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Table 1 Gene structure and transcriptional activity

From: RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome

 

first exon

%GC

internal exons

%GC

last exon

%GC

# of exons

total exon length

# of genes

a) All

314 ± 386

44% ± 8%

180 ± 172

42% ± 5%

246 ± 299

44% ± 8%

5.0 ± 5.1

1006 ± 987

66210

b) Expressed

351 ± 418

45% ± 8%

190 ± 178

43% ± 4%

267 ± 315

45% ± 8%

5.5 ± 5.6

1164 ± 1036

49151

c) Not Expressed

207 ± 247

41% ± 8%

141 ± 142

40% ± 6%

170 ± 218

40% ± 7%

3.4 ± 2.8

550.0 ± 638.8

17059

d) Confident

374 ± 438

45% ± 8%

197 ± 185

43% ± 4%

279 ± 328

45% ±7%

5.8 ± 5.7

1263 ± 1062

46430

e) Not Confident

172 ± 141

41% ± 8%

114 ± 77

40% ± 7%

135 ± 117

41% ± 8%

3.0 ± 2.5

403 ± 308

19780

f) Not Expressed, Not Confident

165 ± 129

40% ± 8%

110 ± 73

39% ± 7%

132 ± 108

40% ± 7%

3.0 ± 2.5

395 ± 283

12604

  1. a) All - All 66,210 predicted genes.
  2. b) Expressed - The subset of the predicted genes that were transcriptionally active according to our definition: total of two counts in one or more tissues.
  3. c) Not Expressed - The subset of the predicted gens that were not transcriptionally active according to our definition.
  4. d) Confident - The subset of genes that were identified in the final draft of the soybean genome as highly-confident.
  5. e) Not Confident - The subset of genes that were not identified in the final draft of the soybean genome as highly-confident.
  6. f) Not Expressed, Not Confident - The subset of genes that comprise the intersection of c and d: the genes are neither expressed or highly-confident.
  7. Relationship between exon length, percent GC content and transcriptional activity for three classes of exons: the first exon (first), the internal exons (internal) and last exon (last). The total number of genes in each group and the total exon length is also indicated.