Table 4

Characteristics of P. tricornutum pre-miRNA sequences.

miRNA name

locationa

mfeb

lenc

P-valued

total reads and 5' homogeneitye

hairpin characteristics f


PT1

PT2

PT3

bulges

mismatched


pti-miR5471

chr_1:1604545:1604822:-

-78.8

278

0.172

0/0

9/9

0/0

0

5


pti-miR5472

chr_10:761305:761625:-

-85.9

321

0.355

64/88

23/30

145/213

0

5


pti-miR5473

chr_11:35406:35506:-

-30.4

101

0.019

6/9

0

9/15

0

4


pti-miR5474

chr_15:663006:663165:+

-42.7

160

0.801

22/23

69/71

20/22

0

6


pti-miR5475

chr_18:415320:415541:-

-62

222

0.44

0/0

226/230

383/385

0

4


pti-miR5476

chr_19:299730:299870:-

-52.8

141

0.043

0/0

0/0

9/15

0

3


pti-miR5477

chr_1:2137385:2137503:-

-26.1

119

0.025

0/0

0/0

6/9

0

6


pti-miR5478

chr_23:97534:97765:+

-76.1

232

0.029

0/0

0/0

5/7

0

4


pti-miR5479

chr_25:444580:444846:+

-79.6

267

0.1

0/0

0/0

18/19

0

4


pti-miR5480

chr_26:278601:278960:+

-105

360

0.146

0/0

0/0

6/8

0

6


pti-miR5481

chr_2:1365749:1366009:+

-70.8

261

0.213

0/0

0/0

5/5

0

4


pti-miR5482

chr_9:128204:128523:+

-101

320

0.561

0/0

0/0

5/6

0

3


pti-miR5483

chr_9:523733:524013:+

-67.6

281

0.126

0/0

0/0

10/12

0

5


aIndicated the chromosome number, start and end site and sense (+) or antisense strand (-) that the pre-miRNAs located.

bMinimum Free Energy (cal/mol) of pre-miRNAs, predicted by mfold.

clength of pre-miRNAs.

dcomputed P-values of miRNA precursors.

enumber of reads that had the same 5' end as the mature miRNA and the total number reads mapped to the precursors.

fasymmetric bulges larger than 2 nt and mismatched miRNA bases in the miRNA region.

Huang et al. BMC Genomics 2011 12:337   doi:10.1186/1471-2164-12-337

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