Two independent BLAST comparisons plotted coordinately: maize gene lg2 (AY180106 from a BAC) with its rice ortholog and maize gene lrs1 (AY180107 from a BAC) with the same rice ortholog (RGP PAC AP003287). The purple alignment line of lg2CNS17 represents how sequences near 5′ exons align. Exons were identified in genomic DNA for all three genes using the complete cDNA of lg2-mRNA (AF036949) and then masked. Bl2seq conditions were modified from those of Kaplinsky et al. (2002b). The BLAST result is represented by the solid, multicolored lines connecting the maize lg2 (Zm LG2) and rice lrs1 (Os LRS1) gene diagrams. The identity match is indicated parenthetically. Each color connects CNSs that are essentially the same. A broken line reflects a maize lg2-lrs1 CNS retention, but just below the 15/15 cutoff. Yellow highlighting denotes those rare CNSs that are fractionated. Fractionation at the DNA level could, hypothetically, explain subfunctionalization at the phenotypic level. An insertion into lg2 promoter is noted. Figure was reproduced with permission from the Genetics Society of America © 2004, from Langham et al. (2004).
