VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10005778

Fusion event

HBV-DGKH 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

1825

Orient

+

Integrated sequence

AGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAACTTTTT| |CACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCGTATAAAGAAT

Host Sequence

Chromosome

chr13

Cytoband

q14.11

Reference genome

GRCh37/hg19

Start

42777103/42202967 (Hg38)

End

42777103/42202967 (Hg38)

Orient

-

Location type

Intron

Target gene

DGKH

miRNAs that regulate target gene

hsa-mir-1-3p ; hsa-mir-4452 ; hsa-mir-183-3p ; hsa-mir-3935 ; hsa-mir-656-3p ; hsa-mir-577 ; hsa-mir-1277-5p ; hsa-mir-575 ; hsa-mir-4676-5p ; hsa-mir-6858-3p ; hsa-mir-4798-3p ; hsa-mir-889-3p ; hsa-mir-19b-3p ; hsa-mir-19a-3p ; hsa-mir-545-5p ; hsa-mir-3163 ; hsa-mir-4709-5p ; hsa-mir-4282 ; hsa-mir-4789-5p ; hsa-mir-466 ; hsa-mir-4643 ; hsa-mir-4789-3p ; hsa-mir-297 ; hsa-mir-3924 ; hsa-mir-568 ; hsa-mir-190a-3p ; hsa-mir-223-5p ; hsa-mir-567 ; hsa-mir-5011-5p ; hsa-mir-30e-3p ; hsa-mir-30d-3p ; hsa-mir-30a-3p ; hsa-mir-1305 ; hsa-mir-6794-3p ; hsa-mir-766-5p ; hsa-mir-4778-3p ; hsa-mir-1304-3p ; hsa-mir-4509 ; hsa-mir-4744 ; hsa-mir-1207-3p ; hsa-mir-4639-3p ; hsa-mir-3161 ; hsa-mir-6804-5p ; hsa-mir-513b-5p ; hsa-mir-4457 ; hsa-mir-125b-2-3p ; hsa-mir-3614-3p ; hsa-mir-6873-5p ; hsa-mir-5680 ; hsa-mir-421 ; hsa-mir-505-3p ; hsa-mir-7159-5p

Nearest miRNA

hsa-mir-2276/Upstream/634572; hsa-mir-1267/Downstream/1993162;

Nearest TSS

ENST00000623511/Upstream/62572; ENST00000489851/Downstream/11540;

Nearest CpG islands

None/Target, chr13-CpG: 551/Upstream/153543, chr13-CpG: 84/Downstream/68750

Upstream sequence

ATACGTAATTTACATGGGTTAAGGAGACTGTTCTATTTATTAACTGAAATAATAATTATATATTGTTTCAAGTTCTGTAAGTACTAAGATACATGAAGAA

Downstream sequence

AAACAAATAACTTTAAAAAACAGTCTTCATCTGTAGGCTATAATGAAATATGTGATTGAGAACAAGTAGTTGTTTAATTCACATTTTTAGTTATTTCAAA

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).