It has previously been shown that the LI family in the mouse (LlMd) contains two alternative 5′ ends called the A- and F-type sequences (1,2). We show here that the F-type element is a major class of murine LI elements and report on the details of organization of the 5′ motif of these F-type elements. Although the A- and F-type 5′ sequences share no detectable sequence homology the organization of an F-type 5′ end is strikingly similar to that of an A-type. That is, the F-type 5′ sequences consist of a tandem array of a small number of 206 bp monomers while the A-type 5′ motif consists of a tandem array of 208 bp monomers. All of the A-type elements characterized to date have a truncated monomer at the 5′ end of the array. Many of the F-type elements are also terminated at the 5′ end by a truncated copy but unlike the A-type elements some F-type elements terminate with a monomer which is within a few nucleotides of being complete. In addition the F-type consensus sequence, in contrast to the A-type sequence, shows homology (70%) to the body of the LIMd starting at the position where the monomer joins the rest of the LI element.
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