Intron density ranges from a handful in the entire genome of some protists ( Mair et al., 2000 Morrison et al., 2007), to about eight per gene in human ( Sakharkar et al., 2004). With the exception of the highly reduced nucleomorph genome of Hemiselmis andersenii ( Lane et al., 2007), introns are found in all fully sequenced eukaryotic genomes, including other nucleomorphs ( Gilson et al., 2006). Spliceosomal introns are one of the eukaryotic defining characters. We suggest a novel criterion of evolutionary conservation, dubbed intron positional conservation, which can identify functional introns. We propose that this great diversity of intronic functions supports the notion that introns were indeed selfish elements in early eukaryotes, but then independently gained numerous functions in different eukaryotic lineages. In this review, we show that introns in contemporary species fulfill a broad spectrum of functions, and are involved in virtually every step of mRNA processing. The intron–exon architecture of many eukaryotic genes raises the intriguing question of whether this unique organization serves any function, or is it simply a result of the spread of functionless introns in eukaryotic genomes. 2 School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.1 Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel.
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