ALK _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10006128
Fusion event
HBV-ALK 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
1200
Orient
+
Integrated sequence
GCCAACTTACAAGGCCTTTCTGTGTAAACAATATCTGCACCTTTACCCCGTTGCCCGGCAACGGTCAGGTCTCTGCCAAGTGTTTGCTGACGCAACCCCC| |ACTGGATGGGGCTTGGCCATAGGCCATCGGCGCATGCGTGGAACCTTTGTGGCTCCTCTGCCGATCCATACTGCGGAACTCCTAGCAGCTTGTTTTGCTC
Host Sequence
Chromosome
chr2
Cytoband
p23.2
Reference genome
GRCh37/hg19
Start
29624941/29402075 (Hg38)
End
29624941/29402075 (Hg38)
Orient
+
Location type
Intron
Target gene
ALK
miRNAs that regulate target gene
hsa-mir-132-3p ; hsa-mir-96-5p
Nearest miRNA
hsa-mir-1301/Upstream/1405626; hsa-mir-10b/Downstream/3130078;
Nearest TSS
ENST00000437798/Upstream/82864; ENST00000421411/Downstream/315625;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/286032, chr2-CpG: 147/Downstream/517890
Nearest cancer related gene
ALK(OG, No orient, 0)
Upstream sequence
GTATTGTTTCTGGGAGCCGGGGCAGCTCTGAGGGCCGGGCTGGTGGGAACCGCAGGTTAGAGTTGGGCTGTGTTTTACATCCCTCCCTTCACAAGAGATC
Downstream sequence
AGTGGAGGAAGGGAAGGCAGACTTTGGCAGCGGGTGTTGAGTGAAAGCCTGGCAGAGCCATTCCCAGGTGAACTCCAGCCCAAACTCTGCTGAAAGCCAG
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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