miRNA display CGI


Results 1 - 16 of 16 are showing below:
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ID Location Perfect MFE.* RefSeq Acc. strand Start Position R_P_ratio# P value
Predicted miRNA align pattern
28354 3' -57.9 NC_005946.1 + 9229 0.66 0.758132
Target:  5'- aGGCAGGUcgcaagcUCCUcAGGAggG-CAGGGGa -3'
miRNA:   3'- -UCGUCCA-------AGGAcUCCUggCaGUCCCC- -5'
28354 3' -57.9 NC_005946.1 + 51733 0.66 0.739669
Target:  5'- cAGUcaAGGUUgugaCUGucaaGGGACUGUCAGGGu -3'
miRNA:   3'- -UCG--UCCAAg---GAC----UCCUGGCAGUCCCc -5'
28354 3' -57.9 NC_005946.1 + 4288 0.67 0.7308
Target:  5'- gGGUGGGUguggaaggacacGAGG-CCGUCGGGGGc -3'
miRNA:   3'- -UCGUCCAagga--------CUCCuGGCAGUCCCC- -5'
28354 3' -57.9 NC_005946.1 + 103017 0.67 0.727827
Target:  5'- cGCGGGUcUCCccggagcaaaggGAGGGCCGggagaCAcGGGGa -3'
miRNA:   3'- uCGUCCA-AGGa-----------CUCCUGGCa----GU-CCCC- -5'
28354 3' -57.9 NC_005946.1 + 83941 0.67 0.679416
Target:  5'- gGGCAGaGUggagggacgUCCUGGGGACaGaCAGGGu -3'
miRNA:   3'- -UCGUC-CA---------AGGACUCCUGgCaGUCCCc -5'
28354 3' -57.9 NC_005946.1 + 14310 0.68 0.658919
Target:  5'- cGGCAGGUacaUCCccGAGGgcuacGCCGaCAuGGGGg -3'
miRNA:   3'- -UCGUCCA---AGGa-CUCC-----UGGCaGU-CCCC- -5'
28354 3' -57.9 NC_005946.1 + 102908 0.68 0.648633
Target:  5'- cGGCAGGUUUCaGGGGA--GaCAGGGGu -3'
miRNA:   3'- -UCGUCCAAGGaCUCCUggCaGUCCCC- -5'
28354 3' -57.9 NC_005946.1 + 2304 0.68 0.648633
Target:  5'- gAGCAGGgugUCCUcgGAcgcGGAccCCGcCGGGGGc -3'
miRNA:   3'- -UCGUCCa--AGGA--CU---CCU--GGCaGUCCCC- -5'
28354 3' -57.9 NC_005946.1 + 76925 0.69 0.576712
Target:  5'- ---cGGaUCCcaaGAGGACCGUCcGGGGa -3'
miRNA:   3'- ucguCCaAGGa--CUCCUGGCAGuCCCC- -5'
28354 3' -57.9 NC_005946.1 + 86882 0.7 0.546343
Target:  5'- --aGGGUU--UGAGGACUGUCuGGGGa -3'
miRNA:   3'- ucgUCCAAggACUCCUGGCAGuCCCC- -5'
28354 3' -57.9 NC_005946.1 + 68964 0.7 0.5067
Target:  5'- cAGCuGGUUCUUGAGGGCgGcUCuGGuGGu -3'
miRNA:   3'- -UCGuCCAAGGACUCCUGgC-AGuCC-CC- -5'
28354 3' -57.9 NC_005946.1 + 95407 0.73 0.364071
Target:  5'- cGGCGGGUccUCCaaaaccggccaaGACCGUCAGGGGg -3'
miRNA:   3'- -UCGUCCA--AGGacuc--------CUGGCAGUCCCC- -5'
28354 3' -57.9 NC_005946.1 + 48295 0.73 0.347412
Target:  5'- gAGCAGGUUggcCCUGAGGcCCGgguaAGGGu -3'
miRNA:   3'- -UCGUCCAA---GGACUCCuGGCag--UCCCc -5'
28354 3' -57.9 NC_005946.1 + 61194 0.74 0.33206
Target:  5'- gGGCAGG---CUGAGGGCCaaCGGGGGg -3'
miRNA:   3'- -UCGUCCaagGACUCCUGGcaGUCCCC- -5'
28354 3' -57.9 NC_005946.1 + 95119 0.75 0.282302
Target:  5'- uGCAGGcggUCCUGAGGAUCGcucccacCAGGGa -3'
miRNA:   3'- uCGUCCa--AGGACUCCUGGCa------GUCCCc -5'
28354 3' -57.9 NC_005946.1 + 14074 1.11 0.001006
Target:  5'- cAGCAGGUUCCUGAGGACCGUCAGGGGg -3'
miRNA:   3'- -UCGUCCAAGGACUCCUGGCAGUCCCC- -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.