VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10015744

Fusion event

HBV-SV2C integration

Validated

No

Detection method

MAPS

Data source

Curated

Sample type

Adjacent tissue

Disease

Hepatocellular carcinoma (HCC)

Quality evaluation

Perfect

Reported year

2012

PubMed ID

23236287

Virus Sequence

Virus name

HBV

Reference genome

AY800389.1;AY800390.1;AY800391.1;AY800392.1

Orient

+

Host Sequence

Chromosome

chr5

Cytoband

q13.3

Reference genome

GRCh37/hg19

Start

75380870/76085045 (Hg38)

End

75380870/76085045 (Hg38)

Orient

+

Location type

Intronic

Target gene

SV2C

miRNAs that regulate target gene

hsa-mir-526a ; hsa-mir-523-5p ; hsa-mir-522-5p ; hsa-mir-520c-5p ; hsa-mir-519c-5p ; hsa-mir-519b-5p ; hsa-mir-519a-5p ; hsa-mir-518f-5p ; hsa-mir-518e-5p ; hsa-mir-518d-5p ; hsa-mir-6502-5p ; hsa-mir-1301-5p ; hsa-mir-517-5p ; hsa-mir-520g-5p ; hsa-mir-3613-3p ; hsa-mir-6856-5p ; hsa-mir-6758-5p

Nearest miRNA

hsa-mir-10397/Upstream/3206382; hsa-mir-103a-1/Downstream/6755110;

Nearest TSS

ENST00000502646/Upstream/859; ENST00000506257/Downstream/206720;

Nearest CpG islands

None/Target, chr5-CpG: 87/Upstream/74, chr5-CpG: 39/Downstream/85734

Upstream sequence

AGAATTAAACGGAAGCTACCGCGCTAGCAGTCAGCTAAGTATGAAGGGAT

Junction sequence

AGAATTAAACGGAAGCTACCGCGCTAGCAGTCAGCTAAGTATGAAGGGATTGAAAAAGTTGCATGGCGCTGGTGAACAGACCAATTTA

* Color: Human Sequence / Virus Sequence / Overlapped sequence / Unknown sequence

Reference

Ding, D., et al. Recurrent targeted genes of hepatitis B virus in the liver cancer genomes identified by a next-generation sequencing-based approach. PLoS Genet ,2010,8(12): e1003065.