VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10004905

Fusion event

HBV-SLCO3A1 integration

Validated

No

Detection method

PCR and Ultra-deep sequencing

Data source

Curated

Sample type

Nontumor

Disease

Hepatocellular carcinoma (HCC)

Quality evaluation

Normal

Reported year

2018

PubMed ID

29861854

Virus Sequence

Virus name

HBV

Reference genome

AP011098

Start

1318

Orient

-

Integrated sequence

ATAGGCCATCGGCGCATGCGTGGAACCTTTGTGGCTCCTCTGCCGATCCATACTGCGGAACTCCTAGCAGCTTGTTTTGCTCGCAGCCGGTCTGGAGCAA| |AACTTATCGGGACTGACAACTCTGTTGTCCTCTCTCGGAAATACACCTCCTTCCCATGGCTGCTCGGGTGTGCTGCCAACTGGATCCTGCGCGGGACGTC

Host Sequence

Chromosome

chr15

Cytoband

q26.1

Reference genome

GRCh37/hg19

Start

92630143/92086913 (Hg38)

End

92630143/92086913 (Hg38)

Orient

+

Location type

Intron

Target gene

SLCO3A1

miRNAs that regulate target gene

hsa-mir-215-5p ; hsa-mir-192-5p ; hsa-mir-218-1-3p ; hsa-let-7e-5p ; hsa-mir-15a-5p ; hsa-mir-16-5p ; hsa-mir-103a-3p ; hsa-mir-107 ; hsa-mir-15b-5p ; hsa-mir-195-5p ; hsa-mir-424-5p ; hsa-mir-497-5p ; hsa-mir-3150b-3p ; hsa-mir-4689 ; hsa-mir-4784 ; hsa-mir-6838-5p ; hsa-mir-6858-5p ; hsa-mir-6809-3p ; hsa-mir-6833-3p ; hsa-mir-4768-5p ; hsa-mir-6873-3p ; hsa-mir-372-5p ; hsa-mir-371a-5p ; hsa-mir-616-5p ; hsa-mir-373-5p ; hsa-mir-371b-5p ; hsa-mir-330-3p ; hsa-mir-5582-3p ; hsa-mir-548x-3p ; hsa-mir-548j-3p ; hsa-mir-548aq-3p ; hsa-mir-548am-3p ; hsa-mir-548aj-3p ; hsa-mir-548ah-3p ; hsa-mir-548ae-3p ; hsa-mir-374b-3p ; hsa-mir-4420 ; hsa-mir-181b-3p ; hsa-mir-181b-2-3p ; hsa-mir-4524b-5p ; hsa-mir-4524a-5p ; hsa-mir-3974 ; hsa-mir-370-5p ; hsa-mir-874-5p ; hsa-mir-4635 ; hsa-mir-149-5p ; hsa-mir-4264 ; hsa-mir-1224-3p ; hsa-mir-622 ; hsa-mir-4650-5p ; hsa-mir-1972 ; hsa-mir-6765-3p ; hsa-mir-210-3p ; hsa-mir-147b ; hsa-mir-933 ; hsa-mir-3907 ; hsa-mir-1470 ; hsa-mir-6887-3p ; hsa-mir-4756-3p ; hsa-mir-3919 ; hsa-mir-4433b-3p ; hsa-mir-6856-5p ; hsa-mir-6758-5p

Nearest miRNA

hsa-mir-10393/Upstream/2080072; hsa-mir-1302-10/Downstream/817486;

Nearest TSS

ENST00000557528/Upstream/145595; ENST00000555210/Downstream/11017;

Nearest CpG islands

None/Target, chr15-CpG: 55/Upstream/170465, chr15-CpG: 170/Downstream/306534

Upstream sequence

aaaaatacaaaaattagccaggcatggtgccacacgcctgtaatcccagctactcaagaggctgaggcaggagaatcacttgaacctggtgtggggacgg

Downstream sequence

cagaggttccagtgagctgagatcaagtcacttcactctaaccggggtgaaaaagcaaaactccgtctcaaaaaaaaaaaaaaaggaatatttctctacc

Reference

Tu, T., et al. Hepatitis B Virus DNA Integration Occurs Early in the Viral Life Cycle in an In Vitro Infection Model via Sodium Taurocholate Cotransporting Polypeptide-Dependent Uptake of Enveloped Virus Particles. J Virol ,2018,92(11).