VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10005299

Fusion event

HBV-PDE4D 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

1548

Orient

+

Integrated sequence

CGCGGACGACCCGTCTCGGGGCCGTTTGGGGCTCTACCGTCCCCTTCTTCATCTGCCGTTCCGGCCGACCACGGGGCGCACCTCTCTTTACGCGGTCTCC| |CCGTCTGTGCCTTCTCATCTGCCGGACCGTGTGCACTTCGCTTCACCTCTGCACGTCGCATGGAGACCACCGTGAACGCCCACCAGGTCTTGCCCAAGGT

Host Sequence

Chromosome

chr5

Cytoband

q12.1

Reference genome

GRCh37/hg19

Start

58920046/59624220 (Hg38)

End

58920046/59624220 (Hg38)

Orient

-

Location type

Intron

Fragile sites / regions

FRA5H

Target gene

PDE4D

miRNAs that regulate target gene

hsa-mir-335-5p ; hsa-mir-340-5p ; hsa-mir-7-5p ; hsa-mir-103a-3p ; hsa-mir-19b-3p ; hsa-mir-18a-5p ; hsa-mir-16-5p ; hsa-mir-3148 ; hsa-mir-4668-5p ; hsa-mir-4457 ; hsa-mir-5590-3p ; hsa-mir-142-5p ; hsa-mir-6783-5p ; hsa-mir-6838-5p ; hsa-mir-497-5p ; hsa-mir-424-5p ; hsa-mir-195-5p ; hsa-mir-15b-5p ; hsa-mir-15a-5p ; hsa-mir-6835-3p ; hsa-mir-548z ; hsa-mir-548h-3p ; hsa-mir-548d-3p ; hsa-mir-548bb-3p ; hsa-mir-7158-3p ; hsa-mir-548ac ; hsa-mir-31-3p ; hsa-mir-302f ; hsa-mir-4760-3p ; hsa-mir-4282 ; hsa-mir-18b-5p ; hsa-mir-4735-3p ; hsa-mir-4439 ; hsa-mir-3136-5p ; hsa-mir-6857-3p ; hsa-mir-6855-3p ; hsa-mir-4513 ; hsa-mir-4502 ; hsa-mir-4682 ; hsa-mir-1324 ; hsa-mir-4422 ; hsa-mir-3611 ; hsa-mir-4325 ; hsa-mir-4266 ; hsa-mir-642b-3p ; hsa-mir-642a-3p ; hsa-mir-6080 ; hsa-mir-6888-5p ; hsa-mir-3120-3p ; hsa-mir-3646 ; hsa-mir-424-3p ; hsa-mir-199a-5p ; hsa-mir-139-5p

Nearest miRNA

hsa-mir-10397/Upstream/1094111; hsa-mir-103a-1/Downstream/79386;

Nearest TSS

ENST00000502646/Upstream/37721; ENST00000502993/Downstream/144289;

Nearest CpG islands

None/Target, chr5-CpG: 87/Upstream/584166, chr5-CpG: 47/Downstream/268999

Upstream sequence

AGAACTAGGCTCATAAAAACTGGTTATATTTGTGACAGATGACCTGAAATCACTGTTTTATGAATGGTAAGCCTGTCTTTCCTGACCAGAGTCACATGGC

Downstream sequence

GGACGTTTCTCCTAATTCCATCCCCTGTTCCATCCTTTGGGGCCTTCTCTGTCTCTGACATCTTCAGTCTATCCCTCCTTTCCTTCACATACTCCTGCCC

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).