miRNA display CGI


Results 1 - 20 of 21 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
1193 3' -43.2 NC_001132.2 + 133204 0.66 1
Target:  5'- aGUA---GUAUGUAgacGACGCCGUccGCGAa -3'
miRNA:   3'- gCAUguaUAUGCAU---UUGUGGCA--UGCU- -5'
1193 3' -43.2 NC_001132.2 + 45684 0.66 1
Target:  5'- uCGUACAcAUGCGUc-GCGuuCCGUACa- -3'
miRNA:   3'- -GCAUGUaUAUGCAuuUGU--GGCAUGcu -5'
1193 3' -43.2 NC_001132.2 + 70018 0.66 1
Target:  5'- uGUACA---ACGUAGACGgCGUAUc- -3'
miRNA:   3'- gCAUGUauaUGCAUUUGUgGCAUGcu -5'
1193 3' -43.2 NC_001132.2 + 81465 0.66 1
Target:  5'- aCGUACGUcuaACGUuAAC-UCGUGCGGu -3'
miRNA:   3'- -GCAUGUAua-UGCAuUUGuGGCAUGCU- -5'
1193 3' -43.2 NC_001132.2 + 148269 0.67 1
Target:  5'- aCGUuuACGUA-ACGUAGACGggUCGUGCGc -3'
miRNA:   3'- -GCA--UGUAUaUGCAUUUGU--GGCAUGCu -5'
1193 3' -43.2 NC_001132.2 + 46187 0.67 1
Target:  5'- gCGUAUGUAUGCGccGACGCCuuuuuGUGgGAu -3'
miRNA:   3'- -GCAUGUAUAUGCauUUGUGG-----CAUgCU- -5'
1193 3' -43.2 NC_001132.2 + 88155 0.66 1
Target:  5'- uGUACGUGUACauuaAAACuCCGUuCGAu -3'
miRNA:   3'- gCAUGUAUAUGca--UUUGuGGCAuGCU- -5'
1193 3' -43.2 NC_001132.2 + 28270 0.68 0.999999
Target:  5'- aCGUugGCGUGUACGcGAAUAUCGUGuuUGAa -3'
miRNA:   3'- -GCA--UGUAUAUGCaUUUGUGGCAU--GCU- -5'
1193 3' -43.2 NC_001132.2 + 141734 0.68 0.999998
Target:  5'- ---cUAUGUGCGUGguuuAACGCgGUGCGGa -3'
miRNA:   3'- gcauGUAUAUGCAU----UUGUGgCAUGCU- -5'
1193 3' -43.2 NC_001132.2 + 15799 0.69 0.999998
Target:  5'- cCGUACGcgGUGgGUAuaAACACuCGUACGu -3'
miRNA:   3'- -GCAUGUa-UAUgCAU--UUGUG-GCAUGCu -5'
1193 3' -43.2 NC_001132.2 + 34750 0.69 0.999995
Target:  5'- --gGCGUGUACGgaGACACCG-ACu- -3'
miRNA:   3'- gcaUGUAUAUGCauUUGUGGCaUGcu -5'
1193 3' -43.2 NC_001132.2 + 42534 0.69 0.999995
Target:  5'- aCGUGCGg--ACGUu--CGCCGUACc- -3'
miRNA:   3'- -GCAUGUauaUGCAuuuGUGGCAUGcu -5'
1193 3' -43.2 NC_001132.2 + 96258 0.69 0.999993
Target:  5'- aCGaGCGuUAUACuu-AACGCCGUACGGg -3'
miRNA:   3'- -GCaUGU-AUAUGcauUUGUGGCAUGCU- -5'
1193 3' -43.2 NC_001132.2 + 12517 0.71 0.999948
Target:  5'- aCGUACA--UACGUAAacGCGCCauagGCGAu -3'
miRNA:   3'- -GCAUGUauAUGCAUU--UGUGGca--UGCU- -5'
1193 3' -43.2 NC_001132.2 + 129759 0.71 0.999908
Target:  5'- aUGUAgAaagGCGUGGAC-CCGUACGGa -3'
miRNA:   3'- -GCAUgUauaUGCAUUUGuGGCAUGCU- -5'
1193 3' -43.2 NC_001132.2 + 107086 0.72 0.999795
Target:  5'- --cACGUAUcCGUcGAACGCUGUGCGGa -3'
miRNA:   3'- gcaUGUAUAuGCA-UUUGUGGCAUGCU- -5'
1193 3' -43.2 NC_001132.2 + 47848 0.72 0.999737
Target:  5'- gCG-ACGUc--CGUAGACGCCGUACGc -3'
miRNA:   3'- -GCaUGUAuauGCAUUUGUGGCAUGCu -5'
1193 3' -43.2 NC_001132.2 + 2057 0.75 0.995572
Target:  5'- gGUGCGUcgAgGgaGACGCCGUGCGu -3'
miRNA:   3'- gCAUGUAuaUgCauUUGUGGCAUGCu -5'
1193 3' -43.2 NC_001132.2 + 2771 0.78 0.979733
Target:  5'- gCGUGCGUAUACGggGGCGgugccCCGUAUGGc -3'
miRNA:   3'- -GCAUGUAUAUGCauUUGU-----GGCAUGCU- -5'
1193 3' -43.2 NC_001132.2 + 154046 0.79 0.961519
Target:  5'- uGUACAUGUaGCG-GAGCACgGUGCGAa -3'
miRNA:   3'- gCAUGUAUA-UGCaUUUGUGgCAUGCU- -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.