A = green
C = blue
G = yellow
T = red

The display also shows all start and stop codons for the six reading frames as green (start) and red (stop) blocks in the light, medium and dark grey lines above (forward) and below (reverse) the DNA sequence lines.  The example to the left shows the beginning of the coding region for the gene Ucp2.  Note that there are two start codons at or near the beginning of the coding region, one in the top reading frame at the start of the coding region (the red bars in the track above) and one in the third reading frame.  However, the start codon in the third reading frame is followed almost immediately by a stop codon.

Click here to view the DNA codon table which shows the three DNA bases which make up each codon for each amino acid in the standard genetic code (that is, the codes most commonly used for standard amino acids in species such as rat, mouse and human).  Amino acid names, three letter abbreviations and one letter abbreviations (such as are used in this JBrowse track) are listed.

Click the down arrow in the track label and select “Save Track Data” to open the save menu.  Here you can give the file a different name if you wish and choose whether you would like to simply view the sequence or download the file to your computer for further analysis.  Because this track does not show genomic objects such as genes (which could, for example, be presented as GFF3), the only option for the data type of the download is FASTA.

The example to the left shows the menu and the sequence for a small segment of DNA but this function is available even when the display is zoomed out far enough that the sequence is not showing in the JBrowse window.  You can download sequence data for regions up to approximately 500 kb using this functionality.