GRIN3A _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10020135
Fusion event
HBV-GRIN3A integration
Validated
No
Detection method
VirusScan
Data source
Curated
Sample type
Tumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Good
Reported year
2016
PubMed ID
27339696
Virus Sequence
Virus name
HBV
Reference genome
NC_003977.1
Start
1181
End
2281
Orient
+
Integrated sequence
GTTTGCTGACGCAACCCCCACGGGTTGGGGCTTGGCCATAGGCCATCGGCGCATGCGTGGAACCTTTGTGGCTCCTCTGCCGATCCATACTGCGGAACTCCTAGCAGCTTGTTTTGCTCGCAGCCGGTCTGGAGCGAAACTTATCGGAACCGACAACTCAGTTGTCCTCTCTCGGAAATACACCTCCTTTCCATGGCTGCTAGGCTGTGCTGCCAACTGGATCCTGCGCGGGACGTCCTTTGTCTACGTCCCGTC
Host Sequence
Chromosome
chr9
Cytoband
q31.1
Reference genome
GRCh37/hg19
Start
104362434/101600152 (Hg38)
End
104363484/101601202 (Hg38)
Orient
+
Location type
Intronic
Target gene
GRIN3A
miRNAs that regulate target gene
hsa-mir-542-5p
Nearest miRNA
hsa-let-7a-1/Upstream/3370935; hsa-mir-12126/Downstream/4999726;
Nearest TSS
ENST00000422679/Upstream/5131; ENST00000374801/Downstream/12320;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/66202, chr9-CpG: 115/Downstream/136365
Upstream sequence
agccataatggtgacactgcactgtagcctggatgacagagtgagacactgtctccaaaaaataagtgttattcaaggacctgccgtgtatgtcatttct
Downstream sequence
gaagtacttgagcaaagtagcagaagatgagctagacagaaccagatgaagcagggttttgaatgtttggctaagacatttagtctctacccagtaggga
Target sequence
actttcaggattaaatgagatagattataagaagaagggtgctcaatgcctatcacatagtaggtacaggaatggtagAGATTATAATTATTGCCTACTTTAGGCTTGCTTAAAAACTCAAGTAGACTGTATGCATACATGCACACAGATATACTCAGCTATTTatttgttttctcaacaaataattattgaggatctactatgtgagaagaatataatactgacctaaagtggatacttttcttgttgtccctg
Reference
Cao, S., et al.Divergent viral presentation among human tumors and adjacent normal tissues. Sci Rep,2016, 6: 28294.
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