VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10005743

Fusion event

HBV-SH3PXD2B 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

1961

Orient

-

Integrated sequence

GTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCGTATAAAGAATTTGGAGCTTCTGTGGAGTTACTCTCTTTTTTGCCTT| |CTGACTTCTTTCCTTCTATTCGAGATCTCCTCGACACCGCCTCTGCTCTGTATCGGGAGGCCTTAGAGTCTCCGGAACATTGTTCACCTCACCATACAGC

Host Sequence

Chromosome

chr5

Cytoband

q35.1

Reference genome

GRCh37/hg19

Start

171754120/172327116 (Hg38)

End

171754120/172327116 (Hg38)

Orient

+

Location type

Intronic

Fragile sites / regions

FRA5G

Target gene

SH3PXD2B

miRNAs that regulate target gene

hsa-mir-1-3p ; hsa-mir-335-5p ; hsa-mir-6749-3p ; hsa-mir-6792-3p ; hsa-mir-4691-5p ; hsa-mir-4673 ; hsa-mir-4645-5p ; hsa-mir-6856-5p ; hsa-mir-1972 ; hsa-mir-6758-5p

Nearest miRNA

hsa-mir-10397/Upstream/940356; hsa-mir-10523/Downstream/335049;

Nearest TSS

ENST00000502646/Upstream/43045; ENST00000520919/Downstream/7119;

Nearest CpG islands

None/Target, chr5-CpG: 87/Upstream/30009, chr5-CpG: 74/Downstream/127015

Upstream sequence

GCGGGGCGTCGGGCTCCGGGCACCACGAATGCCGGACGTGAAGGGGAGGACGGAGGCGCGTAGACGCGGCTGGGGACGAACCCGAGGACGCATTGCTCCC

Downstream sequence

cccaaagtgttgggattacaggcatgaaccaccgcgcctggccTGAAGATTGTTAATCTGAAGATTCTACTCTTCATAGAAACaataaaaattattatgc

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).