KCNMA1 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10014323
Fusion event
HBV-KCNMA1 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
precore/core protein|Core and e antigen|
Start
1941
Orient
+
Integrated sequence
CATCTCTTGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATCGACCCTTATAAAGAATTTGGAGCTACTGTG| |GAGTTACTCTCGTTTTTGCCTTCTGACTTCTTTCCTTCAGTACGAGATCTTCTAGATACCGCCTCAGCTCTGTATCGGGAAGCCTTAGAGTCTCCTGAGC
Host Sequence
Chromosome
chr10
Cytoband
q22.3
Reference genome
GRCh37/hg19
Start
78804459/77044701 (Hg38)
End
78804459/77044701 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA10D
Target gene
KCNMA1
miRNAs that regulate target gene
hsa-mir-211-5p ; hsa-mir-218-5p ; hsa-mir-17-5p
Nearest miRNA
hsa-mir-1265/Upstream/1492148; hsa-mir-107/Downstream/9219993;
Nearest TSS
ENST00000439456/Upstream/5163; ENST00000428936/Downstream/33371;
Nearest CpG islands
None/Target, chr10-CpG: 68/Upstream/932154, chr10-CpG: 220/Downstream/591636
Upstream sequence
ctgcgccactgcactccagcatgggcaacagagagagatcctgtctctaaaataaataaataaaaCCTTGTGTTTAATACTAAGAAAATGAAAGTGAACA
Downstream sequence
AAGAAATCTGGACCAGGTAAagggagttattgtcattatgaattccccttttatagatgataaaactgaggcacagagaggttaagaaacctgctgacag
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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