Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10015133
Fusion event
HBV-RAI1 integration
Validated
No
Detection method
WGS
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2012
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Region type
HBVgp1 Polymerase;HBVgp3 X protein
Start
1606
Orient
+
Integrated sequence
CGTTCCGACCGACCACGGGGCGCACCTCTCTTTACGCGGACTCCCCGTCTGTGCCTTCTCATCTGCCGGACCGTGTGCACTTCGCTTCACCTCTGCACGT| |CGCATGGAGACCACCGTGAACGCCCACCAAATATTGCCCAAGGTCTTACATAAGAGGACTCTTGGACTCTCAGCAATGTCAACGACCGACCTTGAGGCAT
Host Sequence
Chromosome
chr17
Cytoband
p11.2
Reference genome
Start
End
17587733/17684419 (Hg38)
Orient
+
Location type
Intronic
Target gene
miRNAs that regulate target gene
hsa-mir-744-5p ; hsa-mir-769-3p ; hsa-mir-504-5p ; hsa-let-7b-5p ; hsa-mir-3687 ; hsa-mir-190a-3p ; hsa-mir-374a-5p ; hsa-mir-4704-5p ; hsa-mir-4789-5p ; hsa-mir-5007-3p ; hsa-mir-5011-5p ; hsa-mir-7150 ; hsa-mir-8052 ; hsa-mir-3199 ; hsa-mir-4736 ; hsa-mir-4763-3p ; hsa-mir-1207-5p ; hsa-mir-4515 ; hsa-mir-184 ; hsa-mir-5004-5p ; hsa-mir-6868-5p ; hsa-mir-4462 ; hsa-mir-211-3p ; hsa-mir-3937 ; hsa-mir-1197 ; hsa-mir-3924 ; hsa-mir-656-3p ; hsa-mir-5580-3p ; hsa-mir-6749-3p ; hsa-mir-4303 ; hsa-mir-128-2-5p ; hsa-mir-128-1-5p ; hsa-mir-6751-3p ; hsa-mir-1199-5p ; hsa-mir-150-5p ; hsa-mir-4532 ; hsa-mir-6784-5p ; hsa-mir-106a-3p ; hsa-mir-1225-3p ; hsa-mir-1233-3p ; hsa-mir-2681-5p ; hsa-mir-4427 ; hsa-mir-452-5p ; hsa-mir-4676-3p ; hsa-mir-4680-3p ; hsa-mir-4762-3p ; hsa-mir-5187-3p ; hsa-mir-892c-3p ; hsa-mir-943
Nearest miRNA
hsa-mir-1253/Upstream/1402331; hsa-mir-10226/Downstream/129061;
Nearest CpG islands
None/Target, chr17-CpG: 26/Upstream/1372, chr17-CpG: 71/Downstream/10091
Upstream sequence
tctgctggtctgtaatcctttttgttcttgtgtatttgttttttttttaattactgattgctacccacgaaattaattttgcaatccactgatgggtcat
Downstream sequence
acccagaatttgaaaaaaacAAGCCTAGGAAATGAATTTGCCATCTATTCATGCAACAAATGTTAATTGCAACCCTAATAATTCCTCTCATGTTAAACTA
Reference
Sung, W. K., et al. Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat Genet,2012, 44(7): 765-769.