miRNA display CGI


Results 1 - 17 of 17 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
28403 5' -55.1 NC_005946.1 + 53331 0.66 0.876476
Target:  5'- gGCAGCGgcguuggccGAGGCAGUCucaGAGUCUgAg -3'
miRNA:   3'- -CGUUGU---------CUCCGUCAGuc-CUCAGGgUg -5'
28403 5' -55.1 NC_005946.1 + 55055 0.66 0.876476
Target:  5'- aGCAGCcugaGGAGGCuGUUGuGGAGUCUgaACa -3'
miRNA:   3'- -CGUUG----UCUCCGuCAGU-CCUCAGGg-UG- -5'
28403 5' -55.1 NC_005946.1 + 76751 0.66 0.866575
Target:  5'- uCGGCAG-GGCAGgcaggaacggcgcaaAGGGGcCCCGCg -3'
miRNA:   3'- cGUUGUCuCCGUCag-------------UCCUCaGGGUG- -5'
28403 5' -55.1 NC_005946.1 + 43215 0.66 0.852235
Target:  5'- --uACGGAccccuuugGGUAGUCuugcgcggucaccAGGAGUCCCAUc -3'
miRNA:   3'- cguUGUCU--------CCGUCAG-------------UCCUCAGGGUG- -5'
28403 5' -55.1 NC_005946.1 + 18335 0.67 0.818834
Target:  5'- --cACAGAGGaucucaGGUCGGGGGUgagaUCCAUg -3'
miRNA:   3'- cguUGUCUCCg-----UCAGUCCUCA----GGGUG- -5'
28403 5' -55.1 NC_005946.1 + 59603 0.67 0.818834
Target:  5'- --cACAGAGGCcaagAGGGGUCCUAUg -3'
miRNA:   3'- cguUGUCUCCGucagUCCUCAGGGUG- -5'
28403 5' -55.1 NC_005946.1 + 15934 0.67 0.817939
Target:  5'- cGCAagucuGCcGAGGCGGUCGuggccauGGAGgccgccgaUCCCACc -3'
miRNA:   3'- -CGU-----UGuCUCCGUCAGU-------CCUC--------AGGGUG- -5'
28403 5' -55.1 NC_005946.1 + 13648 0.67 0.813435
Target:  5'- gGCuGCGGAGGCcaggaacccgagucaGGUCAGGAGgauggCCgGg -3'
miRNA:   3'- -CGuUGUCUCCG---------------UCAGUCCUCa----GGgUg -5'
28403 5' -55.1 NC_005946.1 + 76656 0.67 0.791222
Target:  5'- gGCAAcCAGGGGCc--CAGGGG-CCCAg -3'
miRNA:   3'- -CGUU-GUCUCCGucaGUCCUCaGGGUg -5'
28403 5' -55.1 NC_005946.1 + 47746 0.68 0.781696
Target:  5'- aCGugAGAGGC-GUCAGG-GUCaCuCACg -3'
miRNA:   3'- cGUugUCUCCGuCAGUCCuCAG-G-GUG- -5'
28403 5' -55.1 NC_005946.1 + 76548 0.69 0.720828
Target:  5'- gGCcuCAGGGGCAGaggggaaUCAGGuGUCCuCAg -3'
miRNA:   3'- -CGuuGUCUCCGUC-------AGUCCuCAGG-GUg -5'
28403 5' -55.1 NC_005946.1 + 31556 0.7 0.616528
Target:  5'- gGUAucGCGGcGGCAGUCAGGAa--CCACa -3'
miRNA:   3'- -CGU--UGUCuCCGUCAGUCCUcagGGUG- -5'
28403 5' -55.1 NC_005946.1 + 71836 0.71 0.605915
Target:  5'- cGCGGgcCAGAGGaCGGg-AGGAgGUCCCGCg -3'
miRNA:   3'- -CGUU--GUCUCC-GUCagUCCU-CAGGGUG- -5'
28403 5' -55.1 NC_005946.1 + 60380 0.71 0.594266
Target:  5'- -gGGCAGAGGCGGUCAGcGccgccccAGccacUCCCGCu -3'
miRNA:   3'- cgUUGUCUCCGUCAGUC-C-------UC----AGGGUG- -5'
28403 5' -55.1 NC_005946.1 + 4274 0.8 0.202286
Target:  5'- -gGACAcGAGGCcGUCGGGGGcUCCCACg -3'
miRNA:   3'- cgUUGU-CUCCGuCAGUCCUC-AGGGUG- -5'
28403 5' -55.1 NC_005946.1 + 29737 0.85 0.09061
Target:  5'- gGUGACAGAGGCGGUCAGG-GUCCUg- -3'
miRNA:   3'- -CGUUGUCUCCGUCAGUCCuCAGGGug -5'
28403 5' -55.1 NC_005946.1 + 64009 0.99 0.009641
Target:  5'- uGCAACAGAGGCAGUCAGGAGUCCacgGCg -3'
miRNA:   3'- -CGUUGUCUCCGUCAGUCCUCAGGg--UG- -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.