KCNT2 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10010529
Fusion event
HBV-KCNT2 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|
Start
3132
Orient
-
Integrated sequence
GGCCTTTTGGGGTGGAGCCCTCAGGCTCAGGGCATACTACAAACTTTGCCAGCAAATCCGCCTCCTGCCTCCACCAATCGCCAGTCAGGAAGGCAGCCTA| |CCCCGCTGTCTCCACCTTTGAGAAACACTCATCCTCAGGCCATGCAGTGG
Host Sequence
Chromosome
chr1
Cytoband
q31.3
Reference genome
GRCh37/hg19
Start
196497592/196528462 (Hg38)
End
196497592/196528462 (Hg38)
Orient
-
Location type
Intronic
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/3391879; hsa-mir-1182/Downstream/53951;
Nearest TSS
ENST00000473358/Upstream/63075; ENST00000496761/Downstream/79897;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/3406368, chr1-CpG: 24/Downstream/80116
Upstream sequence
TCCTCTGAAAAACAGAAAATTCTATGTTGCCATTTCCATTGAAAAAATAAATTATGTGATTCCTTTCCTCACTTCTCTTAGAATTGTTCGAGCTAGAATC
Downstream sequence
AAGTAGAAATGGCATGAACTAACTTCTTATTTTCCGATGATATCTAAGCCAAAGAAGGTGTTATTGACTAAACGGCTATTAAGAAATGAAATAAATCTTT
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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