PDSS2 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10004740
Fusion event
HBV-PDSS2 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
1903
Orient
+
Integrated sequence
CACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATG| |GACATTGACCCGTATAAAGAATTTGGAGCTTCTGTGGAGTTACTCTCTTTTTTGCCTTCTGACTTCTTTCCTTCTATTCGAGATCTCCTCGACACCGCCT
Host Sequence
Chromosome
chr6
Cytoband
q21
Reference genome
GRCh37/hg19
Start
107646521/107325317 (Hg38)
End
107646521/107325317 (Hg38)
Orient
+
Location type
Intron
Fragile sites / regions
FRA6F
Target gene
PDSS2
miRNAs that regulate target gene
hsa-mir-26b-5p ; hsa-mir-142-3p
Nearest miRNA
hsa-mir-10398/Upstream/541097; hsa-mir-1202/Downstream/11743730;
Nearest TSS
ENST00000381078/Upstream/113158; ENST00000618129/Downstream/134246;
Nearest CpG islands
None/Target, chr6-CpG: 120/Upstream/209211, chr6-CpG: 19/Downstream/133714
Nearest cancer related gene
PDSS2(TSG, No orient, 0)
Upstream sequence
CCCTGCACTAGCGGCCCCGGCCGGGAGGGCACGAGGACTGCGCAGCCGGACCCCCGCAGGTCCCCAAGCCAGGGGTCCCGTCCATCCGCCCGCCCCCGCG
Downstream sequence
ttacaatggggttatgtcctgataaatccatttaaaagtcagaaaattttaagttgcatcatggtaagccagggactacctgCATATCATTAATTTAACC
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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