ARHGEF3 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005731
Fusion event
HBV-ARHGEF3 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
298
Orient
-
Integrated sequence
ACAGGCGGGGTTTTTCTTGTTGACAAGAATCCTCACAATACCACAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCACCCACGTGT| |CCTGGCCAAAATTCGCAGTCCCCAACCTCCAATCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGGCTATCGCTGGATGTGTCTGCGGCGTTTTATCA
Host Sequence
Chromosome
chr3
Cytoband
p14.3
Reference genome
GRCh37/hg19
Start
57027682/56993654 (Hg38)
End
57027682/56993654 (Hg38)
Orient
-
Location type
Intron
Target gene
ARHGEF3
miRNAs that regulate target gene
hsa-mir-138-5p ; hsa-mir-373-3p ; hsa-mir-335-5p ; hsa-mir-769-5p ; hsa-mir-377-5p ; hsa-mir-485-5p ; hsa-mir-3680-3p ; hsa-mir-557 ; hsa-mir-507 ; hsa-mir-450b-5p ; hsa-mir-889-3p ; hsa-mir-4793-5p ; hsa-mir-5196-3p
Nearest miRNA
hsa-let-7g/Upstream/1141060; hsa-mir-12124/Downstream/3624151;
Nearest TSS
ENST00000440867/Upstream/16279; ENST00000334325/Downstream/66787;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/191472, chr3-CpG: 112/Downstream/85067
Upstream sequence
TCTGAAATCCAACCACCATGTTTCACAAATCCATATCTACTTATGTTCTTCCTAGGTTTTTAGGTGTATTAGAAATGACATTTTTAGTTTTCTTATTATT
Downstream sequence
atgagccaccgtgcccagcctaactttggatacattgcttaaccttcctgaggttcagtttcctcatgtggaaggagaaatattcatatctcattaaaag
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).
Curate