Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10004723
Fusion event
HBV-SAMD4B 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
1803
Orient
+
Integrated sequence
TACTTCAAAGACTGTTTGTTTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTT| |CACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATG
Host Sequence
Chromosome
chr19
Cytoband
q13.2
Reference genome
Start
End
39854440/39363800 (Hg38)
Orient
+
Location type
Intron
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-744-5p ; hsa-mir-92b-5p ; hsa-mir-93-3p ; hsa-mir-320a ; hsa-mir-30d-5p ; hsa-mir-93-5p ; hsa-let-7a-5p ; hsa-mir-6758-5p ; hsa-mir-6856-5p ; hsa-mir-4726-5p ; hsa-mir-4640-5p ; hsa-mir-6799-5p ; hsa-mir-6851-5p ; hsa-mir-3689d ; hsa-mir-7854-3p ; hsa-mir-3918 ; hsa-mir-6865-5p ; hsa-mir-6815-5p ; hsa-mir-6895-5p ; hsa-mir-6859-5p ; hsa-mir-3916 ; hsa-mir-3125 ; hsa-mir-4700-5p ; hsa-mir-6857-5p ; hsa-mir-3915 ; hsa-mir-92a-2-5p ; hsa-mir-4450 ; hsa-mir-3649 ; hsa-mir-5187-5p ; hsa-mir-1255b-5p ; hsa-mir-1255a ; hsa-mir-4644 ; hsa-mir-4306 ; hsa-mir-185-5p ; hsa-mir-4533 ; hsa-mir-1827 ; hsa-mir-3928-3p ; hsa-mir-1252-5p ; hsa-mir-940 ; hsa-mir-6893-5p ; hsa-mir-6876-5p ; hsa-mir-6808-5p ; hsa-mir-4476 ; hsa-mir-4428 ; hsa-mir-651-3p ; hsa-mir-762 ; hsa-mir-5001-5p ; hsa-mir-4498 ; hsa-mir-4430 ; hsa-mir-4492 ; hsa-mir-3652 ; hsa-mir-765 ; hsa-mir-6894-5p ; hsa-mir-7154-3p ; hsa-mir-766-5p ; hsa-mir-6837-5p ; hsa-mir-3135b ; hsa-mir-4685-5p ; hsa-mir-4446-3p ; hsa-mir-4506 ; hsa-mir-2682-5p ; hsa-mir-34b-5p ; hsa-mir-449c-5p ; hsa-mir-4514 ; hsa-mir-4692 ; hsa-mir-491-5p ; hsa-mir-622
Nearest miRNA
hsa-mir-10395/Upstream/4018173; hsa-let-7e/Downstream/45823;
Nearest CpG islands
None/Target, chr19-CpG: 112/Upstream/20767, chr19-CpG: 72/Downstream/26892
Upstream sequence
attgagttaggtcatggaggcagagctagattttgaatccagcaagtttgcctgttgaacttgtgctcttacttagtatactctgctAGGACCTGAGACA
Downstream sequence
GAGTACACCACTACCTTCCAGGGGACCATCTGGGTTCAATTGTGCAGGTATTCGTTGGGCCTCTGCTGTGCCTCCACTCTGGGCCAGGCTTTTTCTGATC
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).