Reading a gtf file I noticed that some transcripts have 2 lines with start codons, but it looks like there are not 2 different start codons but only one where the bases are not consecutive, what is happening?
In this image you can see one start codon is from 7771384 to 7771385 and the other 7773442. The open reading frame starts at the start codon, would it start at 7771384 or 7773442 in this case?
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bio_elle •
2 answers
Remember how translation comes after splicing.
The coordinates that you see are relative to the genome.
In your case, the region that forms the start codon spans a splice junction. The start codon is continuous relative to the transcript, it is just not continuous relative to the genome.
Note the "phase" as being 1 in the second annotation, it shows how the same codon is being continued.
start codon is split in two by a splicing site.
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