Intron Phase Patterns in Genes: Preservation and Evolutionary Changes

Introns are located either between codons (phase 0) or within codons (phase 1 and 2) and their phases as well as location usually stay unchanged for a long time. A string of intron phases represents a structure which may carry useful additional information about internal rearrangements of a gene. Combined search for intron phase patterns and exon lengths serves as a helpful approach for finding conserved intragenic duplications and other rearrangements. In vertebrate genes intragenic duplications usually are more numerous than in orthologs from other animal taxons. Intron phase patterns and exon lengths are highly conservative in some genes and can be traced back to a common ancestor of mammals and nematodes. Despite this, there are orthologs which show drastic losses of intron-exon structures as found in insects and urochordata. Driving forces behind such changes in exon-intron structures remain unknown and need further investigation.