VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10006104

Fusion event

HBV-GRIK3 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

2342

Orient

+

Integrated sequence

GTTCTTGAGTATTTGGTGTCTTTTGGAGTGTGGATTCGCACTCCTCCCGCTTACAGACCACCAAATGCCCCTATCTTATCAACACTTCCGGAAACTACTG| |TTGTTAGACGACGAGGCAGGTCCCCTAGAAGAAGAACTCCCTCGCCTCGCAGACGAAGGTCTCAATCGCCGCGTCGCAGAAGATCTCAATCTCGGGAATC

Host Sequence

Chromosome

chr1

Cytoband

p34.3

Reference genome

GRCh37/hg19

Start

37382272/36916671 (Hg38)

End

37382272/36916671 (Hg38)

Orient

+

Location type

Intron

Target gene

GRIK3

miRNAs that regulate target gene

hsa-mir-1278 ; hsa-mir-1277-5p ; hsa-mir-190a-3p ; hsa-mir-1185-2-3p ; hsa-mir-1185-1-3p ; hsa-let-7f-2-3p ; hsa-mir-5011-5p ; hsa-mir-101-3p ; hsa-mir-448 ; hsa-mir-144-3p ; hsa-mir-8064 ; hsa-mir-338-3p ; hsa-mir-1226-3p ; hsa-mir-634 ; hsa-mir-362-3p ; hsa-mir-8485 ; hsa-mir-329-3p ; hsa-mir-1228-3p ; hsa-mir-586 ; hsa-mir-4659b-3p ; hsa-mir-4659a-3p ; hsa-mir-6875-3p ; hsa-mir-6749-3p ; hsa-mir-6792-3p ; hsa-mir-4691-5p ; hsa-mir-4778-3p ; hsa-mir-6773-3p ; hsa-mir-5699-3p ; hsa-mir-4421 ; hsa-mir-6748-3p ; hsa-mir-5193 ; hsa-mir-1255b-2-3p ; hsa-mir-493-5p ; hsa-mir-4666a-5p ; hsa-mir-3177-5p ; hsa-mir-6757-3p ; hsa-mir-1238-3p ; hsa-mir-670-3p ; hsa-mir-6071 ; hsa-mir-6881-3p ; hsa-mir-6780a-3p ; hsa-mir-7111-3p ; hsa-mir-5581-3p ; hsa-mir-365b-5p ; hsa-mir-365a-5p ; hsa-mir-3140-3p ; hsa-mir-5589-5p ; hsa-mir-4731-5p ; hsa-mir-617 ; hsa-mir-3692-5p ; hsa-mir-93-3p ; hsa-mir-6728-3p ; hsa-mir-4686

Nearest miRNA

hsa-mir-12136/Upstream/2246977; hsa-mir-101-1/Downstream/244892;

Nearest TSS

ENST00000473358/Upstream/57535; ENST00000642067/Downstream/117454;

Nearest CpG islands

None/Target, chr1-CpG: 111/Upstream/452141, chr1-CpG: 233/Downstream/116105

Upstream sequence

ggacttggtgccctgtgtcccagccactccagcagtgactaaaaggggacaagttacacctcgggctgttgcttcaacgggtggaagccccaagcctcag

Downstream sequence

cagcttccatgtggtgttgagcctgcaggtgcccaaaagtcaagaattgaggtttgggagcctctgcctagatttcagaggatgtatggaaacacctgga

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).