VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10004758

Fusion event

HBV-AFF2 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

1792

Orient

+

Integrated sequence

ACCTTGAGGCATACTTCAAAGACTGTTTGTTTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAA| |ATTGGTCTGTTCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGC

Host Sequence

Chromosome

chrX

Cytoband

q28

Reference genome

GRCh37/hg19

Start

147839825/148758301 (Hg38)

End

147839825/148758301 (Hg38)

Orient

-

Location type

Intron

Fragile sites / regions

FRAXE ; FRAXF

Target gene

AFF2

miRNAs that regulate target gene

hsa-mir-7111-5p ; hsa-mir-6870-5p ; hsa-mir-5698 ; hsa-mir-4723-5p ; hsa-mir-3175 ; hsa-mir-8085 ; hsa-mir-6731-5p ; hsa-mir-4644 ; hsa-mir-4306 ; hsa-mir-185-5p ; hsa-mir-4786-5p ; hsa-mir-6794-5p ; hsa-mir-4716-3p ; hsa-mir-6856-5p ; hsa-mir-6758-5p ; hsa-mir-6502-3p ; hsa-mir-877-5p ; hsa-mir-4784 ; hsa-mir-3150b-3p ; hsa-mir-6859-5p ; hsa-mir-3916 ; hsa-mir-3125 ; hsa-mir-603 ; hsa-mir-8485 ; hsa-mir-2113 ; hsa-mir-3177-5p ; hsa-mir-143-5p ; hsa-mir-3944-5p ; hsa-mir-511-3p ; hsa-mir-4783-5p ; hsa-mir-3180-5p ; hsa-mir-525-5p ; hsa-mir-520a-5p ; hsa-mir-22-5p ; hsa-mir-5584-3p ; hsa-mir-488-5p ; hsa-mir-4773 ; hsa-mir-148a-5p ; hsa-mir-933 ; hsa-mir-1976 ; hsa-mir-26a-1-3p ; hsa-mir-26a-2-3p ; hsa-mir-3653-5p ; hsa-mir-370-3p ; hsa-mir-4279 ; hsa-mir-4720-3p ; hsa-mir-4804-3p ; hsa-mir-548aa ; hsa-mir-548ap-3p ; hsa-mir-548as-3p ; hsa-mir-548at-3p ; hsa-mir-548ay-3p ; hsa-mir-548t-3p ; hsa-mir-645 ; hsa-mir-6893-3p

Nearest miRNA

hsa-let-7f-2/Upstream/1473573; hsa-mir-105-1/Downstream/1469703;

Nearest TSS

ENST00000429181/Upstream/39210; ENST00000448332/Downstream/739965;

Nearest CpG islands

None/Target, chrX-CpG: 62/Upstream/256538, chrX-CpG: 17/Downstream/712719

Upstream sequence

gttttttttcaaaatctgtgaagaatgtcaatggtaggttaacaggaatagcattgaatctacaaattaccaaagtcataataatttatccttacttttt

Downstream sequence

AGACACAGAAACACGTTTCTCAAATATTGGATAGCTGTTTTTGTGATTTTGCTTGTTTAGTTTTAAGGTTGGCCCTTTGGCAGACATTTCCTGTAACTTT

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).