FIGURE 3.

Alignment and ranking of different isoforms. (A) Gene tree multiple sequence alignment color coded by interpro domain. The orange domain is conserved in grass orthologs, but is not identified completely in maize because a retained intron disrupts it and induces a frame shift (shown by arrow). The resulting longer translation was selected for analysis in the gene tree pipeline. Different colors mean different interpro domains, black color means “no domain here,” lightly shaded area indicates a gap in the multiple sequence alignment. The thin red lines show the positions of exon junctions. (B) Ranking of different isoforms of Zm00001d003817 based on different standards. T002 has the longest CDS, but T003 outperforms it in domain length and annotation edit distance.