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- From NCBI or ENSEMBL database.
For example, one can download the TMPRSS2 transcript variant 1 from NCBI Genbank using identifier NM_001135099.1.
This can be also done from UGENE using option Access remote database or Search NCBI Genbank. - Align the genomic and cDNA sequences using spliced aligner.
For this option one has to have both genomic and cDNA sequences. In UGENE the alignment can be performed using the Spidey tool.
To run the alignment open the genomic sequence and select action Align -> Align ‣ Align to mRNA sequence.
The generated exon annotation can be then exported using action Export -> Export ‣ Export sequence of selected annotations
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