Genes Entirely Missed byGenie
| Strand | Begin | End | Other gene-finder hits | Homology hits | Gene names (Ashburner et al. 1999) | Evidence (Ashburner et al. 1999) | Comments |
| R | 230,985 | 240,152 | 3 | 0 | DS08249.5 | gene prediction only | — |
| F | 498,520 | 507,581 | 2 | 0 | DS01514.3 | gene prediction only | — |
| R | 523,395 | 525,283 | 3 | 0 | DS05899.7 | gene prediction plus low P value BLASThit | — |
| R | 533,592 | 536,913 | 3 | 0 | DS05899.6 | gene prediction only | — |
| F | 1,152,128 | 1,152,385 | 0 | 0 | DS07721.1 | cDNA (?) | very suspicious annotation |
| R | 1,285,030 | 1,286,199 | 3 | 1 | DS06874.6 | gene prediction plus low P value BLASThit | — |
| F | 1,300,469 | 1,315,922 | 3 | 0 | DS06874.7 | gene prediction only | — |
| R | 1,368,793 | 1,369,282 | 5 | 0 | Mst35Bb | cDNA | — |
| F | 1,484,701 | 1,489,834 | 2 | 0 | DS00929.16 | gene prediction only | suspicious annotation |
| R | 1,520,808 | 1,521,371 | 1 | 1 | DS00929.7 | gene prediction plus low P value BLAST hit | overlaps gene on opposite strand |
| F | 1,628,242 | 1,628,412 | 0 | 0 | DS003192.3 | cDNA (?) | very suspicious annotation |
| R | 1,663,026 | 1,663,163 | 0 | (2 opposite strand) | DS003192.4 | cDNA (?) | very suspicious annotation |
| R | 1,782,412 | 1,786,409 | 2 | 0 | Ms(2)35Ci | gene prediction only | — |
| R | 1,875,987 | 1,895,879 | 5 | 0 | DS03023.4 | gene prediction only | gene on opposite strand |
| R | 2,109,315 | 2,113,209 | 4 | 0 | BACR44L22.5 | gene prediction only | — |
| F | 2,158,476 | 2,159,460 | 3 | 2 | DS07108.5 | gene prediction plus low P value BLAST hit | — |
| F | 2,236,081 | 2,241,876 | 3 | 0 | DS02252.3 | gene prediction plus low P value BLASThit | 5000-bp single-exon gene |
| R | 2,286,435 | 2,287,433 | 3 | 0 | DS02252.4 | gene prediction plus low P value BLASThit | — |
| F | 2,398,367 | 2,410,394 | 5 | 0 | DS07486.5 | gene prediction only | — |
[i] The gene names from Ashburner et al. (1999) are listed. In addition, the evidence for that gene annotation from that paper is given. The Begin and End gene coordinates are from the std3 annotations. In addition, we list the number of overlaps by other gene finders and the two homology programs.