Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005285
Fusion event
HBV-SHROOM3 integration
Validated
No
Detection method
PCR and Ultra-deep sequencing
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Start
1739
Orient
+
Integrated sequence
GCCCAAGGTCTTACATAAGAGGACTCTTGGACTCTCAGCAATGTCAACGACCGACCTTGAGGCATACTTCAAAGACTGTTTGTTTAAGGACTGGGAGGAG| |TTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAACTTTTTCACCTCTGCCTAAT
Host Sequence
Chromosome
chr4
Cytoband
q21.1
Reference genome
Start
End
77562330/76641177 (Hg38)
Orient
-
Location type
Intron
Target gene
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-6514-3p ; hsa-mir-4314 ; hsa-mir-7977 ; hsa-mir-3649 ; hsa-mir-6847-3p ; hsa-mir-6811-3p ; hsa-mir-214-5p ; hsa-mir-6506-5p ; hsa-mir-619-5p ; hsa-mir-3192-5p ; hsa-mir-4646-5p ; hsa-mir-204-3p ; hsa-mir-383-3p ; hsa-mir-24-3p ; hsa-mir-4284 ; hsa-mir-30e-5p ; hsa-mir-30d-5p ; hsa-mir-30c-5p ; hsa-mir-30b-5p ; hsa-mir-30a-5p ; hsa-mir-1537-5p ; hsa-mir-3607-3p ; hsa-mir-6817-5p ; hsa-mir-4769-3p ; hsa-mir-3925-3p ; hsa-mir-766-3p ; hsa-mir-338-3p ; hsa-mir-4530 ; hsa-mir-646
Nearest miRNA
hsa-mir-12113/Upstream/65551; hsa-mir-1243/Downstream/6112160;
Nearest CpG islands
None/Target, chr4-CpG: 46/Upstream/54991, chr4-CpG: 79/Downstream/47994
Upstream sequence
TAGAAGCATGTTTCTTTAAAAGTCTTTAAGGAATAGAGTTCAATAATAACTATGTCATCTTTCAATGCCTGCCACAGCATTGTTTTCAGTTTGAGTTTAT
Downstream sequence
TGAGGCTTTCCCATGAGCCAAGTCCCATAATATTCAGCTTTGTAACTTGAGTGCCTATCATTCAGTGGATGGACAGGAAGGATGCCTTGATGAATGGATA
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).