Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005427
Fusion event
HBV-ABCF2 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
1800
Orient
+
Integrated sequence
GCATACTTCAAAGACTGTTTGTTTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCT| |GTTCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGC
Host Sequence
Chromosome
chr7
Cytoband
q36.1
Reference genome
End
150909462/151212376 (Hg38)
Orient
-
Location type
Intron
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-16-5p ; hsa-mir-124-3p ; hsa-mir-103a-3p ; hsa-mir-32-5p ; hsa-mir-532-3p ; hsa-mir-193b-3p ; hsa-mir-326 ; hsa-mir-320a ; hsa-mir-186-5p ; hsa-mir-218-5p ; hsa-mir-5047 ; hsa-mir-1301-3p ; hsa-mir-7156-3p ; hsa-mir-939-5p ; hsa-mir-1343-5p ; hsa-mir-122-5p ; hsa-mir-6081 ; hsa-mir-4722-5p ; hsa-mir-1286 ; hsa-mir-873-5p ; hsa-mir-107 ; hsa-mir-5699-3p ; hsa-mir-4421 ; hsa-mir-6748-3p ; hsa-mir-6764-5p ; hsa-mir-1915-3p ; hsa-mir-16-1-3p ; hsa-mir-4433a-3p ; hsa-mir-92b-3p ; hsa-mir-92a-3p ; hsa-mir-367-3p ; hsa-mir-363-3p ; hsa-mir-25-3p ; hsa-mir-4280 ; hsa-mir-4433b-3p ; hsa-mir-6769a-3p ; hsa-mir-3943 ; hsa-mir-4323 ; hsa-mir-3908 ; hsa-mir-5010-3p ; hsa-mir-4743-3p ; hsa-mir-592 ; hsa-mir-6888-3p ; hsa-mir-584-5p ; hsa-mir-4669 ; hsa-mir-3657 ; hsa-mir-550a-3p ; hsa-mir-200c-5p ; hsa-mir-152-5p ; hsa-mir-597-3p ; hsa-mir-182-3p ; hsa-mir-550b-3p ; hsa-mir-3120-5p ; hsa-mir-486-5p ; hsa-mir-758-5p ; hsa-mir-218-2-3p
Nearest miRNA
hsa-mir-10399/Upstream/3834255; hsa-mir-153-2/Downstream/26045;
Nearest CpG islands
None/Target, chr7-CpG: 39/Upstream/7484, chr7-CpG: 60/Downstream/14418
Upstream sequence
TTCCCCTAGGGTAGAGTTATTTTAACATACATATTTATATGACTCTACAAATACTATTGAAGTCCTTAATACAGTAAAGATTTTTAATAAATATTTAGCT
Downstream sequence
CTGTATCCCAATAGGAAGAGAGGTTCACAGACGTTGGTGTGAAAATGCAAACTCCTGGCCATCTCTGCACCTCTCTCATTCTACCAAATGCGATTAATCA
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).