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 |
|
|
|
|
||||||||
|
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 |
||||||||
