VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10005428

Fusion event

HBV-ABCF2 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

1529

Orient

+

Integrated sequence

TCCCGTCGGCGCTGAATCCCGCGGACGACCCGTCTCGGGGCCGTTTGGGGCTCTACCGTCCCCTTCTTCATCTGCCGTTCCGGCCGACCACGGGGCGCAC| |CTCTCTTTACGCGGTCTCCCCGTCTGTGCCTTCTCATCTGCCGGACCGTGTGCACTTCGCTTCACCTCTGCACGTCGCATGGAGACCACCGTGAACGCCC

Host Sequence

Chromosome

chr7

Cytoband

q36.1

Reference genome

GRCh37/hg19

Start

150909440/151212354 (Hg38)

End

150909440/151212354 (Hg38)

Orient

+

Location type

Intron

Fragile sites / regions

FRA7I

Target gene

ABCF2

miRNAs that regulate target gene

hsa-mir-16-5p ; hsa-mir-124-3p ; hsa-mir-103a-3p ; hsa-mir-32-5p ; hsa-mir-532-3p ; hsa-mir-193b-3p ; hsa-mir-326 ; hsa-mir-320a ; hsa-mir-186-5p ; hsa-mir-218-5p ; hsa-mir-5047 ; hsa-mir-1301-3p ; hsa-mir-7156-3p ; hsa-mir-939-5p ; hsa-mir-1343-5p ; hsa-mir-122-5p ; hsa-mir-6081 ; hsa-mir-4722-5p ; hsa-mir-1286 ; hsa-mir-873-5p ; hsa-mir-107 ; hsa-mir-5699-3p ; hsa-mir-4421 ; hsa-mir-6748-3p ; hsa-mir-6764-5p ; hsa-mir-1915-3p ; hsa-mir-16-1-3p ; hsa-mir-4433a-3p ; hsa-mir-92b-3p ; hsa-mir-92a-3p ; hsa-mir-367-3p ; hsa-mir-363-3p ; hsa-mir-25-3p ; hsa-mir-4280 ; hsa-mir-4433b-3p ; hsa-mir-6769a-3p ; hsa-mir-3943 ; hsa-mir-4323 ; hsa-mir-3908 ; hsa-mir-5010-3p ; hsa-mir-4743-3p ; hsa-mir-592 ; hsa-mir-6888-3p ; hsa-mir-584-5p ; hsa-mir-4669 ; hsa-mir-3657 ; hsa-mir-550a-3p ; hsa-mir-200c-5p ; hsa-mir-152-5p ; hsa-mir-597-3p ; hsa-mir-182-3p ; hsa-mir-550b-3p ; hsa-mir-3120-5p ; hsa-mir-486-5p ; hsa-mir-758-5p ; hsa-mir-218-2-3p

Nearest miRNA

hsa-mir-10399/Upstream/3834233; hsa-mir-153-2/Downstream/26067;

Nearest TSS

ENST00000635602/Upstream/1976; ENST00000482173/Downstream/9630;

Nearest CpG islands

None/Target, chr7-CpG: 39/Upstream/7462, chr7-CpG: 60/Downstream/14440

Junction sequence

GCA

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

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).