VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10005594

Fusion event

HBV-PPP1R12C 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

417

Orient

-

Integrated sequence

CCCCAACCTCCAATCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGGCTATCGCTGGATGTGTCTGCGGCGTTTTATCATATTCCTCTTCATCCTGCT| |GCTATGCCTCATCTTCTTGTTGGTTCTTCTGGACTACCAAGGTATGTTGCCCGTTTGTCCTCTACTTCCAGGAACATCAACTACCAGCACGGGACCATGC

Host Sequence

Chromosome

chr19

Cytoband

q13.42

Reference genome

GRCh37/hg19

Start

55614853/55103485 (Hg38)

End

55614853/55103485 (Hg38)

Orient

-

Location type

Exon

Fragile sites / regions

FRA19A

Target gene

PPP1R12C

miRNAs that regulate target gene

hsa-mir-103a-3p ; hsa-mir-32-5p ; hsa-mir-130b-5p ; hsa-mir-125b-2-3p ; hsa-let-7b-5p ; hsa-mir-8057 ; hsa-mir-1260b ; hsa-mir-1260a ; hsa-mir-6778-3p ; hsa-mir-532-3p ; hsa-mir-7107-5p ; hsa-mir-1234-3p ; hsa-mir-1224-3p ; hsa-mir-4793-5p ; hsa-mir-1306-5p ; hsa-mir-92b-3p ; hsa-mir-92a-3p

Nearest miRNA

hsa-let-7e/Upstream/458102; hsa-mir-10394/Downstream/19740;

Nearest TSS

ENST00000633603/Upstream/6421; ENST00000591665/Downstream/10133;

Nearest CpG islands

None/Target, chr19-CpG: 112/Upstream/5805, chr19-CpG: 99/Downstream/13635

Upstream sequence

TGGAACAGACTGGCCCAACTCACCTCATCACCTCAATGTAGCCCTTGGCAGCAGCCACGTGCAGGGCAGAGGCGCCTGTGCGGGGGTGCCGGGCCTCTGG

Downstream sequence

CATGGCGCCCCCATTCAGCCAGCACCTCGTGTCATGAAGGAGCAATTCCTCTTCTGCCCGCTTGGCTGCTTCCACATCCACACCTAGGAGGATAAGAGGC

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).