NDM2 is significantly underrepresented in UPs as compared to the two classes of alternative promoters.
For example, TATA/DMp1 is found in 5.8% of UPs, 5.1-fold and 6.1-fold higher than its occurrence in the two classes of alternative promoters, FAPs and DAPs, respectively.
PASA-generated clusters having more than one assembly were screened for each of the nine classes of alternative splicing classes.
Table 2 has three bins reflecting the transcript support for each of the remaining six classes of alternative splicing.
Using the FL-cDNA as a reference for delineating the likely translated ORF, seven of the nine classes of alternative splicing occur predominantly in the coding sequence and these events have a significant effect on the translated protein.
We conservatively distrusted reads mapped to intronic regions and assembled first or last exons so we classified only the most frequent three classes of alternative splicing, "exon skipping", "alternative 5' splice site" and "alternative 3' site".
Computational analysis of 3'-ends of ESTs suggested the existence of four classes of alternative polyadenylation in human, mouse, and rat: tandem poly(A) sites, composite exons, hidden exons, and truncated exons.
We have assigned labels to rice and Arabidopsis splicing isoforms corresponding to the following nine classes of alternative splicing: a) Alternate Acceptor (AA), b) Alternate Donor (AD), c) Alternate Terminal Exon (ATE), d) Skipped Exon (SE), e) Retained Exon (RE), f) Initiation Within an Intron (IWI), g) Termination Within an Intron (TWI), h) Retained Intron (RI), and i) Spliced Intron (SI).
For these two classes of systems, we also provide an alternative stability proof via the construction of a novel Lyapunov functional.
As such, genomic microarrays may serve as a valuable alternative methodology that helps discriminate between these two classes of compounds.
