PBX3 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005076
Fusion event
HBV-PBX3 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
1434
Orient
+
Integrated sequence
CAACTCTGTTGTCCTCTCTCGGAAATACACCTCCTTCCCATGGCTGCTCGGGTGTGCTGCCAACTGGATCCTGCGCGGGACGTCCTTTGTCTACGTCCCG| |TCGGCGCTGAATCCCGCGGACGACCCGTCTCGGGGCCGTTTGGGGCTCTACCGTCCCCTTCTTCATCTGCCGTTCCGGCCGACCACGGGGCGCACCTCTC
Host Sequence
Chromosome
chr9
Cytoband
q33.3
Reference genome
GRCh37/hg19
Start
128550191/125787912 (Hg38)
End
128550191/125787912 (Hg38)
Orient
+
Location type
Intron
Target gene
PBX3
miRNAs that regulate target gene
hsa-mir-495-3p ; hsa-mir-615-3p ; hsa-mir-93-5p ; hsa-mir-26b-5p ; hsa-mir-760 ; hsa-mir-181b-5p ; hsa-mir-181a-5p ; hsa-mir-320a ; hsa-let-7c-5p ; hsa-mir-98-5p ; hsa-mir-33a-3p ; hsa-mir-144-3p ; hsa-mir-497-5p
Nearest miRNA
hsa-let-7a-1/Upstream/1094114; hsa-mir-12126/Downstream/1902775;
Nearest TSS
ENST00000422679/Upstream/38981; ENST00000491160/Downstream/55801;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/39521, chr9-CpG: 47/Downstream/101799
Upstream sequence
cccgtctctactaaaaatacaaaaaattagctgggtgcggtggtgtgcgcctgtaatcccagctactcaggaggctgaggcaggagaattgtgtgaacct
Downstream sequence
tggagctaaaggtcattggtgatttatttattttttaaggaggtcagagaactgtaaggctaggttgttggttgaatatcttatatgctccctgaagcca
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).
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