Figure 1

GEB histogram and physical map displays. (A) The general structure of LINE-1 (L1) elements in mammals. The arrow indicates internal promoter for transcription. Between the 5' and 3' untranslated regions (UTRs) are two open reading frames (ORFs) which encode proteins essential for autonomous retrotransposition. EN, endonuclease domain; RT, reverse transcriptase domain; AAAA, polyadenylation site. (B) GEB histogram display for mouse Chromosome 4 from centromere to telomere (left to right). The width of each bar represents 1 Mb, and the height of each bar represents the frequency of defined features. (C) GEB physical map display of a 10 Mb region (116–126 Mb), corresponding to the boxed area in (B). Features on the forward and reverse strands are shown above and below the ruler respectively. The power of the two-dimensional display is illustrated by the custom annotation of L1 elements, where each copy varies substantially in size. With the physical length of each individual L1 element plotted on the horizontal axis and the homology of each L1 component to the L1 consensus plotted on the vertical axis, regions with high L1 density (dashed box) are clearly distinguished from relatively L1-poor regions on visual inspection (compare the 5'UTR-ORF1-ORF2–3'UTR plot against the yellow LINE/L1).