RFTN1 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005606
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
277
Orient
-
Integrated sequence
CCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAGAATCCTCACAATACCACAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTT| |CTAGGGGGAGCACCCACGTGTCCTGGCCAAAATTCGCAGTCCCCAACCTCCAATCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGGCTATCGCTGGA
Host Sequence
Chromosome
chr3
Cytoband
p24.3
Reference genome
GRCh37/hg19
Start
16376931/16335424 (Hg38)
End
16376931/16335424 (Hg38)
Orient
+
Location type
Intron
Target gene
RFTN1
miRNAs that regulate target gene
hsa-mir-484
Nearest miRNA
hsa-mir-12127/Upstream/461575; hsa-let-7g/Downstream/597772;
Nearest TSS
ENST00000440867/Upstream/8557; ENST00000607363/Downstream/3884;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/69945, chr3-CpG: 113/Downstream/177396
Upstream sequence
tttgccacatgaggtgatatcaaggttctgaggtttagcaaatgaatggatgattttgagggccaccactcTCCACCCTCTACACTTGGTGGCTTggcct
Downstream sequence
tgcagccttaaaaaggaacgaatcacgtcctttgtggggacatggatggagctggaagctgttatccttagcaaactaacgcaggaacagaaaatcaaac
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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