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VISDB
Viral Integration Site DataBase
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TVIS10006103
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10006103
Fusion event
HBV-GRIK3 integration
Validated
No
Detection method
PCR and Ultra-deep sequencing
Data source
Curated
Sample type
Nontumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
29861854
Virus Sequence
Virus name
HBV
Reference genome
AP011098
Start
3015
Orient
-
Integrated sequence
ATTCTTTCCCGATCACCAGTTGGACCCTGCGTTCGGAGCCAACTCAAACAATCCAGATTGGGACTTCAACCCCAACAAGGATCACTGGCCAGAGGCAAAT| |CAGGTAGGAGCGGGAGCATTCGGGCCAGGGTTCACCCCACCACACGGCGGTCTTTTGGGGTGGAGCCCTCAGGCTCAGGGCATATTGACAACAGTGCCAG
Host Sequence
Chromosome
chr1
Cytoband
p34.3
Reference genome
GRCh37/hg19
Start
37368357/36902756 (Hg38)
End
37368357/36902756 (Hg38)
Orient
-
Location type
Intron
Target gene
GRIK3
miRNAs that regulate target gene
hsa-mir-1278
;
hsa-mir-1277-5p
;
hsa-mir-190a-3p
;
hsa-mir-1185-2-3p
;
hsa-mir-1185-1-3p
;
hsa-let-7f-2-3p
;
hsa-mir-5011-5p
;
hsa-mir-101-3p
;
hsa-mir-448
;
hsa-mir-144-3p
;
hsa-mir-8064
;
hsa-mir-338-3p
;
hsa-mir-1226-3p
;
hsa-mir-634
;
hsa-mir-362-3p
;
hsa-mir-8485
;
hsa-mir-329-3p
;
hsa-mir-1228-3p
;
hsa-mir-586
;
hsa-mir-4659b-3p
;
hsa-mir-4659a-3p
;
hsa-mir-6875-3p
;
hsa-mir-6749-3p
;
hsa-mir-6792-3p
;
hsa-mir-4691-5p
;
hsa-mir-4778-3p
;
hsa-mir-6773-3p
;
hsa-mir-5699-3p
;
hsa-mir-4421
;
hsa-mir-6748-3p
;
hsa-mir-5193
;
hsa-mir-1255b-2-3p
;
hsa-mir-493-5p
;
hsa-mir-4666a-5p
;
hsa-mir-3177-5p
;
hsa-mir-6757-3p
;
hsa-mir-1238-3p
;
hsa-mir-670-3p
;
hsa-mir-6071
;
hsa-mir-6881-3p
;
hsa-mir-6780a-3p
;
hsa-mir-7111-3p
;
hsa-mir-5581-3p
;
hsa-mir-365b-5p
;
hsa-mir-365a-5p
;
hsa-mir-3140-3p
;
hsa-mir-5589-5p
;
hsa-mir-4731-5p
;
hsa-mir-617
;
hsa-mir-3692-5p
;
hsa-mir-93-3p
;
hsa-mir-6728-3p
;
hsa-mir-4686
Nearest miRNA
hsa-mir-12136/Upstream/2233062; hsa-mir-101-1/Downstream/258807;
Nearest TSS
ENST00000473358/Upstream/43620;
ENST00000642067/Downstream/131369;
Nearest CpG islands
None/Target,
chr1-CpG: 111/Upstream/438226
,
chr1-CpG: 233/Downstream/130020
Upstream sequence
taataccaaaggcacgacccatgaaagaaataattgataagctggactacattaaaattaaaattttctgctctgcaaaagacacagtaaagagaatgaa
Downstream sequence
aaatgaagccactgactgggacatatcttatgatggactacttttttttttgaaacagggtcttgctctgttgcccaggctggtgtgcagtggtacaacc
Reference
Tu, T., et al. Hepatitis B Virus DNA Integration Occurs Early in the Viral Life Cycle in an In Vitro Infection Model via Sodium Taurocholate Cotransporting Polypeptide-Dependent Uptake of Enveloped Virus Particles. J Virol ,2018,92(11).
Sample Information
×
Sample name
RK213_NT
Sample type
Nontumor
Age
62
Gender
Male
CpG Island Information
×
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