I'm trying to map a genelist of NCBI Gene IDs from Scomber japonicus (Chub mackerel) to Danio rerio (Zebrafish) for further analysis with tools tailored to Danio that are not available for S japonicus.

I noticed that while Orthology.eg.db is able to convert most Scomber japonicus genes to NCBI Gene IDs, it fails to map LOC genes between species. For my analysis, I don't necessarily care that these genes aren't actually orthologs and that in both species these genes are LOC genes. I am just interested in programmatically converting my genelist of NCBI Gene IDs between the two species while capturing LOC to LOC conversions in addition to ortholog mapping. Is there a way to get around this limitation of Orthology.eg.db for LOC genes or is there another tool that I can use since they are not strictly orthologs?

Example using a genelist of NCBI Gene IDs:

genelist <- c(
  "128378700", "128369139", "128358931", "128359788", "128380930",
  "128362230", "128368409", "128375657", "128355604", "128369136"
)

mappings <- AnnotationDbi::select(
  Orthology.eg.db,
  keys = genelist,
  "Danio.rerio",
  "Scomber.japonicus"
)

This is a screenshot of the results from my example with some annotation added

Thank you for taking the time to answer and sorry if this is a dumb question!

It's not a dumb question.

The LOC genes are things that NCBI thinks might be genes, but are unsure of. They are sure enough to give them an NCBI Gene ID, but since it's uncharacterized, they don't give it a name, and instead just append LOC to the front of the gene ID. The Orthology.eg.db package is mapping between the NCBI Gene IDs for the two species though, so if there is a known orthologous gene in S. japonicus, you should get the mapping.

But it's unlikely for the LOC genes, because of how the orthologs are identified. In this case, transcripts from Scomber japonicus were sequenced using PacBio, and then assembled into full length transcripts using HiFiasm. The transcripts are then identified by comparing to a model organism (maybe D. rerio? I don't know). But usually the transcripts are only identified when they are similar to an existing, known transcript, so if there were a transcript in S. japonicus that is very similar to an uncharacterized LOC gene in D. rerio, it wouldn't be annotated because it's not informative.