Splicing to generate a PTC is evolutionarily conserved in CLK transcripts. The CDC-like kinases (CLKs) are splicing regulators that affect splicing decisions through the phosphorylation of SR proteins. A) A screen of SWISS-PROT performed by Hillman et al revealed that human CLK1, CLK2 and CLK3 paralogs all generate PTC⁺ alternative isoforms.¹⁶ Conserved skipping of exon 4 causes a frameshift and results in a PTC. The percent identities from global alignments between corresponding exons and introns are shown in purple. B) CLK homologs were identified in mouse through existing annotation and in the predicted proteins of the sea squirt C. intestinalis using an hidden Markov model (HMM) constructed from sequences of annotated CLK transcripts from a variety of organisms. An EST analysis revealed that the alternative splicing pattern that generates PTC⁺ alternative isoforms was conserved in all three sets of orthologs in human and mouse. The same splicing pattern was also found in the only identifiable C. intestinalis homolog. A relatively high degree of sequence similarity was found to be present in the introns flanking the alternative exon. ©2004 Hillman et al; license BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL (http://genomebiology.com/2004/5/2/R8).¹⁶