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Table 3 Predicted Brachypodium miRNAs that are responsive to cold stress.

From: Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response

Name

Sequence (5'-3')

L (nt)

Arm/nt

N

Location in the genome

AMFE

(kcal mol-1)

CD

NC/WC

miR901T

UAUGCCAUGUCGUCACAUAUC

21

5'/104

1

super_0:10573853-10573873

-63.46

3/24

miR902T

UAGAUCUUUAAAUAAACGGAUG

22

5'/174

1

super_1:13020674-13020695

-49.71

4/22

miR903T

GGGGAAAAGAGAUUGAGGGAG

21

3'/92

1

super_0:36361618-36361638

-69.34

6/31

miR904T

UGUUCAUACGGUUGAUAGCAC

21

3'/144

1

super_11:5086279-5086299

-47.71

3/22

miR905T

UUCUUUGACCGAGCCUUUGAC

21

5'/140

1

super_4:26389353-26389373

-38.71

7/39

miR906T

UGGACUGCAGGUUUAUUUCGG

21

3'/116

1

super_10:314839-314859

-41.15

4/23

miR910T

UGUAGAUACUCUCUAAGGCUU

21

3'/87

1

super_1:8100215-8100235

-54.13

28/5

miR911T

AAGAAUUUAGGGACGGAGGGA

21

3'/86

2

super_277:408-428

-70.01

35/4

   

3'/88

 

super_2:20949532-20949552

-45.00

 

miR912T

ACUGGAUGGCACGGGAGCUAC

21

3'/103

1

super_4:17219372-17219392

-39.22

67/7

miR913T

UUUGAACUAAGAAGGGUCAAA

21

3'/128

3

super_1:16079568-16079588

-44.14

43/5

   

3'/131

 

super_3:15856277-15856297

-50.91

 
   

3/132

 

super_7:14469193-14469213

-57.34

 

miR914T

UUGAGCUAAGGAGGGUUGGAG

21

3'/100

1

super_11:2194743-2194763

-52.60

37/6

miR915T

UUGAACUAAGGAGGGUCAAUG

21

3'/103

1

super_0:16172946-16172966

-71.94

29/5

miR916T

AGGGCGAGGCAAAUGAUCAAA

21

3'/90

1

super_4:13613574-13613594

-66.22

33/6

miR917T

ACUUAUUUCGGGACGGAGGGC

21

3'/88

1

super_10: 6143242-6143262

-58.75

34/6

miR918T

AAAAUCGAGUAGCAGUCCGCG

21

3'/184

1

super_4:2249267-2249287

-40.59

41/5

miR919T

AAAAUCGAGUAGCAGCCCGUG

21

3'/185

1

super_1:24396584-24396604

-58.75

144/28

miR920T

AUCUUGGGCUCUAGGUAGGUU

21

5'/170

1

super_7:15735308-15735328

-58.58

25/5

miR921T

UUUCGGCUUCUAGGACCGGCU

21

5'/203

1

super_5:18782230-18782250

-54.33

15/3

miR922T

ACUUGUUUUGGGACGGAGGGA

21

3'/88

1

super_1: 22691473-22691493

-75.91

22/4

miR923T

UUAGGUGCUUUCGGCUUUGGC

21

5'/116

1

super_0:7108639-7108659

-57.16

32/6

miR924T

AGUAAUAUGUGUCGGAGGGGG

21

3'/100

1

super_5:7860249-7860269

-58.20

32/5

miR925T

UUACGUGAGUUAAAUCGUCGA

21

3'/100

1

super_0:9973530-9973550

-64.40

16/3

miR926T

AAGAAUUUAGGAAUGGAGGGA

21

3'/86

1

super_1:26695542-26695562

-45.58

36/6

miR927T

AGAAUUUAGGGAAGGAGGGAU

21

3'/88

1

super_0:27230875-27230895

-56.93

37/7

miR928T

ACUUAUUAUGGACCGGAGGGA

21

3'/71

1

super_3:10319482-10319502

-53.80

24/3

  1. Name, the name of predicted cold-responsive Brachypodium miRNAs and underlines denote miRNAs whose miRNA* have been detected in Solexa sequencing analysis; Sequence, sequence cloned in small RNA libraries; L, the length of miRNA; Arm/nt, the miRNA location in the predicted hairpin structure (5' or 3' arm)/the length of the precursor; N, number of loci in the genome; Location, miRNA location in the genome; AMFE, the adjusted minimum free energy (MFE) representing the MFE of 100 nucleotides, it is calculated by (MFE ÷ length of miRNA precursor sequence)× 100; CD, the effect of cold-treatment on miRNA expression, NC/WC, normalized sequencing frequencies in the NC and WC library.
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BMC Genomics

ISSN: 1471-2164

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