RFTN1 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005605
Fusion event
HBV-RFTN1 integration
Validated
No
Detection method
PCR and Ultra-deep sequencing
Data source
Curated
Sample type
Nontumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
29861854
Virus Sequence
Virus name
HBV
Reference genome
AP011098
Start
1811
Orient
+
Integrated sequence
AGACTGTTTGTTTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCA| |CCATGCAACTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGA
Host Sequence
Chromosome
chr3
Cytoband
p24.3
Reference genome
GRCh37/hg19
Start
16376929/16335422 (Hg38)
End
16376929/16335422 (Hg38)
Orient
-
Location type
Intron
Target gene
RFTN1
miRNAs that regulate target gene
hsa-mir-484
Nearest miRNA
hsa-mir-12127/Upstream/461573; hsa-let-7g/Downstream/597774;
Nearest TSS
ENST00000440867/Upstream/8555; ENST00000607363/Downstream/3886;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/69943, chr3-CpG: 113/Downstream/177398
Upstream sequence
ccaataatcccttctgttgaaacataagataataaaatatattattaaatgagataatccatgtaaggtaccttcacatcctaagcactgaataaatact
Downstream sequence
tatgcagccttaaaaaggaacgaatcacgtcctttgtggggacatggatggagctggaagctgttatccttagcaaactaacgcaggaacagaaaatcaa
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).
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