SYNE2 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10016129
Fusion event
HBV-SYNE2 integration
Validated
No
Detection method
RNA-Seq
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
AY033073.1
Start
1802
End
1824
Orient
+
Integrated sequence
GCATCCTGCTGCTATGCCTCATC
Host Sequence
Chromosome
chr14
Cytoband
q23.2
Reference genome
GRCh37/hg19
Start
64506127/64039409 (Hg38)
End
64506181/64039463 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA14B
Target gene
SYNE2
miRNAs that regulate target gene
hsa-mir-155-5p ; hsa-mir-193b-3p ; hsa-mir-148b-3p ; hsa-mir-9-5p ; hsa-mir-1-3p ; hsa-mir-34a-5p ; hsa-mir-26b-5p ; hsa-mir-21-5p ; hsa-mir-484 ; hsa-let-7b-5p ; hsa-mir-543 ; hsa-mir-376a-5p ; hsa-mir-485-5p
Nearest miRNA
hsa-mir-208a/Upstream/3390698; hsa-mir-1185-1/Downstream/55561;
Nearest TSS
ENST00000550708/Upstream/36385; ENST00000557060/Downstream/23319;
Nearest CpG islands
None/Target, chr14-CpG: 35/Upstream/185601, chr14-CpG: 45/Downstream/254550
Upstream sequence
aacactaatttagaaatgctggttttcctcctcttcttatttataaaatgtttcttttcagactcttcacatgcatctttgacttcactatttttatcat
Downstream sequence
tggtcctgcccttaggaggagttcaTGATATTCTTCTCACCTCCTATTCTTTTCCAAACAGACCCAAATGAAAGGAAAGATACATGTTTGAGAAAAAGCA
Target sequence
GCTGAAGTGgaatgttcactttgtgagtcaggggatgtaaagatcaaaatgtcg
Reference
Jiang, S., et al. Re-evaluation of the carcinogenic significance of hepatitis B virus integration in hepatocarcinogenesis. PLoS One ,2012, 7(9): e40363.
Curate