Table 3

Types of splice variants observed

Retained introns


Kingdom

No. of splice variants

Cassette exons

Discarding unspliced ESTs

Keeping unspliced ESTs*

Competing 5' sites

Competing 3' sites

<a onClick="popup('http://genomebiology.com/2008/9/3/R50/mathml/M1','MathML',630,470);return false;" target="_blank" href="http://genomebiology.com/2008/9/3/R50/mathml/M1">View MathML</a> (CE fraction)


D. rerio

Animal

6,137

2,475

1,176

2,324

931

1,555

0.68

T. rubripes

Animal

201

52

47

79

50

52

0.53

B. floridae

Animal

812

516

26

123

121

149

0.95

C. savignyi

Animal

181

93

18

64

22

48

0.84

C. intestinalis

Animal

2,779

834

907

2,084

394

644

0.48

N. vectensis

Animal

108

54

8

33

21

25

0.87

S. purpuratus

Animal

284

147

13

50

63

61

0.92

D. melanogaster

Animal

2,163

453

712

2,343

442

556

0.39

A. aegypti

Animal

983

280

284

606

186

233

0.50

A. gambiae

Animal

882

207

283

635

190

202

0.42

A. mellifera

Animal

561

153

124

338

135

149

0.55

C. elegans

Animal

1,589

361

452

828

285

491

0.44

S. mansoni

Animal

1,236

235

599

974

143

259

0.28

R. oryzae

Fungi

47

0

30

55

5

12

0

C. neoformans

Fungi

1,091

18

768

1,117

101

204

0.02

U. maydis

Fungi

85

8

31

105

16

30

0.21

S. pombe

Fungi

3

0

3

13

0

0

0

S. cerevisiae

Fungi

9

0

2

42

3

4

0

N. crassa

Fungi

20

2

8

30

5

5

0.20

M. grisea

Fungi

151

5

86

194

24

36

0.05

S. nodorum

Fungi

36

2

21

37

5

8

0.09

A. flavus

Fungi

162

3

124

302

13

22

0.02

A. nidulans

Fungi

100

1

74

216

8

17

0.01

H. capsulatum

Fungi

50

1

33

65

6

10

0.03

C. posadasii

Fungi

950

15

648

1,259

120

167

0.02

C. immitis

Fungi

861

8

542

1,035

131

180

0.01

S. sclerotiorum

Fungi

323

9

210

419

49

55

0.04

D. discoideum

Protist

107

6

33

98

29

39

0.15

P. trichocarpa

Plant

664

144

215

392

103

202

0.40

A. thaliana

Plant

3,255

251

1,260

2,609

547

1,197

0.17

O. sativa

Plant

3,893

450

1,339

3,076

706

1,398

0.25

P. patens

Plant

2,068

249

534

1,156

558

727

0.32

C. reinhardtii

Plant

490

60

211

520

86

133

0.22

O. lucimarinus

Plant

17

0

13

60

2

2

0

P. infestans

Protist

406

6

262

564

60

78

0.02

P. sojae

Protist

66

1

32

87

15

18

0.03

P. yoelii

Protist

38

1

22

92

6

9

0.04

P. falciparum

Protist

77

9

34

75

19

15

0.21

P. tetraurelia

Protist

535

0

407

786

35

93

0

T. thermophila

Protist

282

6

202

423

30

44

0.03

E. histolytica

Protist

7

0

6

24

0

1

0

P. tricornutum

Protist

215

0

126

643

27

62

0


*For comparison, we include the total number of RIs predicted when unspliced ESTs are not discarded. Discarding unspliced ESTs primarily affects the number of predicted RIs. Complete results for all forms of alternative splicing, when unspliced ESTs are not discarded, are included in Additional data file 5.

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

Open Data