SPATA9 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10015248
Fusion event
HBV-SPATA9 integration
Validated
No
Detection method
WGS
Data source
Curated
Sample type
Tumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2012
PubMed ID
22634754
Virus Sequence
Virus name
HBV
Reference genome
NC_003977
Region type
HBVgp3 X protein;HBVgp4 precore/core protein
Start
1821
Orient
+
Integrated sequence
TGTTTAAAGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGCGCACCAGCACCATGCAA| |CTTTTTCACCTCTGCCTAATCATCTCTTGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATCGACCCTTATA
Host Sequence
Chromosome
chr5
Cytoband
q15
Reference genome
GRCh37/hg19
Start
95012131/95676427 (Hg38)
End
95012131/95676427 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA5B
Target gene
SPATA9
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-124-3p
Nearest miRNA
hsa-mir-10397/Upstream/2055639; hsa-mir-103a-1/Downstream/402711;
Nearest TSS
ENST00000502646/Upstream/18365; ENST00000515852/Downstream/6564;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/29437, chr5-CpG: 121/Downstream/54569
Upstream sequence
ACGAACGTGGCCAGCGGCAGCACCTCGCGGTAGTGGCTGCGCAGCAGGGAGCGCACGGCTCGGCAGCGGGGAGCGCGCGGCATCGCGGGGGTGGCCGGGG
Downstream sequence
AACTGATTTCTCCATTTGAGCTCTACTCTTTAAATATATATCTTGCTTTTCTTTTTTTATTTTCTTCTTGCTACAGCCATGCCCATTTCTTTGTCATAGG
Reference
Sung, W. K., et al. Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat Genet,2012, 44(7): 765-769.
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