VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS42000998

Fusion event

EBV-DGKH 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

10274

Orient

-

Integrated sequence

TAAAGCCAGGTGATAATTCCATACCCTGGAAGCAGGAGATGGGTGCATTTCACCCCAACCCCCCCTTTCGACTGTCATTTACAATAAAATGAAACCTTTT| |ATTCTTGATTGCCTCTTGTGTTCTTGCCGCCCAGGTACCTTCCTGTGTTCTCCCCACGGGAAAAAGAATAGCTTCTGCAGAAGGCCATTGACGCAAGTTT

Host Sequence

Chromosome

chr13

Cytoband

q14.11

Reference genome

GRCh37/hg19

Start

42710029/42135893 (Hg38)

End

42710029/42135893 (Hg38)

Orient

-

Location type

Intronic

Target gene

DGKH

miRNAs that regulate target gene

hsa-mir-1-3p ; hsa-mir-4452 ; hsa-mir-183-3p ; hsa-mir-3935 ; hsa-mir-656-3p ; hsa-mir-577 ; hsa-mir-1277-5p ; hsa-mir-575 ; hsa-mir-4676-5p ; hsa-mir-6858-3p ; hsa-mir-4798-3p ; hsa-mir-889-3p ; hsa-mir-19b-3p ; hsa-mir-19a-3p ; hsa-mir-545-5p ; hsa-mir-3163 ; hsa-mir-4709-5p ; hsa-mir-4282 ; hsa-mir-4789-5p ; hsa-mir-466 ; hsa-mir-4643 ; hsa-mir-4789-3p ; hsa-mir-297 ; hsa-mir-3924 ; hsa-mir-568 ; hsa-mir-190a-3p ; hsa-mir-223-5p ; hsa-mir-567 ; hsa-mir-5011-5p ; hsa-mir-30e-3p ; hsa-mir-30d-3p ; hsa-mir-30a-3p ; hsa-mir-1305 ; hsa-mir-6794-3p ; hsa-mir-766-5p ; hsa-mir-4778-3p ; hsa-mir-1304-3p ; hsa-mir-4509 ; hsa-mir-4744 ; hsa-mir-1207-3p ; hsa-mir-4639-3p ; hsa-mir-3161 ; hsa-mir-6804-5p ; hsa-mir-513b-5p ; hsa-mir-4457 ; hsa-mir-125b-2-3p ; hsa-mir-3614-3p ; hsa-mir-6873-5p ; hsa-mir-5680 ; hsa-mir-421 ; hsa-mir-505-3p ; hsa-mir-7159-5p

Nearest miRNA

hsa-mir-2276/Upstream/567498; hsa-mir-1267/Downstream/2060236;

Nearest TSS

ENST00000623511/Upstream/87071; ENST00000489851/Downstream/2149;

Nearest CpG islands

None/Target, chr13-CpG: 551/Upstream/86469, chr13-CpG: 84/Downstream/135824

Upstream sequence

tcaccactaccactactaccactactacaaccattaccaccatcactgctataaccaccaccaccaccaccattatcaccatcaccatcacacaccacaa

Downstream sequence

ctaccaccaccaccaccatcaccactataaccactagcaccaccaccactactataaccatcaccaccgctataaccaccatcaccaccaccactaccac

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.