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
17006 3' -55.3 NC_004333.2 + 39255 0.66 0.676486
Target:  5'- cCCCGAgcGGCCggcaggcgcacgcgcGCGCGAUCGcaGGUUGGc -3'
miRNA:   3'- -GGGCUa-CCGG---------------CGUGUUAGC--UCGACUu -5'
17006 3' -55.3 NC_004333.2 + 38826 0.66 0.672039
Target:  5'- gCCCGAc-GCCGCGCGccgacgaCGAGCaUGAAa -3'
miRNA:   3'- -GGGCUacCGGCGUGUua-----GCUCG-ACUU- -5'
17006 3' -55.3 NC_004333.2 + 40124 0.66 0.672039
Target:  5'- cCCCGAUgaaGGCCGC-CGAgcucgucggCGAGUcGAAg -3'
miRNA:   3'- -GGGCUA---CCGGCGuGUUa--------GCUCGaCUU- -5'
17006 3' -55.3 NC_004333.2 + 14882 0.66 0.660897
Target:  5'- gCUCGAUgcGGCCGaCGCAAcgcgcgcgcUCG-GCUGAAc -3'
miRNA:   3'- -GGGCUA--CCGGC-GUGUU---------AGCuCGACUU- -5'
17006 3' -55.3 NC_004333.2 + 37976 0.66 0.649726
Target:  5'- gCCGAcGGCCGCAUGcgCGuGCg--- -3'
miRNA:   3'- gGGCUaCCGGCGUGUuaGCuCGacuu -5'
17006 3' -55.3 NC_004333.2 + 17558 0.66 0.63854
Target:  5'- cCCCGAaGcGCUGCACGA-CGAcCUGAu -3'
miRNA:   3'- -GGGCUaC-CGGCGUGUUaGCUcGACUu -5'
17006 3' -55.3 NC_004333.2 + 37104 0.67 0.603869
Target:  5'- uCCCGGaaugGGCCGCACGcccggcgGUCGAGa---- -3'
miRNA:   3'- -GGGCUa---CCGGCGUGU-------UAGCUCgacuu -5'
17006 3' -55.3 NC_004333.2 + 41309 0.67 0.571644
Target:  5'- gCUCGAUGGCUGCGCAAUgcaGuGCg--- -3'
miRNA:   3'- -GGGCUACCGGCGUGUUAg--CuCGacuu -5'
17006 3' -55.3 NC_004333.2 + 33869 0.67 0.571644
Target:  5'- -aCGGU-GCCGCGCuGAUCGAcauGCUGAAg -3'
miRNA:   3'- ggGCUAcCGGCGUG-UUAGCU---CGACUU- -5'
17006 3' -55.3 NC_004333.2 + 19517 0.68 0.527941
Target:  5'- gCUCG-UGGCCGUauggGCAAUCGuucgcaAGCUGAu -3'
miRNA:   3'- -GGGCuACCGGCG----UGUUAGC------UCGACUu -5'
17006 3' -55.3 NC_004333.2 + 45921 0.68 0.517201
Target:  5'- gCCGAgcUGGCCGCguugcgcgagaaGCAgcucGUCGAGCgGAu -3'
miRNA:   3'- gGGCU--ACCGGCG------------UGU----UAGCUCGaCUu -5'
17006 3' -55.3 NC_004333.2 + 42505 0.69 0.475188
Target:  5'- cCCUGcacAUGGCCGCA--GUCGAGUcGAAg -3'
miRNA:   3'- -GGGC---UACCGGCGUguUAGCUCGaCUU- -5'
17006 3' -55.3 NC_004333.2 + 8928 0.69 0.453822
Target:  5'- gCCUGccGGCCGCucgggguGCGGUCGAGCa--- -3'
miRNA:   3'- -GGGCuaCCGGCG-------UGUUAGCUCGacuu -5'
17006 3' -55.3 NC_004333.2 + 41534 0.7 0.434948
Target:  5'- gCCGAgcgcgcuGCCgaGCGCGAUCGAGUUGAu -3'
miRNA:   3'- gGGCUac-----CGG--CGUGUUAGCUCGACUu -5'
17006 3' -55.3 NC_004333.2 + 45164 0.7 0.425198
Target:  5'- gCCCGAuacUGGCCGCGCuu----GCUGAu -3'
miRNA:   3'- -GGGCU---ACCGGCGUGuuagcuCGACUu -5'
17006 3' -55.3 NC_004333.2 + 18899 0.71 0.378478
Target:  5'- aUCGAaGGCCGCcuguuugugGCGAUCGAGCUa-- -3'
miRNA:   3'- gGGCUaCCGGCG---------UGUUAGCUCGAcuu -5'
17006 3' -55.3 NC_004333.2 + 6856 0.71 0.355585
Target:  5'- aCCGgcGGCUGCGCAcugcauugcgcagccAUCGAGCgGAu -3'
miRNA:   3'- gGGCuaCCGGCGUGU---------------UAGCUCGaCUu -5'
17006 3' -55.3 NC_004333.2 + 19197 0.71 0.342827
Target:  5'- aCCCGgcGGCCGCGCAAcugaucgccgcguUCGAccGCgUGAAc -3'
miRNA:   3'- -GGGCuaCCGGCGUGUU-------------AGCU--CG-ACUU- -5'
17006 3' -55.3 NC_004333.2 + 3625 0.73 0.267009
Target:  5'- gCCUGcgGGCCGUAgCAGUCGAcCUGAu -3'
miRNA:   3'- -GGGCuaCCGGCGU-GUUAGCUcGACUu -5'
17006 3' -55.3 NC_004333.2 + 36373 0.74 0.233541
Target:  5'- gCUGAUGGCCGCGucguacuugcgcuCAAUCGAGCg--- -3'
miRNA:   3'- gGGCUACCGGCGU-------------GUUAGCUCGacuu -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.