SYT12 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10006848
Fusion event
HBV-SYT12 integration
Validated
Yes
Detection method
Alu PCR and sequencing
Data source
Curated
Sample type
Tumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2015
PubMed ID
25627239
Virus Sequence
Virus name
HBV
Subtype
B2
Reference genome
JQ688405
Region type
Polymerase, X protein
Start
1589
Integrated sequence
CGCTTCTCCGCCTGTTGTACCGACCGACCACGGGGCGCACCTCTCTTTACGCGGACTCCCCGTCTGTGCCTTCTCATCTGCCGGACCGTGTGCACTTCGC| |TTCACCTCTGCACGTCGCATGGAGACCACCGTGAACGCCCACAGGAACCTGCCCAAGGTCTTGCATAAGAGGACTCTTGGACTTTCAGCAATGTCAACGA
Host Sequence
Chromosome
chr11
Cytoband
q13.2
Reference genome
GRCh37/hg19
Start
66807269/67039798 (Hg38)
End
66807269/67039798 (Hg38)
Location type
Intronic
Fragile sites / regions
FRA11H
Target gene
SYT12
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-146a-5p
Nearest miRNA
hsa-mir-10392/Upstream/105292; hsa-let-7a-2/Downstream/5845;
Nearest TSS
ENST00000527297/Upstream/9698; ENST00000533360/Downstream/17020;
Nearest CpG islands
None/Target, chr11-CpG: 30/Upstream/15829, chr11-CpG: 57/Downstream/16849
Upstream sequence
GGGGAACTTGGAGATTCGAGAATGAACAGGCCTTACTCATCTCTTTGCCGTCTCCCAGTGACCTTGCCTATGGCCCCCATGATGCTCCCACGTCCCTCTT
Downstream sequence
TCTCACCCCTAGAGAGTGCCTGCCTGGAATGCCCAGCGGGCCAGCACGCGGGGACCACCCAGCCGCAAAGGCAGTCTCAGCATTGAGGACACCTTTGAGA
Reference
Yan, H., et al. Characterization of the genotype and integration patterns of hepatitis B virus in early- and late-onset hepatocellular carcinoma. Hepatology ,2015,61(6): 1821-1831.
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