The sunflower sf21C gene is a member of a small plant gene family related to the human N-myc downstream-regulated gene family (NDRG) involved in stress and hormone responses, cell growth and differentiation. We have shown earlier that this sunflower gene is interrupted by nine introns and generates multiple mRNAs by alternative splicing of its primary transcript (Lazarescu et al. in Gene 374:77-86, 2006). In the present study, we have characterized 20 splice isoforms of this gene encoding 14 different protein variants. We show that these isoforms occur in distinct combinations in the various plant organs. Five identified variants were generated by splicing at novel sites, different from those classically recognized by U2- or U12-type spliceosomes. Twelve transcript variants contain premature termination codons (PTCs), which make them potential candidates for nonsense-mediated RNA degradation (NMD). Interestingly, all 12 transcripts are relatively abundant in at least one organ, suggesting that NMD is not a "default" mechanism for PTC-containing RNA transcripts generated by alternative splicing. These data indicate that alternative splicing of the sunflower sf21C primary transcript as well as the mRNA quality control mechanism by NMD are complex and regulated spatially and developmentally.