miRNA display CGI


Results 1 - 19 of 19 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
28157 3' -55.2 NC_005887.1 + 2432 0.66 0.659182
Target:  5'- gCGuGUCUUCgUCGUcggccugcgAGCGcuggucgcccGCCGGAUCGc -3'
miRNA:   3'- -GC-CAGAAGaAGCG---------UCGU----------CGGCCUAGC- -5'
28157 3' -55.2 NC_005887.1 + 5825 0.66 0.659182
Target:  5'- gCGGccagCgcCUUCGCGGCcucGGCCGGAa-- -3'
miRNA:   3'- -GCCa---GaaGAAGCGUCG---UCGGCCUagc -5'
28157 3' -55.2 NC_005887.1 + 17788 0.66 0.659182
Target:  5'- cCGGUCguggcugUCgUCGCAGgGGCU-GAUCGc -3'
miRNA:   3'- -GCCAGa------AGaAGCGUCgUCGGcCUAGC- -5'
28157 3' -55.2 NC_005887.1 + 41601 0.66 0.625629
Target:  5'- gCGGcCcagg-UGCGGCGGCCGGcgCGg -3'
miRNA:   3'- -GCCaGaagaaGCGUCGUCGGCCuaGC- -5'
28157 3' -55.2 NC_005887.1 + 21607 0.67 0.581018
Target:  5'- cCGGUCgcCUgcagCGUcgugaauuucccGGCAGCCGGcGUCGu -3'
miRNA:   3'- -GCCAGaaGAa---GCG------------UCGUCGGCC-UAGC- -5'
28157 3' -55.2 NC_005887.1 + 10194 0.68 0.50493
Target:  5'- cCGG-CUUCUUCGUcguacguGCAGCC-GAUCa -3'
miRNA:   3'- -GCCaGAAGAAGCGu------CGUCGGcCUAGc -5'
28157 3' -55.2 NC_005887.1 + 12818 0.69 0.48395
Target:  5'- gCGGUgUUC-UCGCGuuGCAGCgCGGcgCGa -3'
miRNA:   3'- -GCCAgAAGaAGCGU--CGUCG-GCCuaGC- -5'
28157 3' -55.2 NC_005887.1 + 619 0.69 0.462381
Target:  5'- gCGGUCUUCgcgcugUauccggcgcggcgCGCGGCGGCCGacgcguucaGAUCGa -3'
miRNA:   3'- -GCCAGAAGa-----A-------------GCGUCGUCGGC---------CUAGC- -5'
28157 3' -55.2 NC_005887.1 + 30583 0.7 0.404665
Target:  5'- uGGUCaUCgUCGCuuCgAGCCGGAUCGc -3'
miRNA:   3'- gCCAGaAGaAGCGucG-UCGGCCUAGC- -5'
28157 3' -55.2 NC_005887.1 + 5448 0.7 0.404665
Target:  5'- cCGGUCgcgcuggCUUCGCcuucgAGCAGUCGGAa-- -3'
miRNA:   3'- -GCCAGaa-----GAAGCG-----UCGUCGGCCUagc -5'
28157 3' -55.2 NC_005887.1 + 37319 0.71 0.376216
Target:  5'- uCGGUCg---UCGCAGCAgcGCCGGcacuggcAUCGg -3'
miRNA:   3'- -GCCAGaagaAGCGUCGU--CGGCC-------UAGC- -5'
28157 3' -55.2 NC_005887.1 + 12677 0.71 0.342392
Target:  5'- uCGGgCUUCUgcgucaGCAcgccgagcgucGCGGCCGGGUCGg -3'
miRNA:   3'- -GCCaGAAGAag----CGU-----------CGUCGGCCUAGC- -5'
28157 3' -55.2 NC_005887.1 + 41432 0.71 0.342392
Target:  5'- aCGGUCUgcucgaacgCUUCcCGGCGGCgcgCGGAUCGu -3'
miRNA:   3'- -GCCAGAa--------GAAGcGUCGUCG---GCCUAGC- -5'
28157 3' -55.2 NC_005887.1 + 9567 0.72 0.325917
Target:  5'- aCGGUgUUCg--GCAGCAuGCCgGGGUCGg -3'
miRNA:   3'- -GCCAgAAGaagCGUCGU-CGG-CCUAGC- -5'
28157 3' -55.2 NC_005887.1 + 40834 0.74 0.227099
Target:  5'- aGGUgaUCUUCGU-GCAGUCGGAUCc -3'
miRNA:   3'- gCCAgaAGAAGCGuCGUCGGCCUAGc -5'
28157 3' -55.2 NC_005887.1 + 11285 0.75 0.209534
Target:  5'- uGGcgUUUCUaccucugcUCGCAGCGGCCGGcUCGg -3'
miRNA:   3'- gCCa-GAAGA--------AGCGUCGUCGGCCuAGC- -5'
28157 3' -55.2 NC_005887.1 + 33167 0.77 0.142366
Target:  5'- gCGGUgCUUCgugcaUUCGUAGCGGCCGGA-CGa -3'
miRNA:   3'- -GCCA-GAAG-----AAGCGUCGUCGGCCUaGC- -5'
28157 3' -55.2 NC_005887.1 + 4535 0.85 0.040661
Target:  5'- uCGG-CacCUUCGCGGCAGCCGGGUCGa -3'
miRNA:   3'- -GCCaGaaGAAGCGUCGUCGGCCUAGC- -5'
28157 3' -55.2 NC_005887.1 + 24902 1.1 0.000683
Target:  5'- uCGGUCUUCUUCGCAGCAGCCGGAUCGg -3'
miRNA:   3'- -GCCAGAAGAAGCGUCGUCGGCCUAGC- -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.