Figure 2

Screenshot of the Annotation Station gene editor. The evidence for gene identification and gene modeling is viewed using proprietary software called Annotation Station, developed by Neomorphic and maintained now by Affymetrix. This tool, similar to Apollo that was developed at Berkley and Sanger [105], is used by human annotators as a genome navigation tool and gene structure modeling tool. The gene models, proteins and transcript alignments are shown for an approximately 4.5 kb window along the minus strand of BAC F10O3 in the region encoding the 3-methylcrotonyl-CoA carboxylase 1 (At1g03090). The curated gene structures are shown in dark green on the white background towards the bottom of the view, with exons filled, and introns and UTRs unfilled. Above this curation within the black background, evidence is shown from bottom to top as follows: splice site predictions, computational gene predictions, protein alignments shown in orange, EST alignments from searching the various plant Gene Indices in varied colors, regions of homology to the genome of Brassica oleracea shown in dark blue at the top of the view, and PASA Arabidopsis transcript alignment assemblies at the top shown in bright pink. The vertical marker line indicates the position of a skipped exon (supported by both PASA FL-cDNA and protein alignments) that results in two protein isoforms.