miRNA display CGI


Results 1 - 20 of 35 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
11452 3' -54.6 NC_003085.1 + 1101 0.7 0.491108
Target:  5'- --aGGAGCGCGCG-UGAgucACUCggagagGCGCAg -3'
miRNA:   3'- cagCUUCGCGCGCaACU---UGAG------CGCGU- -5'
11452 3' -54.6 NC_003085.1 + 2370 0.66 0.721636
Target:  5'- -gCGAGGCcgcgGCGCGc-GAGCUCuCGCAg -3'
miRNA:   3'- caGCUUCG----CGCGCaaCUUGAGcGCGU- -5'
11452 3' -54.6 NC_003085.1 + 2983 0.72 0.35688
Target:  5'- cGUCG-AGCGCGCGUggGAaccGCUCcccgcuggGCGCAc -3'
miRNA:   3'- -CAGCuUCGCGCGCAa-CU---UGAG--------CGCGU- -5'
11452 3' -54.6 NC_003085.1 + 3392 0.68 0.599656
Target:  5'- cGUCGGuaAGCGCgacGCGUacgUGAAagcguaUCGCGCGc -3'
miRNA:   3'- -CAGCU--UCGCG---CGCA---ACUUg-----AGCGCGU- -5'
11452 3' -54.6 NC_003085.1 + 4719 0.67 0.633156
Target:  5'- -cCGAAGCGaGCGcgGAACUCG-GCu -3'
miRNA:   3'- caGCUUCGCgCGCaaCUUGAGCgCGu -5'
11452 3' -54.6 NC_003085.1 + 5543 0.66 0.732407
Target:  5'- -gCGAAGUGCGCGcaaagGGcCUgGCGCc -3'
miRNA:   3'- caGCUUCGCGCGCaa---CUuGAgCGCGu -5'
11452 3' -54.6 NC_003085.1 + 7041 0.73 0.339918
Target:  5'- -gCGggGUGgGCGaUGAGCcCGCGCGa -3'
miRNA:   3'- caGCuuCGCgCGCaACUUGaGCGCGU- -5'
11452 3' -54.6 NC_003085.1 + 7862 0.7 0.480713
Target:  5'- --aGAAGCGCGCGgaacuggggcUUGAGCcguUCGUGCu -3'
miRNA:   3'- cagCUUCGCGCGC----------AACUUG---AGCGCGu -5'
11452 3' -54.6 NC_003085.1 + 7907 0.68 0.599656
Target:  5'- cGUCGggGCgaGCGCGUccUGucggCGUGCAc -3'
miRNA:   3'- -CAGCuuCG--CGCGCA--ACuugaGCGCGU- -5'
11452 3' -54.6 NC_003085.1 + 8541 0.73 0.33166
Target:  5'- cUCucGGCGCGCGgcGAGCUCGUcacgGCAg -3'
miRNA:   3'- cAGcuUCGCGCGCaaCUUGAGCG----CGU- -5'
11452 3' -54.6 NC_003085.1 + 10771 0.67 0.677755
Target:  5'- -gCGAAGC-CGCGUUGucAgUUGUGCAg -3'
miRNA:   3'- caGCUUCGcGCGCAACu-UgAGCGCGU- -5'
11452 3' -54.6 NC_003085.1 + 10944 0.67 0.677755
Target:  5'- -aCGguGCGCGUGUUGGugcucgaugACUUGgGCGg -3'
miRNA:   3'- caGCuuCGCGCGCAACU---------UGAGCgCGU- -5'
11452 3' -54.6 NC_003085.1 + 11125 0.66 0.688822
Target:  5'- cGUUGggGCGCGCGUcGucuCUCggauGUGCc -3'
miRNA:   3'- -CAGCuuCGCGCGCAaCuu-GAG----CGCGu -5'
11452 3' -54.6 NC_003085.1 + 11297 0.66 0.699832
Target:  5'- uUCgGAAGCGCGCGcUGGcGCUUGUGg- -3'
miRNA:   3'- cAG-CUUCGCGCGCaACU-UGAGCGCgu -5'
11452 3' -54.6 NC_003085.1 + 13566 0.66 0.725957
Target:  5'- -gCGAgcaaGGCGCGCG-UGGACgugggcaccggaggCGCGCc -3'
miRNA:   3'- caGCU----UCGCGCGCaACUUGa-------------GCGCGu -5'
11452 3' -54.6 NC_003085.1 + 13913 0.7 0.460253
Target:  5'- -gCGGcguGCGCGCGUUucGGACggggCGCGCGc -3'
miRNA:   3'- caGCUu--CGCGCGCAA--CUUGa---GCGCGU- -5'
11452 3' -54.6 NC_003085.1 + 15219 0.71 0.430456
Target:  5'- --gGAAGUGgGCGaggUGGACUUGCGCc -3'
miRNA:   3'- cagCUUCGCgCGCa--ACUUGAGCGCGu -5'
11452 3' -54.6 NC_003085.1 + 16404 0.68 0.604113
Target:  5'- uGUCGAGG-GCGCGUUGAAgcguCUCuggccccauauccagGCGCc -3'
miRNA:   3'- -CAGCUUCgCGCGCAACUU----GAG---------------CGCGu -5'
11452 3' -54.6 NC_003085.1 + 17012 0.66 0.721636
Target:  5'- --aGAAGCGCG-GaUGGgcgcuGCUCGCGUAu -3'
miRNA:   3'- cagCUUCGCGCgCaACU-----UGAGCGCGU- -5'
11452 3' -54.6 NC_003085.1 + 17265 0.69 0.516466
Target:  5'- -gCGcAGgGCGCGUUGAagcacgcgcgccaccACUgGCGCAg -3'
miRNA:   3'- caGCuUCgCGCGCAACU---------------UGAgCGCGU- -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.