VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10015635

Fusion event

HBV-CDK13 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

chr7

Cytoband

p14.1

Reference genome

GRCh37/hg19

Start

40061643/40022044 (Hg38)

End

40061643/40022044 (Hg38)

Orient

-

Location type

Intronic

Target gene

CDK13

miRNAs that regulate target gene

hsa-mir-133b ; hsa-mir-29b-2-5p ; hsa-mir-4659b-3p ; hsa-mir-4659a-3p ; hsa-mir-6875-3p ; hsa-mir-664b-3p ; hsa-mir-579-3p ; hsa-mir-5696 ; hsa-mir-664a-3p ; hsa-mir-30e-3p ; hsa-mir-30d-3p ; hsa-mir-30a-3p ; hsa-mir-8061 ; hsa-mir-4760-5p ; hsa-mir-6794-3p ; hsa-mir-376a-5p ; hsa-mir-372-5p ; hsa-mir-888-5p

Nearest miRNA

hsa-mir-1183/Upstream/3102612; hsa-mir-10399/Downstream/3128851;

Nearest TSS

ENST00000635602/Upstream/22655; ENST00000642592/Downstream/23886;

Nearest CpG islands

None/Target, chr7-CpG: 39/Upstream/70031, chr7-CpG: 109/Downstream/112238

Upstream sequence

CTCCCAGTTGTAGTGTCATTAAATGGATTTTTACTCTTTATATTCCTACCACCTTTCACGTTGAGGGCGAGT

Junction sequence

CTCCCAGTTGTAGTGTCATTAAATGGATTTTTACTCTTTATATTCCTACCACCTTTCACGTTGAGGGCGAGTACAGACCAATTTATGC

* 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.