Figure 1
The TRα/Rev-erbα locus is conserved in marsupials. A. Structure of TRα and Rev-erbα genes is shown schematically for rat and M. domestica. Rectangular boxes indicate exons, boxes terminating in arrows represent poly(A) sites, dark shading indicates coding sequences and bold vertical lines the alternative 5'ss splice site for exon 9A and stop codons for TRα1 (exon 9) and TRα2 (exon 10). Alternative splicing of TRα2 (exon 9A to exon 10) is indicated by dotted angle line. Percent amino acid identity is indicated above each exon and exon numbering is shown in bold below. Conservation of TRα2 exon 10 is described in Figure 2. Probes for RNase protection assays are indicated by bold lines under TRα exon 9A and Rev-erbα exon 6. Hatched ellipses indicate positions of elements that enhance TRα2 mRNA splicing [38]. B. (top) To-scale enlargement of the antisense overlap showing portions of exons from TRα1, TRα2 and Rev-erbα mRNAs within shaded region in panel A. Shaded horizontal bar indicates eight subregions based on an alignment of eutherian and marsupial sequences across this region (additional file 2). Cn and Gn represent regions that include multiple runs of C and G residues, respectively. Rev pA is the conserved region centered on the Rev-erbα poly(A) site. Table at bottom shows percent identity for selected pairwise comparsions: SAO, South American opossum (M. domestica); NAO, North American opossum (D. viriginiana); potoroo, P. tridactylus. Asterisks indicate highly gapped regions in the alignment.