COL5A2 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005124
Fusion event
HBV-COL5A2 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
1818
Orient
+
Integrated sequence
TTGTTTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCA| |ACTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCGTAT
Host Sequence
Chromosome
chr2
Cytoband
q32.2
Reference genome
GRCh37/hg19
Start
190055761/189191035 (Hg38)
End
190055761/189191035 (Hg38)
Orient
-
Location type
Intronic
Target gene
COL5A2
miRNAs that regulate target gene
hsa-mir-21-5p ; hsa-mir-222-3p ; hsa-mir-143-3p ; hsa-mir-29a-3p ; hsa-mir-29b-3p ; hsa-mir-29c-3p ; hsa-mir-767-5p
Nearest miRNA
hsa-mir-10b/Upstream/57924; hsa-mir-1244-1/Downstream/17592199;
Nearest TSS
ENST00000437798/Upstream/11156; ENST00000631047/Downstream/250398;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/898043, chr2-CpG: 26/Downstream/250396
Upstream sequence
ATCACTGATATCTAACACATAATAAAGGAATGAGTTCTATTATACAAACACACAGAACAATAATAGGAGAACAGCGTATGATAAAAGGACTTGAAGTCAC
Downstream sequence
AAGGAACTTGGAAAGAGGTTCTGGATGTGATAGGATTTAAGCAGAGCTTCAGAAAATGAATAGCACTCCAACAAAGATTGCCTGAAGGGAGATTAGGGAA
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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