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
28396 3' -56.7 NC_005946.1 + 61193 0.66 0.787999
Target:  5'- gGCAGgcugaGGGCCAAcGGGGGGaccgUCCUggaccccGUGGa -3'
miRNA:   3'- -UGUC-----UCCGGUU-CUCCCC----AGGA-------UACCg -5'
28396 3' -56.7 NC_005946.1 + 4626 0.66 0.769894
Target:  5'- -uGGGGGUCAcgccAGAGugcuucaucaGGGcUCCUAUGGUa -3'
miRNA:   3'- ugUCUCCGGU----UCUC----------CCC-AGGAUACCG- -5'
28396 3' -56.7 NC_005946.1 + 48034 0.66 0.769894
Target:  5'- -gGGAGGCCu-GGGuGGGcggCCUccuUGGCg -3'
miRNA:   3'- ugUCUCCGGuuCUC-CCCa--GGAu--ACCG- -5'
28396 3' -56.7 NC_005946.1 + 83879 0.67 0.730333
Target:  5'- gACAG-GGU-GAGGGGGGcCgUGUGGCc -3'
miRNA:   3'- -UGUCuCCGgUUCUCCCCaGgAUACCG- -5'
28396 3' -56.7 NC_005946.1 + 41756 0.67 0.729322
Target:  5'- gUAGAGGuCCAGGAugguGGGGUauccgucgggaccCCUggGGCc -3'
miRNA:   3'- uGUCUCC-GGUUCU----CCCCA-------------GGAuaCCG- -5'
28396 3' -56.7 NC_005946.1 + 97233 0.67 0.720193
Target:  5'- -aGGGGGCUggGGcucuGGGGUCUUG-GGUu -3'
miRNA:   3'- ugUCUCCGGuuCU----CCCCAGGAUaCCG- -5'
28396 3' -56.7 NC_005946.1 + 85151 0.68 0.699686
Target:  5'- -uGGuuGGCCAgaaAGAGGGcUCCgaUGUGGCg -3'
miRNA:   3'- ugUCu-CCGGU---UCUCCCcAGG--AUACCG- -5'
28396 3' -56.7 NC_005946.1 + 71830 0.68 0.689337
Target:  5'- cCAGAGGaCGGGAGGaGGUCCcgcgGGa -3'
miRNA:   3'- uGUCUCCgGUUCUCC-CCAGGaua-CCg -5'
28396 3' -56.7 NC_005946.1 + 13645 0.68 0.689337
Target:  5'- uGCGGAGGCCAGGAacccgagucaGGUCaggaggAUGGCc -3'
miRNA:   3'- -UGUCUCCGGUUCUcc--------CCAGga----UACCG- -5'
28396 3' -56.7 NC_005946.1 + 41668 0.68 0.6883
Target:  5'- cACGG-GGCCAGucGGacacaguGGUCCUAUGGg -3'
miRNA:   3'- -UGUCuCCGGUUcuCC-------CCAGGAUACCg -5'
28396 3' -56.7 NC_005946.1 + 16389 0.68 0.678939
Target:  5'- -aAGAGGCgCAGGGGccaGGUCUUuggaGUGGCg -3'
miRNA:   3'- ugUCUCCG-GUUCUCc--CCAGGA----UACCG- -5'
28396 3' -56.7 NC_005946.1 + 57576 0.68 0.678939
Target:  5'- uCAGAGGCCAAGAGGaGGaCaaaggauUGGa -3'
miRNA:   3'- uGUCUCCGGUUCUCC-CCaGgau----ACCg -5'
28396 3' -56.7 NC_005946.1 + 83009 0.68 0.6685
Target:  5'- cCGGAGGCaCGGcGAGGGGagUCCac-GGCa -3'
miRNA:   3'- uGUCUCCG-GUU-CUCCCC--AGGauaCCG- -5'
28396 3' -56.7 NC_005946.1 + 29734 0.69 0.626523
Target:  5'- gACAGAGGCgGuca-GGGUCCUgguGUGGUu -3'
miRNA:   3'- -UGUCUCCGgUucucCCCAGGA---UACCG- -5'
28396 3' -56.7 NC_005946.1 + 72723 0.69 0.60448
Target:  5'- uGCGGGGuCCGcguccguggacguGGAcGGGGUCCUGUgcGGCg -3'
miRNA:   3'- -UGUCUCcGGU-------------UCU-CCCCAGGAUA--CCG- -5'
28396 3' -56.7 NC_005946.1 + 76417 0.7 0.584615
Target:  5'- gACGGuuuGGCCGgaauGAGGGG-CCUAgaGGCc -3'
miRNA:   3'- -UGUCu--CCGGUu---CUCCCCaGGAUa-CCG- -5'
28396 3' -56.7 NC_005946.1 + 70123 0.7 0.563846
Target:  5'- aGCGGuGGUCAGGAGcuGGUCCaGUGGa -3'
miRNA:   3'- -UGUCuCCGGUUCUCc-CCAGGaUACCg -5'
28396 3' -56.7 NC_005946.1 + 98058 0.73 0.382576
Target:  5'- uCGGAGGCCAcGAuGGGGcugauugccCCUGUGGUg -3'
miRNA:   3'- uGUCUCCGGUuCU-CCCCa--------GGAUACCG- -5'
28396 3' -56.7 NC_005946.1 + 66539 0.75 0.298968
Target:  5'- uGCAGAGGCUcaaccccaagggcGAGAGcguguggacccaucuGGGUCCUgacGUGGCg -3'
miRNA:   3'- -UGUCUCCGG-------------UUCUC---------------CCCAGGA---UACCG- -5'
28396 3' -56.7 NC_005946.1 + 19674 0.76 0.250494
Target:  5'- -gGGAGGCCGAGAGGG--CCUcgGGUc -3'
miRNA:   3'- ugUCUCCGGUUCUCCCcaGGAuaCCG- -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.