Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10015006
Fusion event
HBV-SENP5 integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Good
Reported year
2012
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Region type
HBVgp3 X protein;HBVgp4 precore/core protein
Start
1826
End
1930
Orient
+
Integrated sequence
TCACCTCTGCCTAATCATCTCTTGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATCGACCCTTATAAAGAATTTGG
Host Sequence
Chromosome
chr3
Cytoband
q29
Reference genome
End
196625755/196898884 (Hg38)
Orient
+
Location type
Intronic
Target gene
miRNAs that regulate target gene
hsa-let-7d-5p ; hsa-mir-6516-5p ; hsa-mir-455-3p ; hsa-mir-4763-3p ; hsa-mir-1207-5p ; hsa-mir-650 ; hsa-mir-3612 ; hsa-mir-6499-3p ; hsa-mir-6722-3p ; hsa-mir-1909-3p ; hsa-mir-4537 ; hsa-mir-1827 ; hsa-mir-940 ; hsa-mir-6893-5p ; hsa-mir-6808-5p ; hsa-mir-193b-3p ; hsa-mir-193a-3p ; hsa-mir-1273h-5p ; hsa-mir-149-3p ; hsa-mir-30b-3p ; hsa-mir-3192-5p ; hsa-mir-3689a-3p ; hsa-mir-3689b-3p ; hsa-mir-3689c ; hsa-mir-4728-5p ; hsa-mir-490-3p ; hsa-mir-6779-5p ; hsa-mir-6780a-5p ; hsa-mir-6785-5p ; hsa-mir-6799-5p ; hsa-mir-6883-5p ; hsa-mir-7106-5p ; hsa-mir-7851-3p
Nearest miRNA
hsa-let-7g/Upstream/1016391; hsa-mir-4797/Downstream/394994;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/30171, chr3-CpG: 130/Downstream/42940
Upstream sequence
gaaaggttcaactctgtgagttgaatgcacacaccacaaagaagtttctgagaatgcttctgtctagtttttatgtgaagatattccggtttccaacgat
Downstream sequence
catttgatgatgattccattcgtctctactaaaaatacaaaaaaattagccgggcgtggtggcaggcgcctgtagtcacagctatttgggaggatgaggc
Target sequence
ccattggaagatgattccattcgagaccattcgatgattgcattcaattcattcgatgacgattccattcaattccgttcaatgattccattagattc
Reference
Sung, W. K., et al. Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat Genet,2012, 44(7): 765-769.