APOB _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005450
Fusion event
HBV-APOB integration
Validated
No
Detection method
PCR and Ultra-deep sequencing
Data source
Curated
Sample type
Nontumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
29861854
Virus Sequence
Virus name
HBV
Reference genome
AP011098
Start
616
Orient
-
Integrated sequence
CAAGACCTGCACGATTCCTGCTCAAGGAACCTCTATGTTTCCCTCTTGTTGCTGTACAAAACCTTCGGACGGAAACTGCACTTGTATTCCCATCCCATCA| |TCCTGGGCTTTCGCAAGATTCCTATGGGAGTGGGCCTCAGTCCGTTTCTCCTGGCTCAGTTTACTAGTGCCATTTGTTCAGTGGTTCGTAGGGCTTTCCC
Host Sequence
Chromosome
chr2
Cytoband
p24.1
Reference genome
GRCh37/hg19
Start
21246279/21023407 (Hg38)
End
21246279/21023407 (Hg38)
Orient
-
Location type
Intron
Target gene
APOB
miRNAs that regulate target gene
hsa-mir-885-5p ; hsa-mir-7151-5p ; hsa-mir-6869-5p ; hsa-mir-502-5p ; hsa-mir-1911-5p ; hsa-mir-499b-5p ; hsa-mir-500b-3p ; hsa-mir-6862-3p ; hsa-mir-6784-3p ; hsa-mir-624-5p ; hsa-mir-548p
Nearest miRNA
hsa-mir-3125/Upstream/1674902; hsa-mir-10b/Downstream/4305233;
Nearest TSS
ENST00000437798/Upstream/22490; ENST00000405799/Downstream/20555;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/200233, chr2-CpG: 27/Downstream/20390
Upstream sequence
ACTGAGTTCTTGTCTTATGGCCATACCACTACTGGAGCTAGTGAGGTAGTGCATTCTGGTGGAAGCTTGAAGTTTTTCATAAAAAAATAATGAGGTGATT
Downstream sequence
ACAATGATGAAGCATTTTGTCTTGAAGTGGAAACACATTTTTAAATATGTTTTAACAAGAAATGCACCCTGGAAGAAAGTAATAACCTAAGAAATCAAAA
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).
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