LINGO2 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10012645
Fusion event
HBV-LINGO2 integration
Validated
No
Detection method
NGS
Data source
Curated
Sample type
Nontumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
30271481
Virus Sequence
Virus name
HBV
Reference genome
NC_003977
Region type
Polymerase|large S protein|middle S protein|
Start
49
Orient
-
Integrated sequence
AATTCCACAACCTTCCACCAAACTCTGCAAGATCCCAGAGTGAGAGGCC| |TGTATTTCCCTGCTGGTGGCTCCAGTTCAGGAACAGTAAACCCTGTTCTGACTACTGCCTCTCCCTTATCGTCAATCTTCTCGAGGATTGGGGACCCTGC
Host Sequence
Chromosome
chr9
Cytoband
p21.1
Reference genome
GRCh37/hg19
Start
28282907/28282909 (Hg38)
End
28282907/28282909 (Hg38)
Orient
-
Location type
Intronic
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/6770724; hsa-let-7a-1/Downstream/580717;
Nearest TSS
ENST00000422679/Upstream/453633; ENST00000541043/Downstream/12422;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/708920, chr9-CpG: 74/Downstream/929264
Upstream sequence
ttttgtaataagtgtgatgtggtgctgagaagaatgtatattctattgatttggggtggagagttctgtagatgtctattatgtctgcttggtgcagagc
Downstream sequence
TGACAGAATGTACTAATTATTCAAGAAAGGAGTAAGCCCCTGTGGCAGGTAAACCTAAACTCTTTCTGTTTCAGTCCATACTCAGGAACAGTCCTTATCA
Reference
Yang, L., et al. Molecular Characterization of HBV DNA Integration in Patients with Hepatitis and Hepatocellular Carcinoma. J Cancer ,2018,9(18): 3225-3235.
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