Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005087
Fusion event
HBV-PRPF38A integration
Validated
No
Detection method
PCR and Ultra-deep sequencing
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Start
2431
Orient
-
Integrated sequence
GGAAACTACTGTTGTTAGACGACGAGGCAGGTCCCCTAGAAGAAGAACTCCCTCGCCTCGCAGACGAAGGTCTCAATCGCCGCGTCGCAGAAGATCTCAA| |TCTCGGGAATCTCAATGTTAGTATCCCTTGGACTCATAAGGTGGGAAACTTTACTGGGCTTTATTCTTCTACTGTACCTGTCTTTAATCCTGAGTGGCAA
Host Sequence
Chromosome
chr1
Cytoband
p32.3
Reference genome
Start
End
52871280/52405608 (Hg38)
Orient
-
Location type
Promoter PRPF38A,intron
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-192-5p ; hsa-mir-215-5p ; hsa-mir-31-3p ; hsa-mir-145-3p ; hsa-mir-6893-3p ; hsa-mir-634 ; hsa-mir-370-3p ; hsa-mir-4279 ; hsa-mir-6778-3p ; hsa-mir-1976 ; hsa-mir-3653-5p ; hsa-mir-325 ; hsa-mir-6747-3p ; hsa-mir-6727-3p ; hsa-mir-4722-3p ; hsa-mir-122-3p ; hsa-mir-4258 ; hsa-mir-5089-5p ; hsa-mir-7151-3p ; hsa-mir-5095 ; hsa-mir-6506-5p ; hsa-mir-619-5p ; hsa-mir-150-5p ; hsa-mir-6814-5p ; hsa-mir-6504-3p ; hsa-mir-4438 ; hsa-mir-582-3p ; hsa-mir-335-3p ; hsa-mir-452-3p ; hsa-mir-216b-5p ; hsa-mir-216a-5p ; hsa-mir-106a-3p ; hsa-mir-122-5p ; hsa-mir-1267 ; hsa-mir-1304-3p ; hsa-mir-1307-3p ; hsa-mir-130a-3p ; hsa-mir-130b-3p ; hsa-mir-301a-3p ; hsa-mir-301b-3p ; hsa-mir-3135b ; hsa-mir-3652 ; hsa-mir-3664-5p ; hsa-mir-3666 ; hsa-mir-367-5p ; hsa-mir-4294 ; hsa-mir-4295 ; hsa-mir-4423-5p ; hsa-mir-4430 ; hsa-mir-454-3p ; hsa-mir-4634 ; hsa-mir-4638-5p ; hsa-mir-4639-3p ; hsa-mir-504-3p ; hsa-mir-6501-5p ; hsa-mir-652-3p ; hsa-mir-6794-3p ; hsa-mir-744-3p
Nearest miRNA
hsa-mir-12136/Upstream/569206; hsa-mir-101-1/Downstream/1648471;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/975, chr1-CpG: 115/Downstream/146978
Upstream sequence
tatccattctcaatgtatattagctgttgtCGTTACTGTTATTAATACACATTCGTTCTCCTAATATTACACTGTTGATGTATATTTAGGAGAACCAAAG
Downstream sequence
CTTGAACTAACTCCACTCCAACTAGGAAGAGCTTAGCCCTAATATGTTACTGTATTGTTTTTGTTTTTTAGCTGAACTTGTAGTCGATAAAGCCATGGAG
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).