When GeneSeen comes up, a color key will appear in a separate small window. The features shown in the color key will be explained in the next section. The annotation map The most information-packed portion of the GeneSeen display, the annotation map, shows the locations of sequence gaps, repeats, tRNAs, annotated genes and their transcripts. The numbers along the axis represent base numbers on the chromosome arm. Gene transcripts are represented by blue exons connected by lines that represent introns.
Some genes have alternate transcripts, which appear stacked on top of each other.
Associated with the transcripts are colored arrows that indicate the types of evidence that were used to annotate the gene. A green stripe means that there is sequence similarity to another sequence in GenBank. The gene name appears adjacent to the evidence arrow. The gene name appears on the display only when you zoom in enough for the name to fit. Transcripts are identified by CT ID numbers.