There’s a few different ways to import annotation from the ENSEMBL database browser, as well as other databases.
The easiest way to export from ENSEMBL and keep all annotation is to use the Genbank format. The default format will be FASTA which has no annotation. With Genbank all the annotation is stored in the file and will be imported by MacVector.
Depending on which browser you are using you can just SELECT ALL, COPY then use FILE > NEW FROM CLIPBOARD in MacVector to import the file. MacVector 12.6 and above will recognise the fact the copied data is in Genbank format and create the properly annotated sequence.
If you are using an older version you may first need to create a plain text file (using TEXTEDIT) and save that to your Desktop.
However, using a flat file format is generally a one way operation. If you need to add newer annotation (e.g. from publications from after your initial import) then you unless you like performing lots of manual annotation then you want to stay away from using Genbank a second time.
Instead the most flexible way would be to use the IMPORT FEATURES tool. This allows you to export annotation, using a format such as GFT, GFF or BED, from a genome browser (such as ENSEMBL) and import this to an existing sequence.
This allows you to work on your own sequence, but keep it up to date with published annotation about that sequence.
The Import Features tool was introduced into MacVector 12.5.
Depending on the sequence start and stop points you may need to adjust the sequence numbering. For example if you are trying to annotate a single gene but the GFF is still numbered as if it was on a chromosome.
The easiest way is to adjust the numbering of your original sequence.
To do this:
If you have copy and pasted this sequence from an existing chromosome sequence then the original numbering will be preserved.