LINGO2 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005072
Fusion event
HBV-LINGO2 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
1611
Orient
+
Integrated sequence
GCCGACCACGGGGCGCACCTCTCTTTACGCGGTCTCCCCGTCTGTGCCTTCTCATCTGCCGGACCGTGTGCACTTCGCTTCACCTCTGCACGTCGCATGG| |AGACCACCGTGAACGCCCACCAGGTCTTGCCCAAGGTCTTACATAAGAGGACTCTTGGACTCTCAGCAATGTCAACGACCGACCTTGAGGCATACTTCAA
Host Sequence
Chromosome
chr9
Cytoband
p21.1
Reference genome
GRCh37/hg19
Start
28417858/28417860 (Hg38)
End
28417858/28417860 (Hg38)
Orient
-
Location type
Intron
Fragile sites / regions
FRA9C
Target gene
LINGO2
miRNAs that regulate target gene
hsa-mir-587 ; hsa-mir-7162-5p ; hsa-mir-516b-3p ; hsa-mir-516a-3p ; hsa-mir-2115-5p ; hsa-mir-1976 ; hsa-mir-6893-3p ; hsa-mir-370-3p ; hsa-mir-660-3p ; hsa-mir-5193
Nearest miRNA
hsa-mir-101-2/Upstream/6905675; hsa-let-7a-1/Downstream/445766;
Nearest TSS
ENST00000422679/Upstream/122529; ENST00000541043/Downstream/252425;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/843871, chr9-CpG: 74/Downstream/794313
Upstream sequence
ACTGGACTGCTGGGGTCTGGCCCTGGGTTGGCCACAGAACAATAAAGCACGGGGAGTTGTCTGTTTTGGGGTGTGGTGTGCTTCTCTTCTTTGTAGAAAT
Downstream sequence
gaaaaatatatagcaaaaggtaggttctgaatggatttttatgagtgaactaatCAATGAATTTGTGGCCATCTTCTCAGAAAACTCTAATCATTAACTC
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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