miRNA display CGI


Results 1 - 20 of 22 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
12865 3' -57.7 NC_003387.1 + 49733 0.66 0.590723
Target:  5'- aCGCGGauGCCUUGAGCACCUcggcCUUGc- -3'
miRNA:   3'- -GCGCCc-CGGAGCUUGUGGAa---GAGCua -5'
12865 3' -57.7 NC_003387.1 + 43227 0.66 0.590723
Target:  5'- cCGuCGGGGUaCUCGuuGACGCCguaCUCGGg -3'
miRNA:   3'- -GC-GCCCCG-GAGC--UUGUGGaa-GAGCUa -5'
12865 3' -57.7 NC_003387.1 + 25814 0.66 0.552051
Target:  5'- gGUGGcGGCCUgcucggcggccugggCGGugGCCUgCUCGGUg -3'
miRNA:   3'- gCGCC-CCGGA---------------GCUugUGGAaGAGCUA- -5'
12865 3' -57.7 NC_003387.1 + 3390 0.66 0.547797
Target:  5'- gGCGGGcauCCcgaUCGAGCACCUgcUgUCGAUg -3'
miRNA:   3'- gCGCCCc--GG---AGCUUGUGGA--AgAGCUA- -5'
12865 3' -57.7 NC_003387.1 + 4573 0.67 0.526693
Target:  5'- cCGCGcGGGCCUCGGugGCGCgCUgCgcgCGGg -3'
miRNA:   3'- -GCGC-CCCGGAGCU--UGUG-GAaGa--GCUa -5'
12865 3' -57.7 NC_003387.1 + 23246 0.67 0.526693
Target:  5'- uCGCGGGccguGCCcugcUCGcuGGCGCCgUUCUCGAUc -3'
miRNA:   3'- -GCGCCC----CGG----AGC--UUGUGG-AAGAGCUA- -5'
12865 3' -57.7 NC_003387.1 + 5208 0.67 0.503842
Target:  5'- uGUGGcGCCUCGggUACCgcacgaugcugCUCGAc -3'
miRNA:   3'- gCGCCcCGGAGCuuGUGGaa---------GAGCUa -5'
12865 3' -57.7 NC_003387.1 + 52537 0.67 0.48547
Target:  5'- uCGC-GGGCCgagUCGAGCACCgUCUUGc- -3'
miRNA:   3'- -GCGcCCCGG---AGCUUGUGGaAGAGCua -5'
12865 3' -57.7 NC_003387.1 + 32736 0.67 0.475402
Target:  5'- gCGCGGuGGCCUCGGcgauucggGCugUcaaCUCGAUg -3'
miRNA:   3'- -GCGCC-CCGGAGCU--------UGugGaa-GAGCUA- -5'
12865 3' -57.7 NC_003387.1 + 8996 0.67 0.475402
Target:  5'- uCGCGGGcucccgcaugccGCCgUCGAGCACCUgg-CGGg -3'
miRNA:   3'- -GCGCCC------------CGG-AGCUUGUGGAagaGCUa -5'
12865 3' -57.7 NC_003387.1 + 43799 0.68 0.455586
Target:  5'- uCGCGGuGGCCUCGGACgugagcacguuGCCcUCgcCGAa -3'
miRNA:   3'- -GCGCC-CCGGAGCUUG-----------UGGaAGa-GCUa -5'
12865 3' -57.7 NC_003387.1 + 6780 0.68 0.417345
Target:  5'- uGCGcGGGCCgucggCGAACACg--CUCGGg -3'
miRNA:   3'- gCGC-CCCGGa----GCUUGUGgaaGAGCUa -5'
12865 3' -57.7 NC_003387.1 + 6085 0.68 0.417345
Target:  5'- cCGcCGGGGCgucgucggcaggCUCGAACACCUg--CGAc -3'
miRNA:   3'- -GC-GCCCCG------------GAGCUUGUGGAagaGCUa -5'
12865 3' -57.7 NC_003387.1 + 34782 0.68 0.417345
Target:  5'- cCGCGGGGCCUCgcuuGAGCACUacgUCGc- -3'
miRNA:   3'- -GCGCCCCGGAG----CUUGUGGaagAGCua -5'
12865 3' -57.7 NC_003387.1 + 48289 0.69 0.389983
Target:  5'- gGCGcGGGCUcggCGAACGCCUUgcccagCUCGGc -3'
miRNA:   3'- gCGC-CCCGGa--GCUUGUGGAA------GAGCUa -5'
12865 3' -57.7 NC_003387.1 + 17892 0.69 0.372405
Target:  5'- cCGCGcGGGCCgucgaCGAACAU--UCUCGAc -3'
miRNA:   3'- -GCGC-CCCGGa----GCUUGUGgaAGAGCUa -5'
12865 3' -57.7 NC_003387.1 + 2980 0.7 0.363821
Target:  5'- uCGCucGGGGCCUCGcgaGGCGCUg-CUCGAUc -3'
miRNA:   3'- -GCG--CCCCGGAGC---UUGUGGaaGAGCUA- -5'
12865 3' -57.7 NC_003387.1 + 19004 0.71 0.307637
Target:  5'- gGCGuGGGCCUCGAcgaACCUgUUCGGa -3'
miRNA:   3'- gCGC-CCCGGAGCUug-UGGAaGAGCUa -5'
12865 3' -57.7 NC_003387.1 + 694 0.72 0.271724
Target:  5'- aCGCaGGGCCUUGAuCGCCUcgUCgUCGAg -3'
miRNA:   3'- -GCGcCCCGGAGCUuGUGGA--AG-AGCUa -5'
12865 3' -57.7 NC_003387.1 + 38090 0.72 0.251839
Target:  5'- gCGCGGcGGCCUgaCGGGCACCUg--CGAc -3'
miRNA:   3'- -GCGCC-CCGGA--GCUUGUGGAagaGCUa -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.