Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005436
Fusion event
HBV-RXRA 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
1811
Orient
+
Integrated sequence
AGACTGTTTGTTTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCA| |CCATGCAACTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGA
Host Sequence
Chromosome
chr9
Cytoband
q34.2
Reference genome
End
137314741/134422895 (Hg38)
Orient
+
Location type
Intron
Target gene
miRNAs that regulate target gene
hsa-mir-423-3p ; hsa-mir-128-3p ; hsa-mir-574-3p ; hsa-mir-486-3p ; hsa-mir-7106-5p ; hsa-mir-4734 ; hsa-mir-4532 ; hsa-mir-596 ; hsa-mir-3940-3p ; hsa-mir-3692-3p ; hsa-mir-6817-5p ; hsa-mir-4769-3p ; hsa-mir-1976 ; hsa-mir-6747-3p ; hsa-mir-4722-3p ; hsa-mir-6727-3p ; hsa-mir-660-3p ; hsa-mir-4667-3p ; hsa-mir-4258 ; hsa-mir-2681-5p ; hsa-mir-3180-5p ; hsa-mir-7702 ; hsa-mir-525-5p ; hsa-mir-520a-5p ; hsa-mir-4724-3p ; hsa-mir-488-5p ; hsa-mir-6782-3p ; hsa-mir-27a-3p
Nearest miRNA
hsa-let-7a-1/Upstream/43423; hsa-mir-126/Downstream/426403;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/13546, chr9-CpG: 22/Downstream/16575
Upstream sequence
AACCTACACACTTCCACCAAGAGTTTTTAAAAGAAAAATATTTATTAGGATTTTTGTAAGTAAAAAATACATATTTGAGGGAAAGTTGAACTCTACAGTA
Downstream sequence
TGCCCTTCTCCTCCCACTCCAAGGCCGCAGCTCTCTTTCCATGCGGTAATGGTGGTGCACAGAGCCACTGCACAGAAATGCCTGCTCCACGCGCATCACA
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).