SCAPER _STAD.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS42001009
Fusion event
EBV-SCAPER integration
Validated
No
Detection method
GenCap Enrichment+NGS
Data source
Curated
Sample type
Tumor
Disease
Gastric carcinoma (GC)
Quality evaluation
Normal
Reported year
2015
PubMed ID
25355872
Virus Sequence
Virus name
EBV
Reference genome
NC007605
Start
64253
Orient
-
Integrated sequence
CTCCAAATTGATTGATGAGTTAAAGGTCAAGGCCAACTCAGACCCCGAGGCTGATGTCCTGGCCGGGCGCCTGCTCCACCGCCTTAAGGCCGAGTCAGTT| |ACACACACAGTAGCCGAATATCTGGAGGTCTTCTCTGACAAATTCTACGATGAGGAATTCTTCCAGATGCACCGGGATGAGCTGGAGACCCGAGTCTCTG
Host Sequence
Chromosome
chr15
Cytoband
q24.3
Reference genome
GRCh37/hg19
Start
76927205/76634864 (Hg38)
End
76927205/76634864 (Hg38)
Orient
-
Location type
Intronic
Target gene
SCAPER
miRNAs that regulate target gene
hsa-mir-218-5p
Nearest miRNA
hsa-mir-10393/Upstream/872549; hsa-mir-11181/Downstream/2574924;
Nearest TSS
ENST00000557528/Upstream/13035; ENST00000557805/Downstream/30794;
Nearest CpG islands
None/Target, chr15-CpG: 55/Upstream/287382, chr15-CpG: 77/Downstream/270053
Upstream sequence
ggaagagaatgagtgagactaccatgggtgcgtggcatgagggagaccttttgatggaacaggtgatggaacaggttcgtatcttgattgtggtagtggc
Downstream sequence
gtgtgtgtattatttatgatactgtaagtacagtaagtcctcaatgtagtagataggttcttgaaactgcaattttaacaaggtatagcaaaactaattt
Reference
Cao, S., et al.High-throughput RNA sequencing-based virome analysis of 50 lymphoma cell lines from the Cancer Cell Line Encyclopedia project. J Virol,2015, 89(1): 713-729.
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