PDSS2 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10016112
Fusion event
HBV-PDSS2 integration
Validated
No
Detection method
WGS
Data source
Curated
Sample type
Nontumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2012
PubMed ID
22267523
Virus Sequence
Virus name
HBV
Reference genome
AY033073.1
Start
570
Orient
+
Integrated sequence
GCATATAGACCACCAAATGCCCCTATCTTATCAACACTTCCGGAAACTACTGTTGTTAGACGACGAGGCAGGTCCCCTAGAAGAAGAACTCCCTCGCCTC| |GCAGACGAAGGTCTCAATCACCGCGTCGCAGAAGATCTCAATCTCGGGAATCTCAATGTTAGTATTCCTTGGACTCATAAGGTGGGAAACTTTACGGGGC
Host Sequence
Chromosome
chr6
Cytoband
q21
Reference genome
GRCh37/hg19
Start
107519615/107198411 (Hg38)
End
107519615/107198411 (Hg38)
Orient
-
Location type
Intronic
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/414191; hsa-mir-1202/Downstream/11870636;
Nearest TSS
ENST00000381078/Upstream/83142; ENST00000618129/Downstream/13748;
Nearest CpG islands
None/Target, chr6-CpG: 120/Upstream/82305, chr6-CpG: 19/Downstream/260620
Nearby gene
BEND3(-83979) ; SOBP(+291701) ;
Nearest cancer related gene
PDSS2(TSG, No orient, 0)
Upstream sequence
GAAGGCATAGCTCTGTAATATTATGATCTACTTTCTCAAAGCAGATTCTCATTGTCACCTCTGTCCCAAATTCCTAGTAATTGTGTTCCCAATGGACTTG
Downstream sequence
AATATCCTTTTCATTTTGTCACAATAAATGTTCTAGCTCTATGAAATCATTTTACTCTTGATCACTTTAGCTTGTACATAAAAGTATCATTTATTTTAGG
Reference
Jiang, S., et al. Re-evaluation of the carcinogenic significance of hepatitis B virus integration in hepatocarcinogenesis. PLoS One ,2012, 7(9): e40363.
Curate