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Abstract

Three human LINE families comprise 20.4% of the human genome. LINE-1 sequences with 55 subfamilies account for 16.9% and contain all retrotransposons for which autonomous retrotransposition has been documented although most L1 elements are non-functional. While it is known that there are ~7000 elements in the human genome, the number and distribution of autonomously active LINE-1 elements are less certain. We scanned the draft sequence of the human genome for the essential functional parts, viz. promoter, ORF1 and ORF2. These fragments were assembled by allowing gaps of varying sizes between promoter and ORF1 or between ORF1 and ORF2. This procedure reduces the number of potentially active LINE-1 elements from overall searches (~7000) to 177 potentially autonomously active elements including previously described functional LINE-1 elements. Intact elements are apparently stochastically distributed in the genome, with the potential exception of the X chromosome. Unexpectedly, plots of gap sizes between promoter and ORF1 and ORF1 and between ORF2 revealed that while the distribution of intact LINE-1 parts is also random, their distance is not. This list of candidates of autonomously active LINE -1 elements and their exact position within the human genome provides a basis for functional analyses of retrotransposition.