how to identify exon and intron in sequence bioedit

The first and the third exons are partial (missing the 5’ and 3’ end respectively). CDS translation has three separate regions (three exons). Strings of the tilde symbol (~~~~~) indicate the intronic sequence. The translation shows a partial CDS (the start and the stop codon are missing). The aligned region between the two sequences have one-to-one correspondence. Query aligns in its entire length and the alignment is gapless. See the article on determining the coding strand for more information.įigures 1 and 2 below illustrate an example of the method.įigure 1 : A pairwise alignment of a 274 bp Query on the KC333362.1 (Subject) sequence. In addition, pay attention to the correct coding strand. Gaps within CDS may alter the reading frame. They will adjust to the alignment locations.Īny gaps in the alignment will affect CDS locations. Infer the CDS locations on Query from the FEATURES section in the Subject record.The link will display only the aligned region of the Subject record. Click the GenBank link in the Range row above the alignment.To learn how to verify the above items, see the article on interpreting pairwise alignments.Query (your sequence) aligns to Subject across its entire length.Subject has annotated coding region in the aligned region.Verify the following for the alignment:.Check the CDS feature box to display the CDS feature on the alignments.On the search result page, click the Alignments tab to view pairwise alignments.To find exon locations on your sequence, follow these steps: Only exons contribute to the coding region (CDS). Many genes from eukaryotic genomes contain exons and introns. See the article on blastn and CDS feature set up.

You can utilize the CDS feature display on the BLAST search results page. Nucleotide BLAST (blastn) can help you find coding regions (CDS) on your sequence.

How to identify exon and intron in sequence bioedit