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VISDB
Viral Integration Site DataBase
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TVIS10006143
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10006143
Fusion event
HBV-PCDH7 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
1497
Orient
+
Integrated sequence
CTGGATCCTGCGCGGGACGTCCTTTGTCTACGTCCCGTCGGCGCTGAATCCCGCGGACGACCCGTCTCGGGGCCGTTTGGGGCTCTACCGTCCCCTTCTT| |CATCTGCCGTTCCGGCCGACCACGGGGCGCACCTCTCTTTACGCGGTCTCCCCGTCTGTGCCTTCTCATCTGCCGGACCGTGTGCACTTCGCTTCACCTC
Host Sequence
Chromosome
chr4
Cytoband
p15.1
Reference genome
GRCh37/hg19
Start
30913858/30912236 (Hg38)
End
30913858/30912236 (Hg38)
Orient
-
Location type
Intron
Fragile sites / regions
FRA4D
Target gene
PCDH7
miRNAs that regulate target gene
hsa-mir-1-3p
;
hsa-mir-192-5p
;
hsa-mir-25-3p
;
hsa-mir-4789-5p
;
hsa-mir-3941
;
hsa-mir-4261
;
hsa-mir-3688-3p
;
hsa-mir-4789-3p
;
hsa-mir-8076
;
hsa-mir-603
;
hsa-mir-362-3p
;
hsa-mir-8485
;
hsa-mir-329-3p
;
hsa-mir-6720-5p
;
hsa-mir-1277-5p
;
hsa-mir-6512-3p
;
hsa-mir-190a-3p
;
hsa-mir-338-3p
;
hsa-mir-4530
;
hsa-mir-5011-5p
Nearest miRNA
hsa-mir-12113/Upstream/2092568; hsa-mir-1243/Downstream/5514130;
Nearest TSS
ENST00000502981/Upstream/118266;
ENST00000610830/Downstream/7917;
Nearest CpG islands
None/Target,
chr4-CpG: 46/Upstream/189016
,
chr4-CpG: 100/Downstream/5331773
Junction sequence
TC
* Color:
Human Sequence
/
Virus Sequence
/
Overlapped sequence
/
Unknown sequence
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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