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VISDB
Viral Integration Site DataBase
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TVIS10012202
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10012202
Fusion event
HBV-RTN3 integration
Validated
No
Detection method
NGS
Data source
Curated
Sample type
Nontumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
30271481
Virus Sequence
Virus name
HBV
Reference genome
NC_003977
Region type
X protein|
Start
1787
Orient
-
Integrated sequence
ACGACCGACCTTGAGGCATACTTCAAAGACTGTTTGTTTAAAGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTA| |GGCATAAATTGGTCTGCGCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCTTGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTT
Host Sequence
Chromosome
chr11
Cytoband
q13.1
Reference genome
GRCh37/hg19
Start
63524960/63757488 (Hg38)
End
63524960/63757488 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA11H
Target gene
RTN3
miRNAs that regulate target gene
hsa-mir-155-5p
;
hsa-mir-760
;
hsa-mir-484
;
hsa-mir-378a-3p
;
hsa-mir-106a-5p
;
hsa-mir-17-5p
;
hsa-mir-205-5p
;
hsa-mir-6515-5p
;
hsa-mir-4443
;
hsa-mir-4725-3p
;
hsa-mir-6780b-5p
;
hsa-mir-4271
;
hsa-mir-6797-5p
;
hsa-mir-1249-5p
;
hsa-mir-6783-5p
;
hsa-mir-671-5p
;
hsa-mir-4511
;
hsa-mir-33b-5p
;
hsa-mir-33a-5p
;
hsa-mir-4684-3p
;
hsa-mir-4694-5p
;
hsa-mir-367-5p
;
hsa-mir-802
;
hsa-mir-522-3p
;
hsa-mir-224-3p
;
hsa-mir-4694-3p
;
hsa-mir-335-3p
;
hsa-mir-4775
;
hsa-mir-5692a
;
hsa-mir-590-3p
;
hsa-mir-6793-3p
Nearest miRNA
hsa-mir-129-2/Upstream/964717; hsa-let-7a-2/Downstream/584361;
Nearest TSS
ENST00000527297/Upstream/75915;
ENST00000535820/Downstream/8464;
Nearest CpG islands
None/Target,
chr11-CpG: 30/Upstream/75574
,
chr11-CpG: 188/Downstream/4928
Upstream sequence
cacccaggttgaagtgcagtggcacaagctgaaagctcactgcagccttgacctctgacctcccttgctccaagtgatcctcccaccccagcctcctgag
Downstream sequence
tagctgacactacaggcatgtgccatgccctggcaaattttttattttttatagagatgggggtctcactatgttgcccaggccaggctttaacttctgg
Reference
Yang, L., et al. Molecular Characterization of HBV DNA Integration in Patients with Hepatitis and Hepatocellular Carcinoma. J Cancer ,2018,9(18): 3225-3235.
Sample Information
×
Sample name
791P
Sample type
Nontumor
Gender
Female
CpG Island Information
×
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