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VISDB
Viral Integration Site DataBase
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TVIS10020442
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10020442
Fusion event
HBV-KDM4B 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
1131
End
2231
Orient
+
Integrated sequence
TATCTAAACCTTTACCCCGTTGCCCGGCAACGGTCAGGTCTCTGCCAAGTGTTTGCTGACGCAACCCCCACGGGTTGGGGCTTGGCCATAGGCCATCGGCGCATGCGTGGAACCTTTGTGGCTCCTCTGCCGATCCATACTGCGGAACTCCTAGCAGCTTGTTTTGCTCGCAGCCGGTCTGGAGCGAAACTTATCGGAACCGACAACTCAGTTGTCCTCTCTCGGAAATACACCTCCTTTCCATGGCTGCTAGGC
Host Sequence
Chromosome
chr19
Cytoband
p13.3
Reference genome
GRCh37/hg19
Start
5025684/5025673 (Hg38)
End
5026734/5026723 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA19B
Target gene
KDM4B
miRNAs that regulate target gene
hsa-mir-335-5p
;
hsa-mir-505-5p
;
hsa-mir-106b-3p
;
hsa-mir-615-3p
;
hsa-mir-491-5p
Nearest miRNA
hsa-mir-1227/Upstream/92933; hsa-let-7e/Downstream/1362915;
Nearest TSS
ENST00000633603/Upstream/9348;
ENST00000624683/Downstream/20275;
Nearest CpG islands
None/Target,
chr19-CpG: 112/Upstream/39279
,
chr19-CpG: 48/Downstream/5727
Upstream sequence
agtgctgggattacaggcgtgagccaccgcacctggcTGGGAGTTAGAGGTTTCTAATGCATTGCAGGCAGATAGTGAATACCAGACACGGGGCAGCTGT
Downstream sequence
GGCAGTTTTGTGGTTTTGAAATTGAGTTTGTATCAAGAGCTTTACTGCTTTTGTAAAAACTTACTGGCATGGTACCAAGAGAAATTCAAACAATAGTTGG
Target sequence
ggcctctggggccttagctcttccctggcttcgctgggtccttccctttgcctagactttcctcctgccctggaccgcccAGAACTTGCACCCCTGCGTGTTTGACAATCACTTCCAGACGCAGCCCCGCTGCCACCCAGACCTCTCTGGTCCCAAACCAACTTCATTTGTCTTTTTCCTTTTTTTTAAATTTATTTAtttattttattttacttattaattttttttgagacagagtttcactcgttgcccagg
Reference
Cao, S., et al.Divergent viral presentation among human tumors and adjacent normal tissues. Sci Rep,2016, 6: 28294.
Sample Information
×
Sample name
TCGA-DD-A1EH-11A-11R-A131-07
Sample type
Tumor
Gender
Female
CpG Island Information
×
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