RIMS2 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10006315
Fusion event
HBV-RIMS2 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
1833
Orient
-
Integrated sequence
GAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAACTTTTTCACCTCTG| |CCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCGTATAAAGAATTTGGAGCT
Host Sequence
Chromosome
chr8
Cytoband
q22.3
Reference genome
GRCh37/hg19
Start
105065805/104053577 (Hg38)
End
105065805/104053577 (Hg38)
Orient
+
Location type
Intron
Fragile sites / regions
FRA8A
Target gene
RIMS2
miRNAs that regulate target gene
hsa-mir-1-3p ; hsa-mir-335-3p ; hsa-mir-376b-3p ; hsa-mir-376a-3p ; hsa-mir-3065-3p
Nearest miRNA
hsa-mir-12123/Upstream/898888; hsa-mir-10400/Downstream/430792;
Nearest TSS
ENST00000518652/Upstream/138064; ENST00000523362/Downstream/169758;
Nearest CpG islands
None/Target, chr8-CpG: 109/Upstream/551892, chr8-CpG: 51/Downstream/169579
Upstream sequence
GTCCAAGTGCTCCGGGGTGGGTGGAGTGGTCTGTGGGAAGAAGGCAACAGTGACTCTGAGAAGCTGGTGGGAAATCTGCGGAGAGCCACAGCTCTGAAAA
Downstream sequence
TCTTTTAAAATGCAGTCAATATTTCGGATAATTAAATCACTTAGTATAAATTGTTTTAATATGTAATTGAGTTTAACACTGTATTCggtactatttttat
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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