cDNA sequence

The cDNA view shows the spliced transcript along the protein and CDS sequences (Figure 19).

Figure 19. Compare the transcript sequence, coding sequence, and variation in the cDNA view.

The cDNA view shows three sequences aligned on top of each other: the transcript sequence in the first row, the coding sequence alone (no UTR) in the second row, and the protein sequence in the third row. Use the blue 'Configure this page' button on the left to change which sequences you can see.

The UTR is shown higlighted in bright yellow. Codons are shown in alternating pale yellow highlight and no highlight. Alternating exons are shown by switching between black and blue text.

By default, variants are highlighted on the sequence, coloured by consequence according to the legend at the top. Ambiguity codes for the variants are shown above the sequence. Click on one to open the variant tab, explored further on in this course.  Amino acids affected by sequence variation are marked in red. Hover over a red amino acid with your mouse to view the alternatives. You can turn off the variants by going to the 'Configure this page' menu,.

How do you access the cDNA sequence? Try our guided example.