hsa-mir-6780a-3p _LIHC.png
AFF3 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10006132
Fusion event
HBV-AFF3 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
1192
Orient
+
Integrated sequence
ACTTTCTCGCCAACTTACAAGGCCTTTCTGTGTAAACAATATCTGCACCTTTACCCCGTTGCCCGGCAACGGTCAGGTCTCTGCCAAGTGTTTGCTGACG| |CAACCCCCACTGGATGGGGCTTGGCCATAGGCCATCGGCGCATGCGTGGAACCTTTGTGGCTCCTCTGCCGATCCATACTGCGGAACTCCTAGCAGCTTG
Host Sequence
Chromosome
chr2
Cytoband
q11.2
Reference genome
GRCh37/hg19
Start
100238592/99622130 (Hg38)
End
100238592/99622130 (Hg38)
Orient
-
Location type
Intron
Fragile sites / regions
FRA2S ; FRA2A
Target gene
AFF3
miRNAs that regulate target gene
hsa-mir-574-5p ; hsa-mir-6881-3p ; hsa-mir-6780a-3p ; hsa-mir-7111-3p ; hsa-mir-6867-5p ; hsa-mir-3177-5p ; hsa-mir-7703 ; hsa-mir-6720-5p ; hsa-mir-6512-3p ; hsa-mir-1227-3p ; hsa-mir-4252 ; hsa-mir-4793-3p ; hsa-mir-766-3p ; hsa-mir-1273g-3p ; hsa-mir-508-5p ; hsa-mir-6849-3p
Nearest miRNA
hsa-mir-1285-2/Upstream/2823777; hsa-mir-10b/Downstream/1687320;
Nearest TSS
ENST00000437798/Upstream/43760; ENST00000434301/Downstream/384715;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/28101, chr2-CpG: 138/Downstream/481793
Nearest cancer related gene
AFF3(OG, No orient, 0)
Upstream sequence
CTGGTTTCCTATAGGGTGTGAAGCTGAAATTCTATGAGCAAATCTATGTAATTTAAATAAGACTACACCAACTAGGACGTGCTGAGAACAATACAGGACC
Downstream sequence
AGGGGTCTCCAGCCCCACTTTGGTACAGTCACTGCTGGAGTGGAGGGAAAATGAGTCGAGGGTGGGTGCGTTCTCCTCCAACCATGGCAACTCATTCTGA
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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