VAT1L _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10004912
Fusion event
HBV-VAT1L 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
1733
Orient
+
Integrated sequence
GGTCTTGCCCAAGGTCTTACATAAGAGGACTCTTGGACTCTCAGCAATGTCAACGACCGACCTTGAGGCATACTTCAAAGACTGTTTGTTTAAGGACTGG| |GAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAACTTTTTCACCTCTG
Host Sequence
Chromosome
chr16
Cytoband
q23.1
Reference genome
GRCh37/hg19
Start
77874873/77840976 (Hg38)
End
77874873/77840976 (Hg38)
Orient
-
Location type
Intron
Target gene
VAT1L
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-1185-2-3p ; hsa-mir-1185-1-3p ; hsa-mir-4503 ; hsa-mir-4662a-5p ; hsa-mir-6792-5p
Nearest miRNA
hsa-mir-1225/Upstream/971957; hsa-mir-11401/Downstream/3544042;
Nearest TSS
ENST00000527434/Upstream/52446; ENST00000563850/Downstream/21772;
Nearest CpG islands
None/Target, chr16-CpG: 29/Upstream/51739, chr16-CpG: 39/Downstream/204879
Upstream sequence
TGGTATTGGAAATCATCTTATTACACAATCCAGCATGGATTTCAGAAGGCAAATATTCAAATTACATAAACATGCTTGTTATACACTTTTTCACTCCTCT
Downstream sequence
TCATCTTAAGGGTTATGGTAACTTTAGCTTCAAACCTTAAGCAAGCTACATGGATTTAAAAGTTAACTATTAAATCAAATGGCCTTGTATGCACCAATAA
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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