Figure 1.

Anatomy of the L1 element and its structural variants found in the human genome. (a) A full-length L1 transcript is approximately 6,000 nucleotides long. It has a 5' UTR, two ORFs separated by 63 nucleotides, and a 3' UTR followed by a poly(A) tail. An L1 insertion in the genome is flanked by TSDs; the 3' TSD is immediately preceded by a poly(A) tail. (b) Variations in the structure of L1 insertions are shown. Arrowheads indicate the orientation of the L1 sequence. Most L1s are 5' truncated. In addition, during the process of insertion, a 5' segment of L1 may become inverted with respect to the 3' end of the L1 (5' inversion). Alternatively or additionally, a weak poly(A) signal in the L1 transcript can result in a portion of the 3' flanking DNA being transposed to another locus in the genome along with the L1 element; this process is called 3' transduction. In this case, the 3' TSD can be located hundreds of nucleotides downstream from the end of the L1 element. The numbers in parentheses represent the percentage of all L1s with TSDs that fall into each category. (c) TSD sequences flanking an L1 insertion are underlined. The poly(A) tail has a line over it. Although the poly(A) tail could potentially be extended, this would require the length (and potentially the score) of the TSDs to be reduced; TSDfinder always finds the longest possible TSDs.