VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10016022

Fusion event

HBV-MSH3 integration

Validated

Yes

Detection method

LM PCR

Data source

Curated

Sample type

Nontumor

Disease

Hepatocellular carcinoma (HCC)

Quality evaluation

Normal

Reported year

2012

PubMed ID

22962577

Virus Sequence

Virus name

HBV

Reference genome

Not given

Start

1818

Orient

-

Host Sequence

Chromosome

chr5

Cytoband

q14.1

Reference genome

GRCh37/hg19

Start

80163572/80867753 (Hg38)

End

80163572/80867753 (Hg38)

Orient

-

Location type

Intron

Target gene

MSH3

miRNAs that regulate target gene

hsa-mir-326 ; hsa-mir-92b-3p ; hsa-mir-345-5p ; hsa-mir-520g-3p ; hsa-mir-520h ; hsa-mir-4635 ; hsa-mir-3686 ; hsa-mir-3182 ; hsa-mir-4742-3p ; hsa-mir-216b-3p ; hsa-mir-1246 ; hsa-mir-18a-3p ; hsa-mir-324-3p ; hsa-mir-1913 ; hsa-mir-150-5p ; hsa-mir-7107-5p ; hsa-mir-1234-3p ; hsa-mir-1224-3p ; hsa-mir-186-3p ; hsa-mir-3159 ; hsa-mir-520e ; hsa-mir-520d-3p ; hsa-mir-520c-3p ; hsa-mir-520b ; hsa-mir-520a-3p ; hsa-mir-373-3p ; hsa-mir-372-3p ; hsa-mir-302e ; hsa-mir-302d-3p ; hsa-mir-302c-3p ; hsa-mir-302b-3p ; hsa-mir-302a-3p ; hsa-mir-93-5p ; hsa-mir-526b-3p ; hsa-mir-519d-3p ; hsa-mir-20b-5p ; hsa-mir-20a-5p ; hsa-mir-17-5p ; hsa-mir-106b-5p ; hsa-mir-106a-5p ; hsa-mir-4659b-3p ; hsa-mir-4659a-3p ; hsa-mir-4743-3p ; hsa-mir-498 ; hsa-mir-6783-3p ; hsa-mir-6888-3p ; hsa-mir-1343-3p ; hsa-mir-23b-5p ; hsa-mir-23a-5p ; hsa-mir-3120-5p ; hsa-mir-6787-3p ; hsa-mir-6742-3p ; hsa-mir-6852-5p ; hsa-mir-939-3p ; hsa-mir-4775 ; hsa-mir-4735-5p ; hsa-mir-6872-3p ; hsa-mir-590-3p ; hsa-mir-3163 ; hsa-mir-145-5p ; hsa-mir-7-5p

Nearest miRNA

hsa-mir-10397/Upstream/7989090; hsa-mir-103a-1/Downstream/1972402;

Nearest TSS

ENST00000502646/Upstream/152548; ENST00000514946/Downstream/85227;

Nearest CpG islands

None/Target, chr5-CpG: 87/Upstream/212699, chr5-CpG: 136/Downstream/92380

Upstream sequence

tgatgatatatttgcctcagagtactgctgtgaggtttaagtagaataatgaatgttaagtcattatggcagtatttagcatattgtaagcTTCTTCTTG

Downstream sequence

ttgcctattttttaatgggtttggttttttcttataaatgtaagttccttatagatggtggatattagacctttgtcagatgcatagtttgcaaacattt

Reference

Jiang, S., et al. Re-evaluation of the carcinogenic significance of hepatitis B virus integration in hepatocarcinogenesis. PLoS One ,2012, 7(9): e40363.