Figure 2

Improvement of gene models. (a) Improvement of a gene model for Gli, including the joining of two JGI version 1 scaffolds. 5'-ESTs and 3'-ESTs are shown as yellow and purple boxes and EST pairs are connected by dashed lines. Multiple EST pairs indicate that this locus is artifactually split into two version 1 scaffolds. This Gli gene locus was not precisely predicted in the previous studies (exons are indicated by pink boxes and joined by lines). The new gene model (green boxes) precisely coincides with the structure of a cDNA sequence (yellow boxes) and ESTs. (b) The alignment of ESTs and gene models with the genome sequence around the 5'-end of the Gli locus. The 5'-full-length EST shown here has the spliced leader sequence (red letters), which is not aligned with the genome sequence because it is appended to Gli mRNA by trans-splicing. The acceptor dinucleotide for this trans-splicing is shown in red in the genome sequence. Note that only the new model precisely represents the 5'-end of this locus. (c) A gene locus that had not been modeled in previous annotations. Although 5'-ESTs (yellow boxes) and 3'-ESTs (purple boxes) indicate the existence of genes in this region, no previous model sets have included models in this region. Two gene models for this locus were built on the basis of EST evidence.