COL23A1 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10000142
Fusion event
HBV-COL23A1 integration
Validated
Yes
Detection method
invPCR
Data source
Curated
Sample type
Cell line
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Perfect
Reported year
2018
PubMed ID
29437961
Virus Sequence
Virus name
HBV
Reference genome
U95551.1
End
1823
Integrated sequence
TTTAAAGACTGGGAGGAGTTGGGGGAGGAGATTAGATTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGCGCACCAGCACCATGCAACT| |TTTTCACCTCTGCCTAATCATCTCTTGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATCGACCCTTATAAA
Host Sequence
Chromosome
chr5
Cytoband
q35.3
Reference genome
GRCh38.p7
Start
178313453 (Hg38)
End
178313453 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA5G
Target gene
COL23A1
miRNAs that regulate target gene
hsa-mir-676-5p ; hsa-mir-4474-5p ; hsa-mir-8086 ; hsa-mir-4680-5p ; hsa-mir-484 ; hsa-mir-3155b ; hsa-mir-3155a ; hsa-mir-4714-3p ; hsa-mir-7151-3p ; hsa-mir-767-5p ; hsa-mir-5095 ; hsa-mir-4735-5p ; hsa-mir-1224-3p ; hsa-mir-6504-3p ; hsa-mir-501-3p ; hsa-mir-502-3p ; hsa-mir-4438 ; hsa-mir-32-3p
Nearest miRNA
hsa-mir-10397/Upstream/1683953; hsa-mir-1229/Downstream/1484825;
Nearest TSS
ENST00000502646/Upstream/6519; ENST00000521803/Downstream/37414;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/10988, chr5-CpG: 16/Downstream/23682
Downstream sequence
AATTGGTCTGCGCACCAGCACCATGCAACT
Junction sequence
ACTGTGGGGATGCTGCTGGCAGCCACAGCAAATTGGTCTGCGCACCAGCACCATGCAACT
* 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).
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