Figure 2

R2 SIDE (‘Short Internally Deleted Element’) in Drosophila willistoni. (A) The 3.53 kb R2 element in D. willistoni, R2Dwi, is diagrammed with the 5' and 3' UTRs (untranslated regions) shaded darker. The 529 bp element, R2Dwi_SIDE, has sequence identity at the 5' and 3' ends to the R2 element (percent identity shown); the 197 bp central region (white box) has no significant identity to the R2 element. (B) Sequence reads for full-length R2 and R2Dwi_SIDE elements obtained from the trace archive at NCBI [26]. The majority of 5' junctions for both element types are precise (marked with asterisks). Typical variation at the 5' junction for both elements is also presented. (C) Genomic DNA from D. willistoni was PCR amplified using a 28S primer (32 nucleotides upstream of the R2 site) and a ribozyme primer (conserved region 100 nucleotides into the elements) (arrows). PCR products after Bam HI digestion were separated on a native, 8% polyacrylamide gel. Lane M, DNA length markers with sizes indicated. The product at 200 bp was subsequently determined to correspond to an insertion in the R1 site, R2/R1Dwi_SIDE (bottom diagram). Element type and relative percentage in the genome are to the right of the gel.