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
30491 3' -56.1 NC_006548.1 + 24005 0.66 0.512469
Target:  5'- cGGGCGgugUCCAgccgaUCAGGGCCUUGc--- -3'
miRNA:   3'- -CUCGCaa-AGGU-----GGUCCCGGAACuccu -5'
30491 3' -56.1 NC_006548.1 + 16445 0.66 0.534249
Target:  5'- cAGacaGUUUUCACCuGGGCaucgcUGAGGAu -3'
miRNA:   3'- cUCg--CAAAGGUGGuCCCGga---ACUCCU- -5'
30491 3' -56.1 NC_006548.1 + 15816 0.67 0.491063
Target:  5'- cAGCGcuggaACCAGGGCCa-GAGGAu -3'
miRNA:   3'- cUCGCaaaggUGGUCCCGGaaCUCCU- -5'
30491 3' -56.1 NC_006548.1 + 9846 0.66 0.523316
Target:  5'- aAGCGUUgcUUCACCuggucGGCCgUGAGGGc -3'
miRNA:   3'- cUCGCAA--AGGUGGuc---CCGGaACUCCU- -5'
30491 3' -56.1 NC_006548.1 + 518 1.08 0.000512
Target:  5'- gGAGCGUUUCCACCAGGGCCUUGAGGAu -3'
miRNA:   3'- -CUCGCAAAGGUGGUCCCGGAACUCCU- -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.