USP40 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10020316
Fusion event
HBV-USP40 integration
Validated
No
Detection method
VirusScan
Data source
Curated
Sample type
Tumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Good
Reported year
2016
PubMed ID
27339696
Virus Sequence
Virus name
HBV
Reference genome
NC_003977.1
Start
1322
End
2418
Orient
+
Integrated sequence
TATCGGAACCGACAACTCAGTTGTCCTCTCTCGGAAATACACCTCCTTTCCATGGCTGCTAGGCTGTGCTGCCAACTGGATCCTGCGCGGGACGTCCTTTGTCTACGTCCCGTCGGCGCTGAATCCCGCGGACGACCCGTCTCGGGGCCGTTTGGGCCTCTACCGTCCCCTTCTTCATCTGCCGTTCCGGCCGACCACGGGGCGCACCTCTCTTTACGCGGTCTCCCCGTCTGTGCCTTCTCATCTGCCGGACCG
Host Sequence
Chromosome
chr2
Cytoband
q37.1
Reference genome
GRCh37/hg19
Start
234401117/233492471 (Hg38)
End
234402165/233493519 (Hg38)
Orient
+
Location type
Intronic
Target gene
USP40
miRNAs that regulate target gene
hsa-mir-484
Nearest miRNA
hsa-mir-10b/Upstream/941898; hsa-mir-149/Downstream/4017412;
Nearest TSS
ENST00000437798/Upstream/1132; ENST00000485022/Downstream/18239;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/15387, chr2-CpG: 46/Downstream/72896
Upstream sequence
ttctgcctcagcctcctgagtagctgggattacaggcacgtgccaccgcgactggctaatttttgtatttttagtagagatggggtttcaccatgttggt
Downstream sequence
TGGTACCACCAGATGGGCACCTTCAGGAAACCCTGAAGAATGGAGCATGTTTAACTGCTGTGATTACAAAGATTAAGTGAAACTCTACTTTTACTTCCAT
Target sequence
ATTAAACATGCTTTTACAATCTATATCCAATTCTATATGTAACTAGAATTCTATCACCAAGGCATTTTTAGCATTAGTTAACATGAACTACTGTAACCCAACTAAAAAGTAACTTTATGCCAATTTTATAGCTCATTCAACATTACTCTCTCTATATAATCCTAACTTCAAAGAATAAGGAGATAAGAATTTGACTCATTTATATTAATTTTATTACTGAGGCTGAAAAGATTAAAAAGAAATATAAGTAATATA
Reference
Cao, S., et al.Divergent viral presentation among human tumors and adjacent normal tissues. Sci Rep,2016, 6: 28294.
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