All standard gt-ag splice sites are drawn in turquoise, while non standard sites are shown in blue. This is insufficient, because of a bug in the design of the bubble at time of export. This bubble often overflows, but clicking on more brings a new scrollable and printable window with the same information. When there is alternative splicing, the proper number of full length transcripts are represented side by side. The coding region is indicated as wide solid green rectangles, while the 5' and 3' UTR parts are shown as thinner and empty rectangles.
Introns flanked by consensus splice sites are green, others are blue.
The CDS is defined as the longest ORF encoded by the set of exons, using the genome sequence as a reference. If a stop exists in the frame of the longest ORF in the 5' region, then the CDS is assumed to start at the first Met after the last in frame 5' stop. If no stop is found, the gene is assumed to be incomplete on the 5' side. Similarly on the 3' side. Mouse over any green transcript model gives details such as the total length of the reconstructed transcript, the CDS length, the 5' and 3' lengths.