Obviously there is no 100% exact number, but I came across this on flybase, the gold standard for annotation. I am confused now. "Genes located to the genome", is that what I am looking for? If so, what does "Genes not located to the genome" mean?
Personal correspondence to representative at FlyBase.org
In FlyBase we have been gathering information about genes and phenotypes for over 20 years including information from papers and resources older than that. We annotate gene models on the Drosophila melanogaster genome assembly and when possible associate those annotations with other information (eg. phenotype, function etc) that is known about the gene. However, in some cases, especially for genes and phenotypes that were described in the older literature before the genome was sequenced we still have some information about those genes but have been unable to associate that information with a genome annotation. Those are what we call unlocalized genes (i.e. those without a annotation on the genome).