Cross-kingdom patterns of alternative splicing and splice recognition

McGuire, Abigail M; Pearson, Matthew D; Neafsey, Daniel E; Galagan, James E

doi:10.1186/gb-2008-9-3-r50

Table 3 Types of splice variants observed

From: Cross-kingdom patterns of alternative splicing and splice recognition

				Retained introns
	Kingdom	No. of splice variants	Cassette exons	Discarding unspliced ESTs	Keeping unspliced ESTs*	Competing 5' sites	Competing 3' sites	$\frac{C E}{R I + C E}$ (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.

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