Addendum - Detection of miR395-target pairs by findMiRNA

In our publication 'Computational Prediction of miRNAs in Arabidopsis thaliana', it is stated that the transcripts of APS1 and APS3 were not identified as targets by the findMiRNA algorithm. The reason given was the existence of a relatively even spacing of mismatches (including GU pairs) between the miRNA and the target transcript. This explanation is still valid, however it turns out that findMiRNA did successfully identify the miRNA-target pairs miR395-APS1 and miR395-APS3 for three of the six MIR395 loci (MIR395a, MIR395d and MIR395e). The miRNA-target pairs that were not identified by findMiRNA due to the even spacing of mismatches (i.e. ':' and 'O') are indicated below.


miRNA
loci		Target transcripts
APS1 (At3g22890)APS3 (At4g14680)APS4 (At5g43780)Sultr2;1 (At5g10180)
MIR395a 
target: 5'-3'

miRNA:  3'-5'
 
 GAGUUCCUCCAAACUCUUCA
 |||||||O||||||:|||||
 CUCAAGGGGGUUUGUGAAGU
 
 GAGUUCCUCCAAACUCUUCA
 |||||||O||||||:|||||
 CUCAAGGGGGUUUGUGAAGU
 
 GAGUUCCUCCAAACACUUCA
 |||||||O||||||||||||
 CUCAAGGGGGUUUGUGAAGU
 
AGUUCUCCCAAACACUUCA
|||||O|||||||||||||
UCAAGGGGGUUUGUGAAGU
MIR395b 
target: 5'-3'

miRNA:  3'-5'
 
CGAGUUCCUCCAAACUCUUCAU
:||||O||O||||||:|||||:
UCUCAGGGGGGUUUGUGAAGUC
 
UGAGUUCCUCCAAACUCUUCAU
:||||O||O||||||:|||||:
UCUCAGGGGGGUUUGUGAAGUC
 
AGAGUUCCUCCAAACACUUCA
|||||O||O||||||||||||
UCUCAGGGGGGUUUGUGAAGU
 
AGUUCUCCCAAACACUUCA
|||O|O|||||||||||||
UCAGGGGGGUUUGUGAAGU
MIR395c 
target: 5'-3'

miRNA:  3'-5'
 
CGAGUUCCUCCAAACUCUUCAU
:||||O||O||||||:|||||:
UCUCAGGGGGGUUUGUGAAGUC
 
UGAGUUCCUCCAAACUCUUCAU
:||||O||O||||||:|||||:
UCUCAGGGGGGUUUGUGAAGUC
 
AGAGUUCCUCCAAACACUUCA
|||||O||O||||||||||||
UCUCAGGGGGGUUUGUGAAGU
 
AGUUCUCCCAAACACUUCA
|||O|O|||||||||||||
UCAGGGGGGUUUGUGAAGU
MIR395d 
target: 5'-3'

miRNA:  3'-5'
 
 GAGUUCCUCCAAACUCUUCA
 |||||||O||||||:|||||
 CUCAAGGGGGUUUGUGAAGU
 
 GAGUUCCUCCAAACUCUUCA
 |||||||O||||||:|||||
 CUCAAGGGGGUUUGUGAAGU
 
 GAGUUCCUCCAAACACUUCA
 |||||||O||||||||||||
 CUCAAGGGGGUUUGUGAAGU
 
AGUUCUCCCAAACACUUCA
|||||O|||||||||||||
UCAAGGGGGUUUGUGAAGU
MIR395e 
target: 5'-3'

miRNA:  3'-5'
 
 GAGUUCCUCCAAACUCUUCA
 |||||||O||||||:|||||
 CUCAAGGGGGUUUGUGAAGU
 
 GAGUUCCUCCAAACUCUUCA
 |||||||O||||||:|||||
 CUCAAGGGGGUUUGUGAAGU
 
 GAGUUCCUCCAAACACUUCA
 |||||||O||||||||||||
 CUCAAGGGGGUUUGUGAAGU
 
AGUUCUCCCAAACACUUCA
|||||O|||||||||||||
UCAAGGGGGUUUGUGAAGU
MIR395f 
target: 5'-3'

miRNA:  3'-5'

CGAGUUCCUCCAAACUCUUCAU
:||||O||O||||||:|||||:
UCUCAGGGGGGUUUGUGAAGUC

UGAGUUCCUCCAAACUCUUCAU
:||||O||O||||||:|||||:
UCUCAGGGGGGUUUGUGAAGUC

AGAGUUCCUCCAAACACUUCA
|||||O||O||||||||||||
UCUCAGGGGGGUUUGUGAAGU

AGUUCUCCCAAACACUUCA
|||O|O|||||||||||||
UCAGGGGGGUUUGUGAAGU