Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005767
Fusion event
HBV-LPXN 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
1000
Orient
+
Integrated sequence
GGTACTTTACCACAGGAACATATTGTACGGAAACTCAAGCAATGTTTTCGAAAACTGCCTGTAAATAGACCTATTGATTGGAAAGTATGTCAAAGAATTG| |TGGGTCTTTTGGGCTTTGCTGCCCCTTTTACACAATGTGGCTATCCTGCCTTGATGCCTTTATATGCATGTATACAATCTAAGCAGGCTTTCACTTTCTC
Host Sequence
Chromosome
chr11
Cytoband
q12.1
Reference genome
Start
End
58326054/58558581 (Hg38)
Orient
-
Location type
Intron
Target gene
miRNAs that regulate target gene
hsa-mir-9-5p ; hsa-mir-6881-3p ; hsa-mir-6780a-3p ; hsa-mir-7111-3p ; hsa-mir-4635 ; hsa-mir-138-1-3p ; hsa-mir-877-3p ; hsa-mir-4668-3p ; hsa-mir-1273e ; hsa-mir-1827 ; hsa-mir-219b-3p ; hsa-mir-302f ; hsa-mir-3664-3p ; hsa-mir-3929 ; hsa-mir-4419b ; hsa-mir-4433a-3p ; hsa-mir-4459 ; hsa-mir-4478 ; hsa-mir-4649-3p ; hsa-mir-4695-5p ; hsa-mir-4722-5p ; hsa-mir-4768-3p ; hsa-mir-485-5p ; hsa-mir-510-5p ; hsa-mir-512-5p ; hsa-mir-5690 ; hsa-mir-665 ; hsa-mir-6808-5p ; hsa-mir-6840-3p ; hsa-mir-6884-5p ; hsa-mir-6893-5p ; hsa-mir-7160-5p ; hsa-mir-940
Nearest miRNA
hsa-mir-129-2/Upstream/917295; hsa-let-7a-2/Downstream/1036496;
Nearest CpG islands
None/Target, chr11-CpG: 30/Upstream/805300, chr11-CpG: 132/Downstream/19619
Upstream sequence
agttgtgatcacactactgcatgccagcctggacaacagaagcagaatgagaccctgtcaaaaaaaaaaaaaaaaaaaaaaaagagaaGAAAGGAAAGGA
Downstream sequence
AGAAGAAaaagaaaaacaaataggtcaaaggagtagattagaaaacccagaaacaggctcctgcacctaaaagaacttcctatatgagcaatggggcatt
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).