CSMD3 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10018627
Fusion event
HBV-CSMD3 integration
Validated
No
Detection method
VirusFinder
Data source
Curated
Sample type
Nontumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2017
PubMed ID
29212479
Virus Sequence
Virus name
HBV
Reference genome
NC_003977
Start
1090
Integrated sequence
GTCAACGAATTGTGGGTCTTTTGGGTTTTGCTGCCCCTTTTACACAATGTGGTTATCCTGCGTTGATGCCTTTGTATGCATGTATTCAATCTAAGCAGGC| |TTTCACTTTCTCGCCAACTTACAAGGCCTTTCTGTGTAAACAATACCTGAACCTTTACCCCGTTGCCCGGCAACGGCCAGGTCTGTGCCAAGTGTTTGCT
Host Sequence
Chromosome
chr8
Cytoband
q23.3
Reference genome
GRCh37.55
Start
113684458/112672229 (Hg38)
End
113684458/112672229 (Hg38)
Location type
Intron54
Target gene
CSMD3
Nearest miRNA
hsa-mir-12123/Upstream/28646; hsa-mir-10400/Downstream/4202499;
Nearest TSS
ENST00000518652/Upstream/334654; ENST00000521500/Downstream/17813;
Nearest CpG islands
None/Target, chr8-CpG: 109/Upstream/2696386, chr8-CpG: 21/Downstream/760368
Upstream sequence
cagctaatttttgtattttttgtagatatggggtctcactatgttgctcaggctgatctcaaactcctgagctcaggccatctgcccacctcggcctccc
Downstream sequence
taacagaagtgggacagaataggcagaggTAGGAAGTAAAAAACACTAATCTGTGTGGGGGAAAGTCAAGTGGTTCTTGTTGTTACAACTTATTATTAGT
Reference
Yoo, S., et al. A pilot systematic genomic comparison of recurrence risks of hepatitis B virus-associated hepatocellular carcinoma with low- and high-degree liver fibrosis. BMC Med ,2017, 15(1): 214.
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