How do I create an intron-containing feature based on alignment of a cDNA sequence with a reference genomic sequence?
Align a cDNA to a Reference Sequence
Open a reference genomic DNA sequence, then import and align your cDNA by clicking Tools → Align to Reference DNA Sequence.
In Map view, SnapGene will show the alignment, with gaps inserted if appropriate.
Create a New Feature Based on the Alignment
In Map view or Sequence view, right-click (Windows) or Ctrl-click (macOS) on the cDNA sequence name and click Make Feature from Sequence.
Alternatively, make sure the aligned cDNA is selected, then open the "Aligned Sequences" dropdown menu and click Make Feature from Selected Sequence.
Choose to Annotate Gaps as Introns
Click Annotate Gaps to create a new feature with gaps between the aligned cDNA regions. The gaps will correspond to introns.