KCNT2 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10004833
Fusion event
HBV-KCNT2 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
1856
Orient
+
Integrated sequence
GTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTC| |CTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCGTATAAAGAATTTGGAGCTTCTGTGGAGTTACTCTCTTTTTT
Host Sequence
Chromosome
chr1
Cytoband
q31.3
Reference genome
GRCh37/hg19
Start
196517297/196548167 (Hg38)
End
196517297/196548167 (Hg38)
Orient
-
Location type
Intron
Fragile sites / regions
FRA1K
Target gene
KCNT2
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-335-3p ; hsa-mir-1305 ; hsa-mir-4452 ; hsa-mir-183-3p ; hsa-mir-4775 ; hsa-mir-500a-5p
Nearest miRNA
hsa-mir-101-1/Upstream/3411584; hsa-mir-1182/Downstream/34246;
Nearest TSS
ENST00000473358/Upstream/82780; ENST00000496761/Downstream/60192;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/3426073, chr1-CpG: 24/Downstream/60411
Upstream sequence
TAAGCATAAAATGATGATGTGAGGGAGaatttaagaaaataataataactaaaaaataaaaatagtaaaaaaaaCATTTCTTTGTATTGTACTTCTGTGC
Downstream sequence
TGAGTAGGTAAAGGGAGATCTGTTTTTATAGTTCTTTAAAGTATTCCTTTACCTGCTATATTCTGATAAAACAAAATTTCTCTTTGAatttaacaagtga
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).
Curate