How do you create a ribosomal frameshift in a CDS?
Ribosomal-frameshifting, is also known as ribosomal slippage, translational frameshifting or translational recoding. In certain coding sequences the ribosome can "slip" to an alternative reading frame when translating a coding sequence (CDS).
The most common type of frame-shifting is "−1 frameshifting", where the ribosome slips back one nucleotide (with respect to the initial reading frame) and continues translation in the −1 frame.
By default SnapGene does not allow overlapping feature segments which can be used to denote frameshifting. Follow the instructions below to learn how to generate overlapping CDS segments in SnapGene.
Open the Sequence for a Frame-shifted CDS
Import or open the sequence to be annotated with a CDS.
Create a CDS Feature
In Sequence view, or Map view, select the CDS, start codon to stop codon, then click Features → Add Feature.
Enter a name for the feature, set the Type to CDS, and check the option to "Translate this feature in Sequence view".
Click Split Feature to segment the feature into two parts.
Choose to split into 2 segments.
Allow Segments to Share Endpoints
Click the "Location" link.
Check the option to "Allow segments to share endpoints" and click OK.
Edit the Segment Boundaries
Edit the segment boundaries. For "-1 slippage" the end coordinate of the first segment is the same as the start coordinate of the second segment.
Click OK to close the "Add Feature" dialog.
View the Translation
In Sequence view, navigate to the segment boundary (marked by a vertical line) to view the resulting translation across the boundary.
In the above example, the third nucleotide (T) of the phenylalanine codon (Phe, TTT) is also the first nucleotide of the Cysteine codon (Cys, TGC). SnapGene correctly translates this -1 slippage.
Add a ribosomal_slippage Qualifier to the CDS Feature (optional)
Double click the CDS feature to edit it.
Click the dropdown to choose the qualifier /ribosomal_slippage and select the option Yes.
Add a /note qualifier describing the ribosomal slippage. Click OK.
