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Table 4 Less-conserved soybean miRNAs in four small RNA libraries

From: Genome-wide identification of soybean microRNAs and their targets reveals their organ-specificity and responses to phosphate starvation

miRNA

Sequence (5’ to 3’)

Size (nt)

Ch

Start:End (+/-)

Arm

TPM in HPL

TPM in LPL

TPM in HPR

TPM in LPR

Registered in

          

miRBase or not

MIR1507

miR1507a

TCTCATTCCATACATCGTCTGA

22

13

25849776:25849883:+

3

93418

6787

2 73567

59118

Yes

MIR1508

miR1508d

TAGAAAGGGAAATAGCAGTTG

21

9

28530172:28530267:+

3

6600

7129

1596

1456

No

miR1508e

CTAGAAAGGGAAATAGCAGTTG

22

16

32903737:32903831:+

3

1347

1516

374

317

No

MIR1509

miR1509a

TTAATCAAGGAAATCACGGTCG

22

17

10099759:10099871:+

5

7221

8003

21070

17929

Yes

miR1509c

TTAATCAAGGAAATCACGGTTG

22

5

7774098:7774206: −

5

316

531

2125

2125

No

miR1509d

TTAATCAAGGAAATCACGGTC

21

17

10099759:10099871:+

5

45

50

130

117

No

MIR1510

miR1510b-3p

TGTTGTTTTACCTATTCCACC

21

2

6599300:6599391:+

3

75

125

139

162

Yes

miR1510b-5p

AGGGATAGGTAAAACAACTACT

22

2

6599292:6599401:+

5

1462

3478

968

1980

Yes

miR1510c

AGGGATAGGTAAAACAACTAC

21

2

6599292:6599401:+

5

750

851

697

1377

No

miR1510d

AGGGATAGGTAAAACAATGAC

21

16

31518900:31519009:+

5

136

266

245

822

No

MIR2109

miR2109a

TGCGAGTGTCTTCGCCTCTGA

21

4

28532444:28532532: −

5

50

6

181

220

No

MIR3522

miR3522a

TGAGACCAAATGAGCAGCTGAC

22

15

4318787:4318887:+

5

139

115

7

0.01

No

Family undefined

miR1511

AACCAGGCTCTGATACCATGG

21

18

21161229:21161335:+

3

1099

1034

5415

8419

Yes

miR1511a

AACCAGGCTCTGATACCATGGT

22

18

21161229:21161335:+

3

31

28

77

113

No

miR1512b

TAACTGGAAATTCTTAAAGCAT

22

2

8618690:8618783: −

5

0.01

8

72

102

No

miR3508

TAGAAGCTCCCCATGTTCTCA

21

15

5418778:5418967:+

3

75

355

120

104

No

miR4345

TAAGACGGAACTTACAAAGATT

22

14

49067429:49067781:+

5

77

92

151

139

Yes

miR4345a

TTAAGACGGAACTTACAAAGATT

23

14

49067429:49067781:+

5

131

158

314

260

No

miR4345b

CTAAGACGGAACTTACAAAGAT

22

14

49069094:49069198:+

5

127

141

0.01

0.01

No

miR4376-5p

TACGCAGGAGAGATGACGCTGT

22

13

40845924:40846035:+

5

250

154

0.01

0.01

Yes

miR4376a

ACGCAGGAGAGATGACGCTGT

21

13

40845924:40846035:+

5

352

155

0.01

0.01

No

miR4376b

TACGCAGGAGAGATGACGCTG

21

13

40845924:40846035:+

5

358

216

0.01

0.01

No

miR4413c

TAAGAGAATTGTAAGTCACTG

21

19

1788521:1788616: −

5

46

65

120

119

No

miR4416a

ACGGGTCGCTCTCACCTGGAG

21

2

30498955:30499126: −

3

0.01

11

123

158

No

miR4416b

ATACGGGTCGCTCTCACCTAGG

22

19

40699080:40699213: −

3

8

16

95

139

No

  1. Soybean less-conserved miRNAs were grouped into miRNA families based on Blast analysis of mature miRNA sequences in miRBase 18.0 (http://www.mirbase.org). For less-conserved miRNAs, homology of which can only be found in legume (legume-specific).
  2. Ch, chromosome; HPL, leaf+Pi; HPR, root+Pi; LPL, leaf-Pi; LPR, root-Pi; nt, nucleotide; TPM, transcript per million reads; +, sense strand; −, antisense strand.
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BMC Genomics

ISSN: 1471-2164

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