Figure 1.

Schematic diagram of Sqd protein isoforms. The three Sqd isoforms, SqdA, SqdB, and SqdS, are identical to amino acid position 285 (A). Within this conserved region are the two RNA-binding domains RBD-1 and RBD-2 (depicted by the hatched boxes) and an M9-like nuclear-import domain (represented by the black box). At the carboxyl termini of the proteins, all three contain a glycine-rich domain, which in the SqdS and SqdB isoforms continues to the end of the protein. The SqdB and SqdS isoforms use the same 3′ exon; however, the splice site in the SqdB isoform results in a protein with 27 fewer amino acids than SqdS. In addition, SqdS contains another M9 nuclear import motif (amino acids 300–338) that is not present in either SqdA or SqdB. The SqdA isoform uses an alternative 3′ exon and encodes a protein with a unique carboxyl terminus. A comparison of the human hnRNPA1 M9 domain with the M9 domains found in Sqd is shown in B. The M9 motif found only in SqdS shares 16 of 38 amino acid identity with human hnRNPA1 M9 (top), whereas the M9-like motif found in all three Sqd isoforms shares 13 of 38 amino acid identity with hnRNPA1 (bottom). Alignment of the M9 motifs was accomplished using the ClustalW Multiple Sequence Alignment Program.