Argo mRNA Sequence Panel

The mRNA Sequence panel shows marked up mRNA sequence for selected features. It is a tab on the Inspector panel.

The mRNA sequence consists of the concatenated exons of the dna sequence. Alternating exons are drawn with alternating white and grey backgrounds, so you can easily recognize exon boundaries. Mouseover a nucleotide to see mRNA position, feature map sequence position, codon (with amino acid translation) starting at that nucleotide, frame of codon, and exon number.

Possible start and stop codons for current frame are drawn with green and red font, respectively. The current frame can be set using the right click menu option described below. By default, the current frame will be that of the best possible ORF. The start and stop codons of this best possible ORF (longest start to stop codon without any in frame stops) are drawn with green and red background for additional emphasis. Other ORFs can be selected using right click menu options described below. The protein translation of the selected orf is shown in the Protein Sequence panel.

As with all Inspector panel sequence windows, highlighting a region in the mRNA panel also highlights it in the feature map, so you can easily orient yourself in both scales. A valid fasta header is provided for easy copy and paste into other applications.

Right click to see mRNA panel specific options, described below:

Name Description
Copy Copy highlighted sequence to clipboard.
Find Matching Pattern... Use regular expressions to highlight matching sequence.
Find Matching Protein... Use regular expressions to highlight matching protein sequence.
PolyA Signal View Opens the polyA signal view on this feature.
Set selected ORF For editable features, this updates the data model with the currently selected ORF.
Select Orf > This submenu provides a number of ways to select the ORF.
Frame > Set the frame for which to mark up codons. Choose 1, 2, 3 or view codons in all 3 frames at the same time (busy).

argo mrna sequence panel


Last Updated: Sept 18 2006
Contact: Reinhard Engels
argo-support@broad.mit.edu