Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS42000952
Fusion event
EBV-SLC38A2 integration
Validated
No
Detection method
GenCap Enrichment+NGS
Data source
Curated
Sample type
Disease
Gastric carcinoma (GC)
Quality evaluation
Normal
Reported year
2015
PubMed ID
Virus Sequence
Virus name
EBV
Reference genome
Start
79793
Orient
-
Integrated sequence
TTTTGCCCCCGACATCGAAATTGATAGTTACATTGACATCTGCCGTGCAAACATTGCATGTGGGGTAAAATGGGAATTCCGGAATCTCAACATTGAAAAA| |ACCAGGATCTTCACCCGTGAGATGGATCAGGCTCTGGATGGTGTACTGACACACAAGCAAGGCTGCCTCCATTGTCTCGGCACCGATTTCTAGGCAGCAT
Host Sequence
Chromosome
chr12
Cytoband
q13.11
Reference genome
Start
End
46763666/46369883 (Hg38)
Orient
-
Location type
Intronic
Target gene
miRNAs that regulate target gene
hsa-mir-30a-5p ; hsa-mir-335-5p ; hsa-mir-124-3p ; hsa-mir-101-3p ; hsa-mir-16-5p ; hsa-let-7b-5p ; hsa-mir-18a-3p ; hsa-mir-193b-3p ; hsa-let-7e-5p ; hsa-mir-3161 ; hsa-mir-9-3p ; hsa-mir-3145-3p ; hsa-mir-4789-5p ; hsa-mir-599 ; hsa-mir-4704-5p ; hsa-mir-1245b-3p ; hsa-mir-19a-3p ; hsa-mir-19b-3p ; hsa-mir-130a-3p ; hsa-mir-301a-3p ; hsa-mir-130b-3p ; hsa-mir-454-3p ; hsa-mir-301b-3p ; hsa-mir-4295 ; hsa-mir-3666 ; hsa-mir-6857-5p ; hsa-mir-6878-3p ; hsa-mir-491-5p ; hsa-mir-4450 ; hsa-mir-6744-3p ; hsa-mir-4757-5p ; hsa-mir-194-3p ; hsa-mir-4699-3p ; hsa-mir-1296-3p ; hsa-mir-4801 ; hsa-mir-4731-3p ; hsa-mir-212-3p ; hsa-mir-132-3p ; hsa-mir-340-5p ; hsa-mir-199b-5p ; hsa-mir-199a-5p ; hsa-mir-1825 ; hsa-mir-152-3p ; hsa-mir-148b-3p ; hsa-mir-148a-3p ; hsa-mir-455-3p ; hsa-mir-5590-3p ; hsa-mir-142-5p ; hsa-mir-4429 ; hsa-mir-320d ; hsa-mir-320c ; hsa-mir-320b ; hsa-mir-320a ; hsa-mir-8081 ; hsa-mir-4642 ; hsa-mir-1269b ; hsa-mir-1269a ; hsa-mir-4515 ; hsa-mir-1288-3p ; hsa-mir-4740-5p ; hsa-mir-4711-5p ; hsa-mir-6857-3p ; hsa-mir-4682 ; hsa-mir-2355-3p ; hsa-mir-4646-3p ; hsa-mir-4474-3p ; hsa-mir-3912-5p ; hsa-mir-548at-5p ; hsa-mir-26b-5p ; hsa-mir-26a-5p ; hsa-mir-181d-5p ; hsa-mir-181c-5p ; hsa-mir-181b-5p ; hsa-mir-181a-5p
Nearest miRNA
hsa-mir-1244-3/Upstream/4046024; hsa-let-7i/Downstream/817929;
Nearest CpG islands
None/Target, chr12-CpG: 104/Upstream/100258, chr12-CpG: 163/Downstream/1468
Upstream sequence
GAAAGTGTAGTGATACTTTATTCTTTTTATGATTTCTTTCTTAATAGAGTTCTCTTCACTTTTTATAGGTATAAGGGGCACCCTCAGTTATACATAGGGC
Downstream sequence
ATTATTTAAAATATTTCCTCTATTTGCATGAACAGTCAGCATGCCCCACAAGAAGAGCCATGATAGTTAGTCTGGTCATTTTTAAATTTCAACCCACACT
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.