Should all annotations for a modified residue be included within the sequence listing, or can there be included a reference to a table in the description instead?
The sequence listing should be comprehensive and include all of the necessary annotations so it should not provide details of the modified residue/s in the description only.
As you note, WIPO ST.26 strongly recommends that the sequence should contain the unmodified nucleotide (or if not possible variable ‘n’) and a modified base feature. If there is a specific modified nucleotide which is not listed in Part 2 of Annex I of ST.26, then there should be both:
- a mod_base with qualifier value ‘OTHER’
- a note with qualifier value including the full name of the modified base.
Otherwise the mod_base qualifier should have the abbreviation provided in Part 2. Please refer to the ‘Representation of Modified Residues’ section of Annex VI of WIPO ST.26. Example 7(a)-6 of Annex VI may also be relevant for you.
Otherwise there are modifications which are missing from the resulting sequence listing once it is published as part of the INSDC database, for instance.