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VISDB
Viral Integration Site DataBase
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TVIS10005719
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005719
Fusion event
HBV-ABCC6 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
2343
Orient
-
Integrated sequence
TTCTTGAGTATTTGGTGTCTTTTGGAGTGTGGATTCGCACTCCTCCCGCTTACAGACCACCAAATGCCCCTATCTTATCAACACTTCCGGAAACTACTGT| |TGTTAGACGACGAGGCAGGTCCCCTAGAAGAAGAACTCCCTCGCCTCGCAGACGAAGGTCTCAATCGCCGCGTCGCAGAAGATCTCAATCTCGGGAATCT
Host Sequence
Chromosome
chr16
Cytoband
p13.11
Reference genome
GRCh37/hg19
Start
16267145/16173288 (Hg38)
End
16267145/16173288 (Hg38)
Orient
+
Location type
Exon
Fragile sites / regions
FRA16A
Target gene
ABCC6
miRNAs that regulate target gene
hsa-mir-4739
;
hsa-mir-4665-5p
;
hsa-mir-1275
;
hsa-mir-3191-5p
;
hsa-mir-4447
;
hsa-mir-4472
;
hsa-mir-6769b-5p
;
hsa-mir-6769a-5p
;
hsa-mir-92a-2-5p
;
hsa-mir-654-5p
;
hsa-mir-541-3p
;
hsa-mir-5010-5p
;
hsa-mir-4525
;
hsa-mir-7111-5p
;
hsa-mir-6870-5p
;
hsa-mir-5698
;
hsa-mir-4723-5p
;
hsa-mir-6825-5p
;
hsa-mir-625-5p
;
hsa-mir-7106-5p
;
hsa-mir-765
;
hsa-mir-6081
;
hsa-mir-7978
;
hsa-mir-4456
;
hsa-mir-548q
;
hsa-mir-4299
;
hsa-mir-6824-3p
;
hsa-mir-6764-3p
;
hsa-mir-330-5p
;
hsa-mir-326
;
hsa-mir-518c-5p
;
hsa-mir-761
;
hsa-mir-3619-5p
;
hsa-mir-214-3p
;
hsa-mir-6838-5p
;
hsa-mir-6165
;
hsa-mir-497-5p
;
hsa-mir-424-5p
;
hsa-mir-195-5p
;
hsa-mir-16-5p
;
hsa-mir-15b-5p
;
hsa-mir-15a-5p
;
hsa-mir-4531
;
hsa-mir-5703
;
hsa-mir-4516
;
hsa-mir-4434
;
hsa-mir-4773
;
hsa-mir-8485
;
hsa-mir-3941
;
hsa-mir-603
;
hsa-mir-362-3p
;
hsa-mir-329-3p
Nearest miRNA
hsa-mir-1225/Upstream/529916; hsa-mir-11401/Downstream/126871;
Nearest TSS
ENST00000527434/Upstream/7345;
ENST00000574883/Downstream/4233;
Nearest CpG islands
None/Target,
chr16-CpG: 29/Upstream/223218
,
chr16-CpG: 30/Downstream/50091
Upstream sequence
gagtATCACTGCCAAGTGCTACATTTGGTGGGAAGACTTGGGCCCCTGGAGGTGGCAGCAGTGGGTGGGGAGGGGTGGGTGAAGCTGGTGGTTACCCTGC
Downstream sequence
CGTATTGGATGCTGTCCTTTCCTGCTGGCCATCCTGCCCTGTCAGGGTCATCCAGAGGAACCTCTGTCTGGGCTTCTGAAGTGGTACGGTCCTTCTCAGG
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
RK130_NT
Sample type
Nontumor
Age
42
Gender
Male
CpG Island Information
×
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