PRPF6 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10006245
Fusion event
HBV-PRPF6 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
1832
Orient
-
Integrated sequence
GGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAACTTTTTCACCTCT| |GCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCGTATAAAGAATTTGGAGC
Host Sequence
Chromosome
chr20
Cytoband
q13.33
Reference genome
GRCh37/hg19
Start
62650972/64019619 (Hg38)
End
62650972/64019619 (Hg38)
Orient
+
Location type
Intron
Target gene
PRPF6
miRNAs that regulate target gene
hsa-mir-1226-3p ; hsa-mir-149-5p ; hsa-mir-23b-3p ; hsa-mir-7977 ; hsa-mir-675-5p ; hsa-mir-4466 ; hsa-mir-24-3p ; hsa-mir-4284 ; hsa-mir-4746-3p ; hsa-mir-4798-3p ; hsa-mir-6750-3p ; hsa-mir-383-3p
Nearest miRNA
hsa-mir-1-1/Upstream/76893; hsa-mir-6813/Downstream/57336;
Nearest TSS
ENST00000382410/Upstream/38484; ENST00000444463/Downstream/14725;
Nearest CpG islands
None/Target, chr20-CpG: 39/Upstream/38185, chr20-CpG: 28/Downstream/9989
Upstream sequence
CCTCCCGGACACCAGGGCCCTGGGCACAGCATCACTTGATCCTGTGGGTGTTCAGGCCACTCTCGGGTTGCTTGTGAAGGTCCAAGGAGGCGATGGAGAA
Downstream sequence
TCTGAAATGCTTTGTCACCAACCCTCAGGACTTGGATCAGAAATCACAGAGAGGGGCATAGACCAGAGTGCTCTATCCAGGGCCTGACCCTCACCGGCAT
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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