Hello, I am currently annotating viral genomes, poxviridae specifically, and I am having issues with how to annotate the fragmented genes. I am referring to the genes as "fragmented" based on the fact that they are similar in sequence but truncated on either end, or both, compared to the reference gene. This may be due to simply a premature stop codon, loss of the first Met, or deletions or insertions interrupting the genes. However, we have no wet lab evidence as to whether or not they are translated still, or if they maintain the original function.
Basically we hope to at least flag them, as not noting the ORFs would give a false idea that there is nothing present, and that they are not translated (which we don't know for sure), and annotating them simply as genes is assuming that they are translated and functional.
For submission purposes NCBI has suggested labeling the entire area as a "misc_feature".
How do you handle similar situations? Are there standards in place for how to approach fragmented eukaryotic or prokaryotic genes during genome annotation? Any suggestions?