VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10005881

Fusion event

HBV-PLXDC2 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

1784

Orient

+

Integrated sequence

AACGACCGACCTTGAGGCATACTTCAAAGACTGTTTGTTTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGT| |AGGCATAAATTGGTCTGTTCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCT

Host Sequence

Chromosome

chr10

Cytoband

p12.31

Reference genome

GRCh37/hg19

Start

20256536/19967607 (Hg38)

End

20256536/19967607 (Hg38)

Orient

-

Location type

Intron

Target gene

PLXDC2

miRNAs that regulate target gene

hsa-mir-148b-3p ; hsa-mir-1-3p ; hsa-mir-181a-5p ; hsa-let-7b-5p ; hsa-mir-573 ; hsa-mir-3616-5p ; hsa-mir-3152-3p ; hsa-mir-4635 ; hsa-mir-4694-5p ; hsa-mir-574-5p ; hsa-mir-1277-5p ; hsa-mir-599 ; hsa-mir-3912-5p ; hsa-mir-3924 ; hsa-mir-190a-3p ; hsa-mir-6755-3p ; hsa-mir-6867-5p ; hsa-mir-223-5p ; hsa-mir-198 ; hsa-mir-193a-5p ; hsa-mir-1273f ; hsa-mir-1304-3p ; hsa-mir-4781-3p ; hsa-mir-5011-5p ; hsa-mir-3976 ; hsa-mir-4789-3p ; hsa-mir-8485 ; hsa-mir-302f ; hsa-mir-3675-3p ; hsa-mir-136-3p ; hsa-mir-5698 ; hsa-mir-744-3p ; hsa-mir-6805-3p ; hsa-mir-5691 ; hsa-mir-4423-5p ; hsa-mir-6501-5p ; hsa-mir-143-5p ; hsa-mir-4430 ; hsa-mir-3652 ; hsa-mir-3622b-5p ; hsa-mir-122-5p ; hsa-mir-504-3p ; hsa-mir-3135b ; hsa-mir-3194-3p ; hsa-mir-6499-3p ; hsa-mir-367-5p ; hsa-mir-1267 ; hsa-mir-103b ; hsa-mir-5693 ; hsa-mir-7705 ; hsa-mir-617 ; hsa-mir-3605-3p ; hsa-mir-8087 ; hsa-mir-6854-5p ; hsa-mir-6885-3p ; hsa-mir-147a ; hsa-mir-5010-3p ; hsa-mir-6818-5p

Nearest miRNA

hsa-mir-1265/Upstream/2122414; hsa-mir-107/Downstream/584363;

Nearest TSS

ENST00000439456/Upstream/151368; ENST00000377238/Downstream/75713;

Nearest CpG islands

None/Target, chr10-CpG: 68/Upstream/149590, chr10-CpG: 149/Downstream/1205592

Upstream sequence

TCGAACTAGAAAAAATAGAATAAACATACTAAGAGAAAACAATTATAATAATAAGTATAATAATAAACATAAGAGGAGATTAAATATGTGAAAATATGTT

Downstream sequence

AAAATCAGACCTTACCACTTAAAATCAGCTGAAGATTCCAGGTACAAATGAGCGATGTTACAGCATACTGAAAAAACATTGCAGATACTATGTCATGTCC

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).