Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10004793
Fusion event
HBV-RAD23B 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
258
Orient
-
Integrated sequence
AGAGCACAACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAGAATCCTCACAATACCACAGAGTCTAGACTCGTG| |GTGGACTTCTCTCAATTTTCTAGGGGGAGCACCCACGTGTCCTGGCCAAAATTCGCAGTCCCCAACCTCCAATCACTCACCAACCTCTTGTCCTCCAATT
Host Sequence
Chromosome
chr9
Cytoband
q31.2
Reference genome
End
110078091/107315810 (Hg38)
Orient
-
Location type
Intron
Target gene
miRNAs that regulate target gene
hsa-mir-373-3p ; hsa-mir-30a-5p ; hsa-mir-155-5p ; hsa-mir-1301-3p ; hsa-mir-106b-5p ; hsa-mir-197-3p ; hsa-mir-106a-5p ; hsa-mir-92a-3p ; hsa-mir-494-3p ; hsa-mir-15a-5p ; hsa-mir-16-5p ; hsa-mir-15b-5p ; hsa-mir-195-5p ; hsa-mir-424-5p ; hsa-mir-497-5p ; hsa-mir-6838-5p ; hsa-mir-30c-5p ; hsa-mir-30d-5p ; hsa-mir-30b-5p ; hsa-mir-30e-5p ; hsa-let-7a-2-3p ; hsa-mir-96-3p ; hsa-let-7g-3p ; hsa-mir-371a-5p ; hsa-mir-372-5p ; hsa-mir-373-5p ; hsa-mir-616-5p ; hsa-mir-1182 ; hsa-mir-3154 ; hsa-mir-371b-5p ; hsa-mir-573 ; hsa-mir-595 ; hsa-mir-3611 ; hsa-mir-3616-5p ; hsa-mir-4795-5p ; hsa-mir-7978 ; hsa-mir-361-5p ; hsa-mir-2052 ; hsa-mir-2115-3p ; hsa-mir-3074-3p ; hsa-mir-4328 ; hsa-mir-3144-3p ; hsa-mir-485-5p ; hsa-mir-3650 ; hsa-mir-493-5p ; hsa-let-7c-3p ; hsa-mir-514b-5p ; hsa-mir-513c-5p ; hsa-mir-342-3p ; hsa-mir-4762-5p ; hsa-mir-6793-3p ; hsa-mir-510-3p ; hsa-mir-524-5p ; hsa-mir-520d-5p ; hsa-mir-127-5p ; hsa-mir-7843-3p
Nearest miRNA
hsa-let-7a-1/Upstream/714788; hsa-mir-12126/Downstream/1730419;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/31788, chr9-CpG: 67/Downstream/149876
Nearest cancer related gene
RAD23B(TSG, No orient, 0)
Upstream sequence
acacataacatgcgagatggttgtgggtagaaccgaggaaaataacacagggtaagggaaaaagggaatgtcagtgataggcaggggtgccttgctattt
Downstream sequence
ccTCTCTAGTTCTTTTTACAAGTCATTTGCCTTTGGACTTTTAAGATCTAAAAAGTATCACATTGCTTATGGGTATTTTTTTGAGATTGTATAATTTAAC
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).