CSMD3 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10016520
Fusion event
HBV-CSMD3 integration
Validated
No
Detection method
WGS
Data source
Curated
Sample type
Tumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Good
Reported year
2012
PubMed ID
22267523
Virus Sequence
Virus name
HBV
Reference genome
NC_003977
Start
1606
End
1641
Orient
+
Integrated sequence
CGCATGGAGACCACCGTGAACGCCCACCAAATATTG
Host Sequence
Chromosome
chr8
Cytoband
q23.3
Reference genome
GRCh37/hg19
Start
113579530/112567301 (Hg38)
End
113579565/112567336 (Hg38)
Orient
-
Location type
Intronic
Target gene
CSMD3
Nearest miRNA
hsa-mir-12123/Upstream/8082836; hsa-mir-10400/Downstream/76157;
Nearest TSS
ENST00000518652/Upstream/229726; ENST00000521500/Downstream/122706;
Nearest CpG islands
None/Target, chr8-CpG: 109/Upstream/2591458, chr8-CpG: 21/Downstream/865261
Upstream sequence
ACCTCTTATTTGTAATTATTAAAGATATTTTACATATGGCTTTTTAATTTTAACTTTAAAATACTTTATAACTTTTTTGTACTTTCTGATTTGTATGAAC
Downstream sequence
ccattgccctgttttaaattacttctaaatgtagttctcttaccttttgttcataactttcttttatgtcttgccccactaaaaagttagtttgttatgg
Target sequence
aattagctaaagtggtctcatctgtactatctatc
Reference
Jiang, S., et al. Re-evaluation of the carcinogenic significance of hepatitis B virus integration in hepatocarcinogenesis. PLoS One ,2012, 7(9): e40363.
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