SKA3 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10007238
Fusion event
HBV-SKA3 integration
Validated
No
Detection method
NGS
Data source
Curated
Sample type
Tumor
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
3162
Orient
-
Integrated sequence
GGCATACTACAAACTTTGCCAGCAAATCCGCCTCCTGCCTCCACCAATCGCCAGTCAGGAAGGCAGCCTACCCCGCTGTCTCCACCTTTGAGAAACACTC| |ATCCTCAGGCCATGCAGTGG
Host Sequence
Chromosome
chr13
Cytoband
q12.11
Reference genome
GRCh37/hg19
Start
21727908/21153769 (Hg38)
End
21727908/21153769 (Hg38)
Orient
-
Location type
UTR3
Target gene
SKA3
miRNAs that regulate target gene
hsa-mir-193b-3p ; hsa-let-7a-5p ; hsa-mir-1276 ; hsa-mir-3160-3p ; hsa-mir-3667-5p ; hsa-mir-6719-3p
Nearest miRNA
hsa-mir-4499/Upstream/719923; hsa-mir-1267/Downstream/3008647;
Nearest TSS
ENST00000623511/Upstream/7305; ENST00000309594/Downstream/18944;
Nearest CpG islands
None/Target, chr13-CpG: 551/Upstream/12793, chr13-CpG: 123/Downstream/22379
Upstream sequence
tcctacttcactggcctcagtctcctttgctagattactctgcccctttccatcctctaaagttgggagaactccaggatttggtccttggtacactttg
Downstream sequence
aatatattccctccctaagcagctcatccggttctgtggatttatatacACACGGTACACAGTGAAAGGCTGGTATACATTTCAGAGTCAATGGCATACA
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.
Curate