Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005916
Fusion event
HBV-SLC4A4 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
1761
Orient
+
Integrated sequence
ACTCTTGGACTCTCAGCAATGTCAACGACCGACCTTGAGGCATACTTCAAAGACTGTTTGTTTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAA| |AGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACT
Host Sequence
Chromosome
chr4
Cytoband
q13.3
Reference genome
Start
End
72320958/71455241 (Hg38)
Orient
+
Location type
Intron
Target gene
miRNAs that regulate target gene
hsa-mir-5585-3p ; hsa-mir-498 ; hsa-mir-4279 ; hsa-mir-6783-3p ; hsa-mir-1343-3p ; hsa-mir-23b-5p ; hsa-mir-23a-5p ; hsa-mir-6778-3p ; hsa-mir-1976 ; hsa-mir-3653-5p ; hsa-mir-6742-3p ; hsa-mir-6852-5p ; hsa-mir-939-3p ; hsa-mir-6747-3p ; hsa-mir-6727-3p ; hsa-mir-4722-3p ; hsa-mir-660-3p ; hsa-mir-6829-3p ; hsa-mir-6791-3p
Nearest miRNA
hsa-mir-12113/Upstream/5178313; hsa-mir-1243/Downstream/5118327;
Nearest CpG islands
None/Target, chr4-CpG: 46/Upstream/267489, chr4-CpG: 30/Downstream/576606
Upstream sequence
TATTGAATCCAGTTCTATGTGTGTGACAAAGTATTCTTGACAGGTTCCTAAAAAGACATGTGAATGTAGTCAGTGGTTTTCTTTTTAAAGTCTAATATTT
Downstream sequence
cacatacctctgtgTTACCAGTGAGAGATCTGCAGCATGGGTTATGAGAACCAACTCTAATAGGACATAGAGATGAAATAGACAGAGCATGTTTTTCTCC
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).