Fig. 1.

Splice variants for MlDmrtA and MlDmrtB. (Top) MlDmrtA is a three-exon gene with the start site located in the first exon, the DM DNA binding domain spanning exons 1 and 2 and the stop codon located in the third exon. The DM domain is indicated in the alignment with a box and the double zinc binding modules indicated by circles (Zn-binding module 1) and squares (Zn-binding module 2) below the alignment [regions defined as in 81]. We recovered a splice variant sharing the same start and stop positions but lacking exon 2 and thus the complete DM domain. The splice variant lacking exon 2 also had a shorter 3′ UTR indicated by a different polyadenylation site. (Bottom) MlDmrtB is a ten-exon gene locus. However, both our RACE sequencing and the assembled gene models (Trinity and Cufflinks) available at the Mnemiopsis genome database indicated two nine-exon genes, none with all ten exons. Both isoforms shared the same start and stop codons. IsoformA lacks exon 3, and IsoformB lacks exon 4. Contrary to the splice variant for MlDmrtA, both splice variants of MlDmrtB appear to have complete, but different, DM domains (indicated by white and black symbols), with a portion of each Zn-finger domain located in exon 2 and shared by both splice variants. The DM domain for IsoformB is indicated with a box. Like MlDmrtA, the two splice variants have different polyadenylation sites