Should all annotations for a modified nucleotide be included within the sequence listing, or can there be included a reference to a table in the description instead?
A sequence in a sequence listing should be comprehensive and include all of the necessary feature keys, qualifiers, and qualifier values to accurately represent the sequence without the need to refer to an external document. It is not acceptable to define a modified nucleotide by referring to a table or paragraph in the patent application description. The sequence listing should not rely on a reference to any external source of information, for example a table in the description of the patent specification.
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 sequences once it is published as part of the INSDC database, for instance.