Basic Information
VIS ID
TVIS10014861
Fusion event
HBV-LINC01942 integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Tumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2012
PubMed ID
22634756
Virus Sequence
Virus name
HBV
Reference genome
NC_003977.1
Start
1879
Integrated sequence
GCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAACTTTTTCCCCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTG| |TGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCGTATAAAGAATTTGGAGCTTCTGTGGAGTTACTCTCTTTTTTGCCTTCTGACTTCTTTCCTTCTA
Host Sequence
Chromosome
chr5
Cytoband
q35.2
Reference genome
GRCh37/hg19
Start
173125603/173698600 (Hg38)
End
173125603/173698600 (Hg38)
Location type
Intronic
Fragile sites / regions
FRA5G
Target gene
LINC01942
Nearest miRNA
hsa-mir-10397/Upstream/351064; hsa-mir-1229/Downstream/1053134;
Nearest TSS
ENST00000502646/Upstream/9141; ENST00000518141/Downstream/21092;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/81708, chr5-CpG: 23/Downstream/189328
Upstream sequence
TTTTTATAACAGTGAAAAGTAATATAAACCAACTTTTTCCATGGCCATTGGCAAATTTTCTCCAATTTATTTTTGTTCAAGTCAAATCAAAGTGTGAGAA
Downstream sequence
ccattttattgtgcacaccttgaggcaagtacagggccttccttaatttgacattcccaggacctgggcctgacccgtggaaggtccatggtgaagactg
Reference
Fujimoto, A., et al. Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators. Nat Genet,2012, 44(7): 760-764.
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