Table 4

Intron and exon lengths for controls and splice variants

Kingdom

Intron density*

Genome assembly size (Mb)

Average intron length

Average RI length§¶

Average intron length next to CE¥

No. of CEs with unambiguous boundaries#

% introns >200 bp**

Average exon length¶††

Average internal exon length¶‡‡

Average CE length§§


D. rerio

Animal

7.2

1,547

2,940

130

3,485

903

71%

180

132

113

T. rubripes

Animal

8.1

393

582

126

641

22

45%

140

119

103

B. floridae

Animal

5.7

923

1,283

115

1,424

135

91%

151

124

111

C. savignyi

Animal

9.1

164

710

87

595

20

82%

148

130

123

C. intestinalis

Animal

7.4

117

457

152

544

327

76%

181

143

122

N. vectensis

Animal

4.1

357

823

167

820

26

79%

165

110

90

S. purpuratus

Animal

907

1,819

176

2,085

40

99%

174

141

133

D. melanogaster

Animal

3.9

120

829

90

1,632

218

25%

279

246

167

A. aegypti

Animal

3.1

1,384

4,614

106

7,752

112

42%

309

252

204

A. gambiae

Animal

3.2

278

1,154

110

2,905

83

26%

286

236

181

A. mellifera

Animal

5.4

454

1,171

107

2,969

98

40%

195

172

153

C. elegans

Animal

5.5

100

259

84

497

176

30%

189

181

151

S. mansoni

Animal

4.8

381

2,222

42

2,387

127

77%

179

167

130

R. oryzae

Fungi

2.3

46

58

66

-

0

1%

201

161

-

C. neoformans

Fungi

5.4

19

64

67

95

8

5%

228

179

56

U. maydis

Fungi

0.8

20

168

134

288

5

18%

256

143

52

S. pombe

Fungi

1.3

13

108

58

-

0

14%

309

102

-

S. cerevisiae

Fungi

0.1

12

241

244

-

0

49%

596

46

-

N. crassa

Fungi

1.8

39

115

126

171

2

11%

206

142

78

M. grisea

Fungi

1.7

42

109

110

103

5

7%

238

160

64

S. nodorum

Fungi

1.7

37

70

82

88

2

3%

257

178

17

A. flavus

Fungi

2.3

40

76

76

76

1

2%

249

161

90

A. nidulans

Fungi

2.8

30

74

87

78

1

2%

204

151

8

H. capsulatum

Fungi

2.5

33

112

114

114

1

8%

227

155

25

C. posadasii

Fungi

2.2

27

80

87

137

10

2%

395

289

81

C. immitis

Fungi

2.5

29

80

83

89

3

2%

349

244

54

S. sclerotiorum

Fungi

1.8

38

84

98

71

7

5%

316

213

56

D. discoideum

Protist

1.3

34

145

107

252

3

13%

265

231

110

P. trichocarpa

Plant

3.1

308

431

140

637

80

50%

204

125

103

A. thaliana

Plant

4.9

119

180

118

242

138

23%

201

143

101

O. sativa

Plant

4.4

371

462

134

725

299

46%

212

135

116

P. patens

Plant

3.8

480

295

188

394

188

57%

220

137

113

C. reinhardtii

Plant

7

118

264

148

376

30

56%

172

121

103

O. lucimarinus

Plant

0.5

13

157

97

-

0

28%

437

135

-

P. infestans

Protist

2

229

76

78

88

5

1%

214

146

92

P. sojae

Protist

86

87

107

75

1

2%

213

147

111

P. yoelii

Protist

1.2

23

179

151

157

1

25%

229

127

18

P. falciparum

Protist

1.8

23

157

119

176

8

24%

189

112

113

P. tetraurelia

Protist

2.5

72

25

26

-

0

0%

246

233

-

T. thermophila

Protist

3.3

104

132

103

136

3

17%

234

166

83

E. histolytica

Protist

23

72

62

-

0

2%

296

168

-

P. tricornutum

Protist

0.8

26

128

109

-

0

12%

446

410

-


*(Number of introns in genome/Number of genes in genome), calculated from genome annotations. The length of the assembly used in our analysis. Calculated from constitutive introns in EST alignments. §Average length of RIs seen in our EST alignments. See Table S2 in Additional data file 4 for average lengths based on genome annotations. ¥Average length of the two introns surrounding each predicted CE in our EST alignments. #Number of CEs considered for 'Average intron length next to CE' in the previous column and in Figure 5. This excludes those CEs where the introns next to the CEs do not have identical boundaries between transcripts with and without that CE. **Fraction of constitutive introns longer than 200 bp. ††Calculated from constitutive exons in our EST alignments. ‡‡Calculated from constitutive exons in our EST alignments (excluding exons that cannot be CEs, namely, the first and last exons in a gene, and exons in genes without introns). §§Average length of CEs seen in our EST alignments.

McGuire et al. Genome Biology 2008 9:R50   doi:10.1186/gb-2008-9-3-r50

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