron
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-186-5p ; hsa-mir-183-5p ; hsa-mir-20a-5p ; hsa-mir-106b-5p ; hsa-mir-3065-5p ; hsa-mir-590-3p ; 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-410-3p ; hsa-mir-133b ; hsa-mir-133a-3p ; hsa-mir-6792-3p ; hsa-mir-4691-5p ; hsa-mir-1228-3p ; hsa-mir-6813-3p ; hsa-mir-362-3p ; hsa-mir-329-3p ; hsa-mir-8485 ; hsa-mir-4674 ; hsa-mir-4437 ; hsa-mir-4313 ; hsa-mir-378g ; hsa-mir-939-3p ; hsa-mir-6850-3p ; hsa-mir-4292 ; hsa-mir-6791-5p ; hsa-mir-331-3p ; hsa-mir-873-5p ; hsa-mir-3914 ; hsa-mir-941 ; hsa-mir-519d-3p ; hsa-mir-93-5p ; hsa-mir-17-5p ; hsa-mir-20b-5p ; hsa-mir-4428 ; hsa-mir-498 ; hsa-mir-561-5p ; hsa-mir-6830-5p
Nearest miRNA
hsa-mir-101-1/Upstream/760672; hsa-mir-1182/Downstream/1258776;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/40712, chr1-CpG: 49/Downstream/20517
Upstream sequence
CTTTAGTGAATGAGATTCAGACTTCCTTGGGGAGGAGCTGTGGAAGATAAAAGAAGCTGAAAGTGGTATAGGAGACAGGCAGGGCAGCCACTCCAGCATC
Downstream sequence
TGGGGCACCTCCAGCCTTTGTTCTCCATCTCTAGTCCCTTTTTCTCTGCAAGTTGAGCCTCAGGAGGAGGTGTATATTTACAGGGAGAGTCTAGCTGTAT
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).