Table 4

Potential miRNAs and their targets found only in seed coats at different developmental stages
miRNA Tissue Target Target Annotation C.Site Location Category TP100M P-Value
gma-miR319 SC100 Glyma12g33640.1 TCP family transcription factor 740 CDS 0 106.396 0.0231
SC100 Glyma15g09910.1 TCP family transcription factor 959 CDS 0 69.5668 0.0121
gma-miR393 SC100 Glyma19g27280.1 LRR containing protein 2207 CDS 2 20.4608 0.032
SC100 Glyma03g36770.1 LRR containing protein 1750 CDS 3 167.779 0.031
SC100 Glyma16g05500.1 LRR containing protein 2279 CDS 3 20.4608 0.0132
SC100 Glyma19g39420.1 LRR containing protein 1751 CDS 3 167.779 0.031
gma-miR1508 SC100 Glyma13g35890.1 EF-hand containing protein 517 3' UTR 1 8.18433 0.0385
gma-miR1518 SC100 Glyma15g12180.1 Ubiquitin-protein ligase 273 CDS 1 16.3687 0.02
gma-miR1523 SC25 Glyma20g02470.1 LRR containg protein 407 CDS 1 5.26902 0.0419
gma-miR1526 SC100 Glyma08g09640.1 No Functional Annotation 424 CDS 0 163.687 0.048
SC100 Glyma08g09640.2 No Functional Annotation 424 CDS 0 163.687 0.048
gma-miR2119 SC100 Glyma14g24860.1 Alcohol dehydrogenase 99 CDS 2 2488.04 0.0462
gma-miR4374 SC100 Glyma01g36660.1 Ankyrin repeat containing protein 2124 3' UTR 1 8.18433 0.009
gma-miR4377 SC25 Glyma06g04910.1 Cyclin family protein 910 CDS 4 2.63451 0.0297
gma-miR4399 SC100 Glyma17g34370.1 No functional annotation 637 3' UTR 4 4.09216 0.0491
gma-miR4406 SC25 Glyma03g17300.1 Glyoxal oxidase related protein 1489 CDS 0 73.7663 0.0082
gma-miR4407 SC100 Glyma08g15670.1 Peptide transporter family protein 1078 CDS 1 1076.24 0.0159
SC100 Glyma05g04810.1 Peptide transporter family protein 918 CDS 1 1076.24 0.0159

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.

* and bold is miRNA whose target is shown in the target plot (t-plot) (Figure 1).

Shamimuzzaman and Vodkin

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

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