Table 3

Potential miRNA targets found only in cotyledons at different seed developmental stages
miRNA Tissue Target Target Annotation C.Site Location Category TP100M P-Value
gma-miR171 C25 Glyma15g01820.1 Protein tyrosine kinase 1359 CDS 1 24.2379 0.0013
C300 Glyma12g08490.1 Putative methyltransferase 434 CDS 1 12.3961 0.0462
gma-miR394 C100 Glyma06g13230.3 Ferredoxin related protein 1070 CDS 1 104.088 0.027
C100 Glyma06g13230.2 Ferredoxin related protein 685 CDS 1 104.088 0.027
C100 Glyma14g25810.1 GTPase-activating protein 1013 CDS 1 57.8265 0.0035
C100 Glyma06g13230.1 Ferredoxin related protein 952 CDS 1 104.088 0.027
gma-miR398 C100 Glyma03g40280.2 Copper/Zinc superoxide dismutase 156 5' UTR 2 57.8265 0.0379
C100 Glyma03g40280.3 Copper/Zinc superoxide dismutase 156 5' UTR 2 57.8265 0.0379
gma-miR1509 C300 Glyma18g03980.2 No Functional Annotation 2155 3' UTR 0 7.43768 0.0041
gma-miR1513 C300 Glyma08g27950.1 F-box domain containing protein 190 CDS 0 29.7507 0.0402
gma-miR1514 C25 Glyma07g05360.2 No apical meristem protein 773 CDS 0 16.1586 0.0371
gma-miR1515 C300 Glyma09g02920.1 PAZ domain containing protein 2750 CDS 0 57.0223 0.003
gma-miR1531 C100 Glyma16g33400.1 Serine protease inhibitor family 536 3' UTR 3 46.2612 0.0414
gma-miR1532 C25 Glyma10g28900.1 Universal stress protein family 626 3' UTR 4 4.03965 0.015
gma-miR1535 C25 Glyma08g22920.1 Ribose 5-phosphate isomerase 168 CDS 1 60.5947 0.0242
gma-miR2109 C25 Glyma03g14900.1 LRR containing protein 46 CDS 0 88.8723 0.0165
gma-miR4357 C300 Glyma13g01500.1 Alg9-like mannosyltransferase 779 CDS 1 22.3131 0.0089
C300 Glyma01g35530.1 Transferase family protein 522 CDS 1 9.91691 0.0114
gma-miR4369 C25 Glyma19g43800.1 Calcineurin-like phosphoesterase 1257 3' UTR 4 4.03965 0.0468
gma-miR4371 C300 Glyma15g08400.4 No Functional Annotation 452 3' UTR 0 17.3546 0.0017
gma-miR4380 C300 Glyma06g10840.1 MYB family transcription factor 630 CDS 1 9.91691 0.0347
gma-miR4387 C300 Glyma08g43670.1 Uncharacterized conserved protein 1501 CDS 0 4.95846 0.0068
gma-miR4390 C100 Glyma15g06380.1 Dynamin family protein 287 CDS 3 104.088 0.0251
gma-miR4398 C25 Glyma02g25150.1 Integrase domain containing protein 199 5' UTR 4 4.03965 0.0444
gma-miR4402 C300 Glyma02g18090.1 Lectin domain containing protein 783 CDS 4 2.47923 0.0293
gma-miR4403 C300 Glyma19g36500.1 No Functional Annotation 1860 3' UTR 4 2.47923 0.0484
gma-miR4408 C25 Glyma16g34800.1 No functional annotation 434 CDS 1 68.674 0.0057
gma-miR4409 C25 Glyma16g04060.3 BTB/POZ domain containing protein 1304 3' UTR 0 12.1189 0.0144
gma-miR4415 C100 Glyma02g20490.2 Transferase family protein 502 CDS 1 57.8265 0.0463
C100 Glyma02g20490.1 Transferase family protein 502 CDS 1 57.8265 0.0463
C100 Glyma15g12430.1 Transferase family protein 464 CDS 1 57.8265 0.0463
gma-miR4416 C100 Glyma01g44970.1 BTB/POZ domain containing protein 434 CDS 0 161.914 0.0318

CDS: Coding Sequence; UTR: Untranslated Region; TP100M: Transcripts per 100 million; C.site (Cleavage site): Nucleotide number from 5’ end of cDNA; P-value ≤0.05 using Cleaveland pipeline.

Shamimuzzaman and Vodkin

Shamimuzzaman and Vodkin BMC Genomics 2012 13:310   doi:10.1186/1471-2164-13-310

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