Fig. 1

Cis-spliceosomal introns in S. vortens. (a, b) 5′ RACE and/or EST-confirmed (RP and FolC-like genes) and predicted (Hypothetical genes) spliceosomal intron sequences from S. vortens genomic sequences were aligned using ClustalW2 software (see Additional file 2 for gene sequences and EST accession numbers). The 5 nt of exonic sequences flanking each intron are in upper case with a slash representing the exon-intron boundary and mRNA start ‘ATG’ codons in bold. Predicted intron 5′ and 3′ splice sites (SS) and branch point (BP) sequences are highlighted in grey with the putative reactive branch point adenosine in bold and underlined. A conserved pyrimidine-rich motif (‘AAC [T/C]_3-4R’) found upstream of the branch point sequence is underlined. Nucleotide identities shared between all aligned introns are indicated by asterisks under the alignment. b Consensus sequences from the identified S. vortens spliceosomal introns are compared to those from the related diplomonad Spironucleus salmonicida [18], Giardia lamblia [20] and parabasalid Trichomonas vaginalis [15]. An ‘R’ indicates a purine, ‘Y’ is a pyrimidine, ‘W’ is A/T, ‘V’ is A/C/G and ‘H’ is A/C/T. c Secondary structural potential for S. vortens long cis-introns with predicted internal stem loops (See Fig. 3 for Rpl30). Predicted 5′/3′ SS and BP motifs are underlined. Lengths of ‘single-stranded’ distances between splice donor and acceptor sites are indicated in nucleotides (nt) above the intron sequences