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
6056 3' -53 NC_001815.1 + 4702 1 0.000674
Target:  5'- uGCCUUacAACUCUACCAGCUCCGGGCu -3'
miRNA:   3'- -CGGAAguUUGAGAUGGUCGAGGCCCG- -5'
6056 3' -53 NC_001815.1 + 1516 0.71 0.133455
Target:  5'- gGCCUUUucAGCUCUGCCAGggaacacccgcgaccCaUCCuGGGCa -3'
miRNA:   3'- -CGGAAGu-UUGAGAUGGUC---------------G-AGG-CCCG- -5'
6056 3' -53 NC_001815.1 + 835 0.69 0.187329
Target:  5'- uCCUcCAAGCcgcCUACCGGCUacaacCUGGGCc -3'
miRNA:   3'- cGGAaGUUUGa--GAUGGUCGA-----GGCCCG- -5'
6056 3' -53 NC_001815.1 + 6966 0.67 0.239897
Target:  5'- uCCUUCu-GCUCUuccGCCAGCcccUCCGG-Cg -3'
miRNA:   3'- cGGAAGuuUGAGA---UGGUCG---AGGCCcG- -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.