Alternative splicing (AS) has been extensively studied in mammalian systems but much less in plants. Here exon skipping ͉ intron retention ͉ non-sense-mediated decay ͉ spliced alignment ͉ conserved alternative splicing A lternative splicing (AS) is an important posttranscriptional regulatory mechanism that can increase protein diversity and affect mRNA stability (1, 2). Relative to the predominant transcript isoform, different types of AS have been observed, including exon skipping (ExonS), alternative donor (AltD) or acceptor (AltA) site, and intron retention (IntronR) ( Fig. 1; reviewed in ref.3). AS has been extensively studied by EST͞ cDNA-based analysis in mammalian systems, and 35-60% human genes were suggested to be alternatively spliced (4-9). In humans, ExonS is the most common type (58% of the total number of AS events are ExonS events involving a single exon, and 11% are ExonS events in which multiple exons are skipped in tandem) (4). IntronR is the least common type of AS in humans (5%) (4); Ϸ70-88% of the AS events occur in protein coding regions (reviewed in ref. 10), and approximately onethird produce premature termination codons (PTCs) (11). These PTC-containing transcripts are apparent targets for non sensemediated mRNA decay (NMD) (11). Not all of the predicted AS are real and functional, because many possible sources of false positives exist (10). An AS event has been defined as functional ''if it is required during the life cycle of the organism and activated in a regulated manner'' (12). To identify functional AS events, conserved AS events between human and mouse were studied (12-17), with the assumption that conservation indicates function. Twenty-five percent of a set of 980 ExonS events in human were found to be conserved in mouse (12). Another study reported that Ϸ10% of human gene loci with mouse orthologs show conserved AS events (15).The splicing mechanism in plants is generally conserved compared with mammals (18, 19). However, introns in plant are usually short in length and U-rich (18-20), with a much less apparent polypyrimidine tract near the 3Ј splice site than in mammals (21). Our recent genomewide survey on Arabidopsis splicing-related genes revealed variations in SR proteins and hnRNP proteins between plants and mammals, suggesting plantspecific differences in splicing-regulation mechanisms (22). A few AS events were identified experimentally in plants, including genes involved in splicing (23, 24), transcription (25), flowering regulation (26), disease resistance (27), enzyme activities (28, 29), and many other physiological processes and functions (19). A database (PASDB) collecting known alternatively spliced genes in plants is available at http:͞͞pasdb.genomics.org.cn (30).