Figure 6

Splice models of some duplicons with evidence of alternatively splicing. (A) SjCP1084 protein coding mRNA [GenBank:AY570737] and a non-coding transcript [GenBank:FN328299] are products of alternative splicing. Based on gene prediction from the contigs using GeneQuest and GeneMark, and alignment of cDNAs to genome sequences using Spling program, we observed that two mRNA transcript variants were produced from [GenBank:CABF01020060]. An extra splice site was evolved in the first exon of the non-coding transcript [GenBank:FN328299]. When the splice site is recognized, an ORF encoding a protein coding mRNA [GenBank:AY570737] variant is created. The images were created from computer simulation of real DNA sequences using Vector NTI program. Also see a supplementary figure in Additional file 8 for more details. (B) SjCP1531 protein coding mRNA [GenBank:AY570742] and a non-coding transcript [GenBank:FN329677] are products of alternative splicing. Two mRNA transcript variants can be produced from a contig representing on of the duplicated loci [GenBank:CABF01023364]. Two extra splice sites were not utilized in the transcription of the non-coding transcript [GenBank:FN329677]. When the splice sites were recognized, exons 5 and 6 of a translatable ORF were created to produce a protein coding mRNA [GenBank:AY570742] variant. Refer to RT-PCR result in Figure 5 (C) where two bands of exact size and sequence as the two variants described above are apparent on the agarose gel electrophoresis image. Also see Additional file 9 for more details.