Sequence of Dictyostelium DIRS-1: an apparent retrotransposon with inverted terminal repeats and an internal circle junction sequence

Abstract

The Dictyostelium discoideum transposon DIRS-1 contains long terminal repeats that are inverted (ITRs) and nonidentical. We show here that the internal sequence contains 4158 nucleotides and encodes three open reading frames (ORFs). Two of the ORFs (ORFs 2 and 3) are colinear and overlap for more than 2000 bases. Unusual sequence conservation between the two DIRS-1 elements in the overlap region is discussed. The conserved reading frame (ORF3) contains a 200 amino acid region that bears significant homology to retrovirus reverse transcriptase. Based on this homology, we classify DIRS-1 as a possible retrotransposon and propose a model by which the nearly genomic length 4.5 kb DIRS-1 RNA could be used to generate a genomic DNA copy of DIRS-1 with nonidentical inverted terminal repeats.