In general, see How to describe CDS feature, when termination codon is found in the range.
You can also see Protein Coding Sequence; CDS feature to describe CDS feature.
Following items are case study for the error.
1. Did you correctly specify /codon_start qualifier to indicate reading frame of the CDS feature?
Select 1, 2 or 3, appropriately.
- Offset of the frame at translation initiation by codon_start
- How to fix error message: “First codon [***] is not a start codon.” / “Final codon [***] is not a stop codon.”?
- How to fix error message: "Value of [ codon_start ] is not 1, but [
- The Genetic Codes
- About /transl_table qualifier
- How to fix error message: "Invalid value [***] for [transl_table] qualifier."?
3. Are there really some stop codons in the range of CDS feature because of frame shift, nonsense mutation, or some other reason?
3-1. In case of pseudogene
Click [Select Qualifier] button beside CDS and add /pseudogene qualifier. Then, you can specify /pseudogene qualifier with its controlled vocabularies.
See also b) considered pseudogene in detail.
3-2. In cases of unsure whether it is pseudogene or not, the reason of stop codon is uncertain, or on the process of diversity increasing related to acquired immunity, describe misc_feature, not CDS feature.
See a) Putative nonsense mutation, frameshift caused by uncertain reason, or on the process of diversity increasing related to acquired immunity for IgG etc. in detail.