miRNA display CGI


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ID Location Perfect MFE.* RefSeq Acc. strand Start Position R_P_ratio# P value
Predicted miRNA align pattern
1316 3' -53.1 NC_001331.1 + 984 0.67 0.20539
Target:  5'- uGAAGGCCaUUG-GCGCUacaucgUCGGC-GCCCu -3'
miRNA:   3'- -UUUCUGG-AGCuCGCGA------AGCUGaUGGG- -5'
1316 3' -53.1 NC_001331.1 + 3196 1.09 0.000086
Target:  5'- aAAAGACCUCGAGCGCUUCGACUACCCc -3'
miRNA:   3'- -UUUCUGGAGCUCGCGAAGCUGAUGGG- -5'
1316 3' -53.1 NC_001331.1 + 5249 0.66 0.247649
Target:  5'- --uGGCCUCGGGgGaggucaUUGGCUGCCg -3'
miRNA:   3'- uuuCUGGAGCUCgCga----AGCUGAUGGg -5'
1316 3' -53.1 NC_001331.1 + 7038 0.69 0.139358
Target:  5'- cGAGugCUCggGAGCGCggggCGgagaaGCUGCCCc -3'
miRNA:   3'- uUUCugGAG--CUCGCGaa--GC-----UGAUGGG- -5'
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Note:
      When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.

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TDL, Institute of Biomedical Science, Academia Sinica, Taipei, Taiwan.
Copyright © 2007 TDL. All rights reserved.