Fine control of editing requires close examination of the gene structure. This is accomplished in the exon editor panel, which provides a sequence-level view of gene models. When the exon editor is launched, the region displayed is highlighted in the main Apollo display (blue rectangle in lower panel), and this main display rectangle can be moved along the sequence to control the region shown in the exon editor. Using the contextual menu in the exon editor panel, changes can be made to introns and exons, as well as to precise splice junctions and translation starts. Annotations appear in the viewer with alternating colors for individual exons, and clicking on a transcript selects it and causes a graphical representation (or glyph) of the transcript to appear at the bottom of the window. This transcript glyph shows the translation start and stop sites, and can be displayed with or without introns. In the case illustrated, the intron-exon structure of the gene is shown; the numbers in the exons indicate which frame of the translated genomic sequence is utilized in that exon. Clicking on the different portions of the glyph allows one to quickly navigate to specific regions of the transcript. A sequence search query is also available, as is retrieval of genomic and translated sequence.
Lewis et al. Genome Biology 2002 3:research0082.1-0082.14 doi:10.1186/gb-2002-3-12-research0082