PmDscam is a tool for sequence alignment of hypervariable shrimp Dscam (Down syndrome cell adhesion molecule).
Dscam is a member of the immunoglobulin (Ig) superfamily gene. Hypervariability of Dscam only occurs in arthropods. For example,Drosophila Dscam may generate 38,016 isoforms from one genome locus via alternative splicing. Arthropod Dscam may have important roles in neuronal connections and immune responses.
Using NGS and Sanger sequencing, a 260-kbp Dscam genome draft from Black tiger shrimp (Penaeus monodon) was completed. Based on our analysis, hypervariability of PmDscam occurs both on the extracellular region and the cytoplasmic tail. From one PmDscam genome locus and through alternative splicing, there are 54,756 potential combinations involving extracellular regions, plus 512 potential combinations of cytoplasmic tails. Therefore, PmDscam has super-hypervariability all derived from one PmDscam genome locus.
To simplify and standardize alignment of PmDscam isoforms, we inputted 175 exons into this website, ranging from Ig1 to the end of cytoplasmic tail. With 175 exons, numbers of spliced exon variants of N-terminal Ig2 and Ig3 and entire Ig7 were 26, 81 and 26, respectively.