Reference Sequence Track

The "Reference Data" category in the Rat Genome Database v5 JBrowse, or the "Reference Sequence" category in the v3.4 and v6 versions, contains a track which, when you are sufficiently zoomed in, will show the reference DNA sequence and the corresponding 6-frame translation of that sequence (i.e. the translation in all three possible frames on both the forward and reverse strands of the DNA reference).

 

When you are zoomed out too far for JBrowse to display the sequence itself, a message appears in the track that says "Zoom in to see sequence".  Zoom in using either one of the "magnifying glass" icons with the minus sign (-), or by clicking and dragging on the detail section's position bar (the bar between the navigation buttons and the track displays;  in the example to the left, the detail section's position bar is displaying the numbers 171,705,000 and 171,710,000).


Click here to view the DNA sequence example at this zoom level in JBrowse.

The point at which the DNA track will begin showing the sequence depends on the size of the window you are using to display JBrowse and the resolution of your screen.  The first DNA display shows the sequence as color-coded blocks without displaying the letters to indicate the bases for the DNA sequence and the amino acids for the protein sequence.  The colors of the bases are as follows:

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 sequence example at this zoom level in JBrowse.

Zooming in even further yields a display which shows both the DNA sequence and the putative amino acid sequences in all three reading frames for both directions (that is, for all six possible reading frames).

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 here to view this DNA and amino acid sequence example in JBrowse.

You can use the "Save Track Data" function from the context-specific menu to download the DNA sequence as a FASTA file.

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.

Click here and follow the steps above to view and/or download the 495 kb region around the gene Ucp2.
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