PCOLCE2 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10006249
Fusion event
HBV-PCOLCE2 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
1346
Orient
+
Integrated sequence
TTGTGGCTCCTCTGCCGATCCATACTGCGGAACTCCTAGCAGCTTGTTTTGCTCGCAGCCGGTCTGGAGCAAAACTTATCGGGACTGACAACTCTGTTGT| |CCTCTCTCGGAAATACACCTCCTTCCCATGGCTGCTCGGGTGTGCTGCCAACTGGATCCTGCGCGGGACGTCCTTTGTCTACGTCCCGTCGGCGCTGAAT
Host Sequence
Chromosome
chr3
Cytoband
q23
Reference genome
GRCh37/hg19
Start
142564753/142845911 (Hg38)
End
142564753/142845911 (Hg38)
Orient
+
Location type
Intron
Target gene
PCOLCE2
miRNAs that regulate target gene
hsa-mir-215-5p ; hsa-mir-192-5p ; hsa-mir-26b-5p ; hsa-mir-182-5p
Nearest miRNA
hsa-let-7g/Upstream/8408005; hsa-mir-1224/Downstream/8719965;
Nearest TSS
ENST00000440867/Upstream/16056; ENST00000479792/Downstream/2411;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/120775, chr3-CpG: 103/Downstream/42442
Upstream sequence
CTCTCTCTGGTTGACTGACTAAATCAATGaatgattctaacaagtaaatattgtaatcctcattttttagatgcaaggactaaggttcagggattgtttc
Downstream sequence
ttgcagtgggccgagatagcaccactgcactccagcctggtcaacaagagtgaaactcagtctcaaaaaaaatactatgacactgccttctggcttccag
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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