Table 3

Validation of miRNAs identified by parameterized miRDeep.

miRNA Family

miRNA name

Confirmation by RACE

Seedling RPM

If identified by parameterized miRDeep

Reads aligned

Star (count)


miR156

zma-MIR156d

14111.2

5932

1


miR156

zma-MIR156l

12645.91

1659

1


miR160

zma-MIR160b

292.65

miRNA overlapping with CDS


miR162

zma-MIR162

2.74

poor abundance of reads


miR166

zma-MIR166d

314.6

328

1


miR166

zma-MIR166k

6.52

miRNA homologous to CDS


miR166

zma-MIR166m

49.75

miRNA homologous to CDS


miR167

zma-MIR167b

2860.25

17402

1


miR167

zma-MIR167c

2872.95

72684

0


miR168

zma-MIR168a

10364.43

32179

1


miR169

zma-MIR169f

1234.4

3371

0


miR171

zma-MIR171f

15483.87

78

1


miR171

zma-MIR171m

4.12

508

1


miR172

zma-MIR172b

134.49

81

1


miR390

zma-MIR390b

2220.41

6504

1


miR394

zma-MIR394a

4.46

MiRNA overlapping with CDS


miR396

zma-MIR396f

849.46

2503

1


miR396

zma-MIR396g

43.23

miRNA homologous to CDS


miR397

zma-MIR397b

556.13

1628

1


miR399

zma-MIR399h

43.23

129

1


miR399

zma-MIR399i

90.57

272

0


miR529

zma-MIR529

359.2

1050

1


miR827

zma-MIR827

711.89

miRNA overlapping with CDS


Unclassified

?

-

334

0


The candidates were compared against a recently discovered set of miRNAs, from chromosome 5 of maize, expressed in seedlings [14]. The data in third and fourth columns are from [14], while those in last two columns are from current study. The cases missed out by parameterized miRDeep appeared mainly due to a filter which discarded reads mapped to coding sequences (CDS). Even chance homology of a miRNA, either complete or at least in mature/star region, to any CDS can result into the miRNA being unidentified. RPM: Reads Per Million.

Thakur et al. BMC Genomics 2011 12:108   doi:10.1186/1471-2164-12-108

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