RTP2 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10018520
Fusion event
HBV-RTP2 integration
Validated
No
Detection method
VirusFinder
Data source
Curated
Sample type
Nontumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Good
Reported year
2017
PubMed ID
29212479
Virus Sequence
Virus name
HBV
Reference genome
NC_003977
Start
1475
End
1809
Integrated sequence
TTGGGACTCTCTCGTCCCCTTCTCCGTCTGCCGTTCCGACCGACCACGGGGCGCACCTCTCTTTACGCGGACTCCCCGTCTGTGCCTTCTCATCTGCCGGACCGTGTGCACTTCGCTTCACCTCTGCACGTCGCATGGAGACCACCGTGAACGCCCACCAAATATTGCCCAAGGTCTTACATAAGAGGACTCTTGGACTCTCAGCAATGTCAACGACCGACCTTGAGGCATACTTCAAAGACTGTTTGTTTAAAG
Host Sequence
Chromosome
chr3
Cytoband
q27.3
Reference genome
GRCh37.55
Start
187416193/187698405 (Hg38)
End
187416444/187698656 (Hg38)
Location type
Exon1
Fragile sites / regions
FRA3C
Target gene
RTP2
Nearest miRNA
hsa-let-7g/Upstream/911628; hsa-mir-28/Downstream/990125;
Nearest TSS
ENST00000440867/Upstream/28006; ENST00000437407/Downstream/3657;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/28017, chr3-CpG: 24/Downstream/67
Upstream sequence
GTGGAGGTTTGGCTTAGAGCAGGAACACGAGGCTCCCGTTTGGGGAACAAGGAGCCTCAGGAGGCCCTTTCAGCACTAGACAGGCCAGAGATGCTGAAAA
Downstream sequence
CTCCAGCAGCTTCTCGCTGGGCTTCCAGTGAACGATGCCCTCCTGGCAGGCCTCACAGAACTCTGCACGATGCGGCCCGCTGTCCGGGCGGCTGGCCACG
Target sequence
gtcatatgttgaatctgtagcaggatcaagtccagactgtgtcctccccactctcaagcccatgtgccctctcCCACCCTTAACCAGCTCCACTAAAAGAAGGCAGGACTGAGGAAGGAGAACTGCAGGTAAACAACGAGCAGGCAGAGAGAGGCCCAGAAGAGGCACCAGCGAAGAGACAAGAAGTTGTAGCCGGATCCCGCCTGGGCCCTCGGCTTGGAGGCTTCAGAGGTGTAGGTGGTCACCTCCTC
Reference
Yoo, S., et al. A pilot systematic genomic comparison of recurrence risks of hepatitis B virus-associated hepatocellular carcinoma with low- and high-degree liver fibrosis. BMC Med ,2017, 15(1): 214.
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