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
 Math (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