miRNA display CGI


Results 1 - 15 of 15 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
1961 3' -55.7 NC_001347.2 + 64881 0.66 0.960618
Target:  5'- cGAGAAAGuCCCCGCGGaguGCCccgaacuaaCGCGu -3'
miRNA:   3'- -UUUUUUCuGGGGCGCC---CGGaa-------GCGCu -5'
1961 3' -55.7 NC_001347.2 + 197120 0.66 0.957026
Target:  5'- ---cAAGGCCCCGCuggaacucGGGCCcgccgucgUCGCc- -3'
miRNA:   3'- uuuuUUCUGGGGCG--------CCCGGa-------AGCGcu -5'
1961 3' -55.7 NC_001347.2 + 206697 0.66 0.944931
Target:  5'- ----cGGGCCuCUGgGGGCCgcacggagCGCGAc -3'
miRNA:   3'- uuuuuUCUGG-GGCgCCCGGaa------GCGCU- -5'
1961 3' -55.7 NC_001347.2 + 129153 0.67 0.935738
Target:  5'- ----uGGGCaCCGCGGGCUUcCGUGGc -3'
miRNA:   3'- uuuuuUCUGgGGCGCCCGGAaGCGCU- -5'
1961 3' -55.7 NC_001347.2 + 29867 0.67 0.925624
Target:  5'- ---uAAGACUuuGCGGGCCUcgGCu- -3'
miRNA:   3'- uuuuUUCUGGggCGCCCGGAagCGcu -5'
1961 3' -55.7 NC_001347.2 + 73704 0.67 0.924028
Target:  5'- gAGAAGGGGCCgggguCCGCGGGCaccgccgccggaggCGCGGu -3'
miRNA:   3'- -UUUUUUCUGG-----GGCGCCCGgaa-----------GCGCU- -5'
1961 3' -55.7 NC_001347.2 + 167214 0.67 0.920221
Target:  5'- ---cGAGGCCgCGCcGGCCgcgcCGCGAg -3'
miRNA:   3'- uuuuUUCUGGgGCGcCCGGaa--GCGCU- -5'
1961 3' -55.7 NC_001347.2 + 166156 0.68 0.90076
Target:  5'- -----cGugCCCGCGGGCCaggUcaucggcgcuagcgCGCGAu -3'
miRNA:   3'- uuuuuuCugGGGCGCCCGGa--A--------------GCGCU- -5'
1961 3' -55.7 NC_001347.2 + 196250 0.68 0.883015
Target:  5'- -uGAAGGACCUcuaCGCGGcCUUUUGCGAg -3'
miRNA:   3'- uuUUUUCUGGG---GCGCCcGGAAGCGCU- -5'
1961 3' -55.7 NC_001347.2 + 228893 0.69 0.868855
Target:  5'- -uAGAGGugUUgGCGGGCCUgugCGCa- -3'
miRNA:   3'- uuUUUUCugGGgCGCCCGGAa--GCGcu -5'
1961 3' -55.7 NC_001347.2 + 182113 0.7 0.821633
Target:  5'- ----cAGAucgUCCCGCGGGUCUUCGaCGu -3'
miRNA:   3'- uuuuuUCU---GGGGCGCCCGGAAGC-GCu -5'
1961 3' -55.7 NC_001347.2 + 136001 0.7 0.79922
Target:  5'- gGGGAGGGACCCCcggccgagguccggaGCGGGCCg-CGCc- -3'
miRNA:   3'- -UUUUUUCUGGGG---------------CGCCCGGaaGCGcu -5'
1961 3' -55.7 NC_001347.2 + 78391 0.71 0.768444
Target:  5'- uGGGAGGA-CCCGCGGGCCacgUCGgGc -3'
miRNA:   3'- uUUUUUCUgGGGCGCCCGGa--AGCgCu -5'
1961 3' -55.7 NC_001347.2 + 1060 0.72 0.720819
Target:  5'- ----uAGaACCCCGCGGGCCgccgggCGCc- -3'
miRNA:   3'- uuuuuUC-UGGGGCGCCCGGaa----GCGcu -5'
1961 3' -55.7 NC_001347.2 + 51567 0.78 0.363092
Target:  5'- -----cGGCCCCGCGGGgucuCCUUCGCGc -3'
miRNA:   3'- uuuuuuCUGGGGCGCCC----GGAAGCGCu -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.