Characterization of Polymorphic SINE Insertions and Genes in Dog Retrotransposon Free Regions

We have identified 1375 “free regions” in the reference dog genome that are at least 10,000 bp long and contain no SINEs, LINEs, or assembly gaps. Using PANTHER, we analyzed the genes found in these dog SINE+LINE free regions to see which GO terms are overrepresented. We have also studied the patterns of polymorphic SINE insertion into our free regions to check if SINEs in these loci have lower than average insertion frequencies or tend to prefer certain locations. To make this possible, we Illumina sequenced 434 libraries created by extending into flanking non-repeat sequence from a primer hybridizing to conserved SINEC_Cf sequence. The libraries represent 356 dogs from 125 breeds.