Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10010235
Fusion event
HBV-SHISA3 integration
Validated
No
Detection method
NGS
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Region type
precore/core protein|Core and e antigen|
Start
2121
Orient
+
Integrated sequence
AGCCTTAGAGTCTCCTGAGCATTGTTCACCTCACCATACTGCACTCAGGCAAGCAATTCTTTGCTGGGGGGAACTAATGACTCTAGCTACCTGGGTGGGT| |GTTAATTTGGAAGATCCAGCGTCTAGAGACCTAGTAGTCAGTTATGTCAACACTAATATGGGCCTAAAGTTCAGGCAACTCTTGTGGTTTCACATTTCTT
Host Sequence
Chromosome
chr4
Cytoband
p13
Reference genome
Start
End
42402049/42400032 (Hg38)
Orient
-
Location type
Intronic
Target gene
Nearest miRNA
hsa-mir-12113/Upstream/1897913; hsa-mir-1243/Downstream/5252637;
Nearest CpG islands
None/Target, chr4-CpG: 46/Upstream/1247, chr4-CpG: 116/Downstream/256229
Nearest cancer related gene
SHISA3(TSG, No orient, 0)
Upstream sequence
attccatttcattccattctgttccgttccgttccattccattccattccattccattccattccattccattgcattccataccattccattccattct
Downstream sequence
cagggtctccaagagactttaatcagataatgaataagaaagagccaggcacacagtagggacttagtcaatgcaggctttcttTCTTCTACCTGTAAGC
Reference
Yang, L., et al. Molecular Characterization of HBV DNA Integration in Patients with Hepatitis and Hepatocellular Carcinoma. J Cancer ,2018,9(18): 3225-3235.