Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10015226
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
HBVgp1 Polymerase;HBVgp2 pre-S2/S;HBVgp2
Start
417
End
543
Orient
+
Integrated sequence
CTGCTATGCCTCATCTTCTTGTTGGTTCTTCTGGACTATCAAGGTATGTTGCCCGTTTGTCCTCTAATTCCAGGATCCTCAACAACCAGCACGGGACCATGCCGGACCTGCATGACTACTGCTCAAG
Host Sequence
Chromosome
chr3
Cytoband
q29
Reference genome
End
196625744/196898873 (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/1016388; hsa-mir-4797/Downstream/395005;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/30168, chr3-CpG: 130/Downstream/42951
Upstream sequence
ggtctgaaaagaaatattaatgcaccaagttgttatccctaagtgctatgattatgagtgcttttatttttcttcacatctttttttaacttccaaattt
Downstream sequence
ccattagattccatttgatgatgattccattcgtctctactaaaaatacaaaaaaattagccgggcgtggtggcaggcgcctgtagtcacagctatttgg
Target sequence
attccattggaagatgattccattcgagaccattcgatgattgcattcaattcattcgatgacgattccattcaattccgttcaatgatt
Reference
Sung, W. K., et al. Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat Genet,2012, 44(7): 765-769.