Possible Wrong Annotations in std3
| Strand | Begin | End | Genie | Genie EST | Genie ESTHOM | Other gene finder hits | Homology hits | Gene name | Evidence (Ashburner et al. 1999) | Evidence |
| R | 213,507 | 217,188 | X | X | X | 7 | 1 | DS08249.3 | gene prediction only | last exon questionable |
| F | 281,649 | 284,052 | X | X | X | 6 | 2 | D00797.5 | cDNA (partial?) | missing 10 leading exons |
| R | 941,115 | 944,598 | X | X | X | 4 | — | DS08340.1 | gene prediction only | four extra 3′ exons |
| F | 1,205,439 | 1,213,325 | X | X | X | 5 | — | DS07721.3 | gene prediction only | first exon and last 3 exons questionable |
| R | 1,371,813 | 1,372,351 | — | X | X | 3 | — | TFIIS | known gene | longer first and shorter last exon |
| R | 1,549,142 | 1,549,933 | X | X | X | 6 | — | DS07295.4 | gene prediction only | initial exon and first EST verified intron missed |
| F | 1,721,863 | 1,728,736 | X | — | — | 1 | — | DS07295.4 | gene prediction only | at least first seven exons very questionable |
| R | 1,913,374 | 1,914,948 | X | X | X | 6 | 1 | wor | gene prediction plus BLAST homology hits | additional first EST-verified exon |
[i] Genes from the std3 annotations are listed for which multiple evidence from Genie and other programs exists implying wrong annotations. The Begin and End coordinates are from the std3 annotations. The evidence for the annotation in std3 is given as noted in Ashburner et al. (1999) In addition, comments for rejecting the annotated gene structure by Genie are listed.