Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10017462
Fusion event
HBV-GTSF1 integration
Validated
No
Detection method
TS
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2016
PubMed ID
Virus Sequence
Virus name
HBV
Subtype
C
Reference genome
Region type
core protein;X protein;
Start
1826
Integrated sequence
AGACTGGGAGGAGTTGGGGGAGGAGATTAGATTAAAGGTCTTTGTACTGGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAACTTTTTC| |ACCTCTGCCTAATCATCTCATGTTCATGTCCCACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCGTATAAAGAATT
Host Sequence
Chromosome
chr12
Cytoband
q13.13
Reference genome
Start
End
54854631/54460847 (Hg38)
Location type
Intronic
Fragile sites / regions
Target gene
Nearest miRNA
hsa-mir-1244-3/Upstream/123533; hsa-let-7i/Downstream/2733657;
Nearest CpG islands
None/Target, chr12-CpG: 104/Upstream/41440, chr12-CpG: 66/Downstream/127302
Upstream sequence
AATCAGAACTTTTGTTAGGAAGCACAGAAATTCAAGTGCCACAATGTTGACAAAGAGAAGAATCCACATTACTTTATTAGTTTACTCATTACTTCATTGA
Downstream sequence
gcactccaaatatccaatttcagactctacaaaaagaatgtttcataactgctctatccaaagaaaatttcagctctgcgagttcaatgcacacatccca
Reference
Chiu, Y. T., et al. Novel pre-mRNA splicing of intronically integrated HBV generates oncogenic chimera in hepatocellular carcinoma. J Hepatol ,2016,64(6): 1256-1264.