hsa-mir-6780a-3p _LIHC.png
UPF3A _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10014883
Fusion event
HBV-UPF3A integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Cell line
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Perfect
Reported year
2014
PubMed ID
24582836
Virus Sequence
Virus name
HBV
Reference genome
NC_003977.1
Region type
Surface
Start
241
End
459
Orient
+
Integrated sequence
CAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCACCCACGTGTCCTGGCCAAAATTCGCAGTCCCCAACCTCCAATCACTCACCAACCTCTTGTCCTCCAACTTGTCCTGGCTATCGCTGGATGTGTCTGCGGCGTTTTATCATATTCCTCTTCATCCTGCTGCTATGCCTCATCTTCTTGTTGGTTCTTCTGGACTACCAAGGT
Host Sequence
Chromosome
chr13
Cytoband
q34
Reference genome
GRCh37.p10
Start
115070262/114304787 (Hg38)
End
115070459/114304984 (Hg38)
Orient
+
Location type
Intronic
Target gene
UPF3A
miRNAs that regulate target gene
hsa-mir-484 ; hsa-mir-4439 ; hsa-mir-3136-5p ; hsa-mir-6780a-3p ; hsa-mir-3118 ; hsa-mir-134-5p ; hsa-mir-4268 ; hsa-mir-1236-5p ; hsa-mir-6857-3p ; hsa-mir-6855-3p ; hsa-mir-4513 ; hsa-mir-2277-3p ; hsa-mir-4526 ; hsa-mir-3660 ; hsa-mir-6728-3p ; hsa-mir-6736-3p ; hsa-mir-888-3p
Nearest miRNA
hsa-mir-1267/Upstream/30879;
Nearest TSS
ENST00000623511/Upstream/18402; ENST00000478022/Downstream/9351;
Nearest CpG islands
None/Target, chr13-CpG: 551/Upstream/22228, chr13-CpG: 92/Downstream/9205
Downstream sequence
AAGGACCGGCCAGCCTTGCAGCTGTATGATCCAAGAGCTCGCTTCCGAGCGCGAGAGTGTGGCGGAAACAGGAGGATCTGCAAGGCAGAAGGTTCGGGGACTGGTCCTGAGAAGAGGGAAGAGGCAGAGTGAGTCACTGCACGCACCTGGCCTCCATGGACGAGCAAGGGCATCCCAGAAACGT
Target sequence
GGACCGGCCAGCCTTGCAGCTGTATGATCCAGGAGCTCGCTTCCGAGCGCGAGAGTGTGGCGGAAACAGGAGGATCTGCAAGGCAGAAGGTTCGGGGACTGGTCCTGAGAAGAGGGAAGAGGCAGAGTGAGTCACTGCACGCACCTGGCCTCCATGGACGAGCAAGGGCATCCCAGAAACGTGTAAATGACCCCGAG
Junction sequence
AGTCCCCAACCTCCAATCACTCACCAACCTCTTGTCCTCCAATTTGTCTTGGCTATCGCTGGATGTGTCTGCGGCGTTTTATCATATTCCTCTTCACCCTGCTGCTATGCCTCATCTTCTTGTTGGTTCTTCTGGACTACCAAGGACCGGCCAGCCTTGCAGCTGTATGATCCAAGAGCTCGCTTCCGAGCGCGAGAGTGTGGCGGAAACAGGAGGATCTGCAAGGCAGAAGGTTCGGGGACTGGTCCTGAGAAGAGGGAAGAGGCAGAGTGAGTCACTGCACGCACCTGGCCTCCATGGACGAGCAAGGGCATCCCAGAAACGT
* Color:  Human Sequence / Virus Sequence / Overlapped sequence / Unknown sequence
Reference
Lau, C. C., et al. Viral-human chimeric transcript predisposes risk to liver cancer development and progression. Cancer Cell ,2014,25(3): 335-349.
Curate