cDNA sequence
This highly customisable sequence shows, by default, the transcript sequence (cDNA), the coding sequence underneath it, and the protein sequence in the third line. Line numbering is different for all three sequences.
Line numbering
- First line: 1 at the start of the cDNA (i.e. the UnTranslated Region or UTR, if it is annotated)
- Second line: 1 at the start of the coding sequence (i.e. from the first A of ATG)
- Third line: 1 at the start of the protein sequence
Variations are drawn along the sequence, and an IUPAC ambiguity code represents the variation at the top of the relevant nucleotide. Click any ambiguity code for more information. A table of possible codes is described here.
Highlighted nucleotides are coloured according to the key at the top of the view. Red amino acids indicate that, due to sequence variation, one or more other amino acids are possible that that position.
Sequence colouring
- UTR or UnTranslated Region is highlighted in dark yellow.
- Exons are indicated by alternating black and blue nucleotide sequence.
- Codons are marked by light yellow highlight, alternating with no highlight.
- Variations are highlighted according to the key above the sequence. Red amino acids indicate more than one possible amino acid at that position. Hover over a red amino acid to see the alternative(s).
To turn off variations, coding sequence, UTR, and other markup, use the Configure this page tool button at the left. Note the view can be downloaded to open in Microsoft Word, using the Download view as RTF to do so.
To BLAST sequence, select your sequence of interest with your mouse then click on the pop-up button.
