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My student is annotating contig54 of the D. ficusphila 3L control and has run into an interesting problem when annotating Atox1-PB. In melanogaster this particular isoform is hypothesized to result in a longer protein than PA via stop codon read-through, past the stop codon that ends the Atox1-PA isoform coding region. It looks as if we see this also conserved in ficusphila. In other words, the last CDS maps to the third reading frame for both isoforms but there are two possible stop codons, the earlier one used for PA and the later for PB. Is there a way to indicate read-through in the gene model checker? If not, he will get error messages for his PB annotation even though we think it's correct. What would you recommend we do?
No. However, your students can include a note in the GEP Annotation Report after the screenshot of the Gene Model Checker checklist. The note will justify the error in the checklist with the explanation that the B isoform of Atox1 contains a read-through stop codon in D. melanogaster (see screenshot below)