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Table 3 Validation of selected miRNA targets by a modified 5’RACE assay

From: Genome organization and characteristics of soybean microRNAs

miRNA

Target name and function

Target prediction

score1

             5’RACE result2

gma-miR169c

and

gma-miR169g3

Glyma10g10240

TRANSCRIPTION FACTOR NF-Y ALPHA-RELATED

0.78

5’ UAGGCAACUCAUCCUUGGCUC 3’

 |    |  |  |  |  |      |  |   |  |  |  | |  |  |  |   | |      (A/G)GCCGUUCAGUAGGAACCGA(A)

4/6

 

Glyma15g18970

TRANSCRIPTION FACTOR NF-Y ALPHA-RELATED

0.79

 5’ CAGGCAAAUCAUCCUUGGCUU 3’

      |  |  |  |  |   |  |  |  |  |  | |  |  |  |  |   |  |

(A/G)GCCGUUCAGUAGGAACCGA(A)

11/16

 

Glyma17g05920

TRANSCRIPTION FACTOR NF-Y ALPHA-RELATED

0.79

 5’ CUGGCAAAUCAUCCUUGGCUU 3’

         |   |  |  |   |    |   |  |  |   |   |  |  |  |  |  |  |  |   

(A/G)GCCGUUCAGUAGGAACCGA(A)

7/15

 

Glyma19g38800

TRANSCRIPTION FACTOR NF-Y ALPHA-RELATED

0.72;

0.78

 5’ UAGGCAAUCCAUCCUUGGCUC 3’

        |      |  |  |  |  |         |  |  |  |  |  |  |  |  |  |  |               

(A/G)GCCGUUCAGUAGGAACCGA(A)

7/15

gma-miR2118/2218a

Glyma12g03040

LRR;TIRdomain; NB-ARCdomain;Apoptotic ATPase

0.7

 5’ AUGGAACCGGUGGAAUUGGCAA 3’

               |   |  |  |          |  |  | |  |  |  |   |      |  |  |  |  |    

AUCCUUACCCACCUUAGCCGUU

14/16

 

Glyma20g06780

LRR;TIRdomain; NB-ARCdomain;Apoptotic ATPase

0.71

 5’ AUGGAACUGGUGGAAUUGGCAA 3’

          |  |  |   |      |  |  |   |  |  |   |  |       |  |  |  |  |

AUCCUUACCCACCUUAGCCGUU

3/13

  1. 1. Ratio of minimum free energy compared to perfect complementary pairing between miRNA and target.
  2. 2. Base-pairing between miRNA and its target are shown. Numbers indicate number of clones indicating cleavage at the predicted cleavage site and the number of clones sequenced.
  3. 3. miRNAs sequences are : miR169c 5’-AAGCCAAGGAUGACUUGCCGA-3’ and miR169g 5’-AGCCAAGGAUGACUUGCCGG-3’.
  4. 4. miRNA is shown in bold face.