Table 4.

Using the annotation derived from FL-cDNAs, the alternative splicing effects are classified relative to the CDS and UTRs.

Rice
Type	AA	AD	ATE	SE	RE	IWI	TWI	SI	RI
CDS contained	1,508	679	390	311	184	1,224	1,353	351	2,111
CDS overlaps UTRs	1	1	113	75	2	0	0	342	0
3' UTRs contained	183	71	47	21	25	34	147	416	146
3' UTR overlaps CDS	1	1	49	23	0	0	0	246	0
5' UTR contained	468	336	200	80	65	136	84	367	165
5' UTR overlaps CDS	0	0	178	56	2	0	0	98	0
Totals	2,161	1,088	977	566	278	1,394	1,584	1,820	2,422
Arabidopsis
Type	AA	AD	ATE	SE	RE	IWI	TWI	SI	RI
CDS contained	1,206	509	97	138	65	330	441	211	1,789
CDS overlaps UTRs	0	0	37	26	0	0	0	106	0
3' UTRs contained	56	24	4	3	1	6	49	74	57
3' UTR overlaps CDS	0	0	11	4	0	0	0	63	0
5' UTR contained	234	160	58	24	20	86	16	202	140
5' UTR overlaps CDS	0	0	109	22	0	0	0	43	0
Totals	1,496	693	316	217	86	422	506	699	1,986

The categories are mutually exclusive in this analysis (i.e. those isoforms in one category are not present in any of the other five categories).