What does it mean when the ortholog of an isoform is N/A?
I have now compared cassette exons, alternative 5′ and 3′ splice sites, mutual exclusions and intron retentions across human, mouse and rat. Currently, the comparison is done by matching exon junctions, which are 50 oligos used as probes. Pairwise alignments of the probe sequences were done between two species using clustal w. Only matches greater than 0.6 in nucleotide identities were kept. However, note that this threshold is not very high. Spurious matches do exist. Note that for intron retentions only the spliced isoform is compared now. So ‘N/A’ for the RETENTION isoform does not necessarily mean that it is not conserved. I just did not do the comparison for the RETENTION isoform. Also, it is possible that an isoform might be conserved but not detected by transcript evidence. In this case, it is not detected here either. I will update this section in the near future to improve the accuracy. First, two halves of a splice junction will be aligned separately. Second, exon alignment w
