This is a pretty basic question but I cannot find an answer anywhere. For plasmids on Addgene such as this one, there is supposed to be a GtCCR1 rhodopsin domain insert with a EYFP tag. However on the plasmid viewer shown below, there is only an arrow indicating the EYFP tag but not the CCR1 rhodopsin domain itself. Is the rhodopsin domain there but just doesn't show up in the image, or am I misunderstanding the nature of the plasmid? Many plasmids I have been looking at had the same issue, I am new to this so any help would be appreciated.
The GtCCR rhodopsin domain is shown by the thin brown and green arrows on the right of the image that overlap with the EYFP domain and are flanked by the CMV promoter and bGH poly(A) signal. These arrows show the coding region.
The sequences for the plasmid are automatically annotated by Addgene with common features (I think they use Snapgene software for this, at least the features and way they are done are very similar). The actual insert is supplied by the depositor and is not automatically annotated, though an ORF between promoter and terminator signals can (will?) be.
If you don't have Snapgene, I recommend it for plasmids. The viewer (linked above) is free to use. It has some features that you can only use by annual subscription. I have no affiliation with this product or company.
There are a couple of ways of visualizing the sequence and features, but they all give the same result in the end. I'll take you through the most obvious:
- From the front page for your plasmid of interest (POI), click on View All Sequences
- A new page will load, click on the Analyze Sequence button or just click on the map of the plasmid.
- This will load a new page with a number of tabs. You will be on the Map tab. In this tab you can hover over the features and get a little pop-up description and base positions. For example the gTCCR rhodopsin will pop up with ORF: 789 .. 2414 = 1626 bp as well as a protein length and mass assessment.
- Now click on the Sequences tab and it will show the full sequence. You can scroll through and see all the features, base positions for each, restriction enzymes, translations etc. I've added the bit at the start of the ORF for the GtCCR and a bit of the CMV promoter.