RYR2 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005938
Fusion event
HBV-RYR2 integration
Validated
No
Detection method
PCR and Ultra-deep sequencing
Data source
Curated
Sample type
Nontumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
29861854
Virus Sequence
Virus name
HBV
Reference genome
AP011098
Start
1760
Orient
+
Integrated sequence
GACTCTTGGACTCTCAGCAATGTCAACGACCGACCTTGAGGCATACTTCAAAGACTGTTTGTTTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTA| |AAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTAC
Host Sequence
Chromosome
chr1
Cytoband
q43
Reference genome
GRCh37/hg19
Start
237481754/237318454 (Hg38)
End
237481754/237318454 (Hg38)
Orient
+
Location type
Intron
Target gene
RYR2
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-25-3p ; hsa-mir-17-5p ; hsa-let-7c-5p
Nearest miRNA
hsa-mir-101-1/Upstream/1465394; hsa-mir-3123/Downstream/152665;
Nearest TSS
ENST00000473358/Upstream/47957; ENST00000609253/Downstream/356310;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/275110, chr1-CpG: 22/Downstream/465433
Upstream sequence
ctttatacattcttatctcttttaaagacgttaagaaataaaatttttacagtcttttatgttaatccacacattttcaatttctgacattttttattta
Downstream sequence
tttctttggaattgaaggaagctccttcagaactttcttttgtatttaactgtgctaggaacaaattctcagtctttgtttatctgcaaatgtctatttt
Reference
Tu, T., et al. Hepatitis B Virus DNA Integration Occurs Early in the Viral Life Cycle in an In Vitro Infection Model via Sodium Taurocholate Cotransporting Polypeptide-Dependent Uptake of Enveloped Virus Particles. J Virol ,2018,92(11).
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