Figure 5.

The rat genome contains a potential homologue of the mouse KCNMB3 1b' exon. (A) A lower stringency conservation screen, using the candidate mouse KCNMB3 1b' sequence (build mm8), identified a segment of potential homology in the rat. The rat segment contains a 120-bp insert of no homology that connects two segments sharing homology with the mouse 1b' exon. This rat 1b' homologue occurs in a position similar to that in the mouse within the overall KCNMB3 gene map (Fig. S5). (B) The cloned mouse 1b' exon is aligned directly with the candidate rat 1b' exon highlighting the insert (yellow) in the rat sequence. Both candidate exons share a similar consensus sequence for an appropriate intron–exon splice site. The 120-bp insert appears to be a repeatable genetic element occurring on multiple chromosomes in the rat. A homologue of ∼90% identity is also found in the mouse. The position of the mouse 1b exon is, in build mm8, chr3:32,400,082-32,400,204, while in build mm8, the position is chr3:32,692,709-32,692,831. Alignments based on mm8 use a 17-way vertebrate species set while alignments based on mm9 use a 30-way Multiz alignment. The UCSC alignment procedures use an additional filtering step in the generation of the 30-way conservation track that reduces the number of paralogues and pseudogenes from the high-quality assemblies.