title: Gene Model Annotations for Drosophila melanogaster: The Rule-Benders.
abstract: In the context of the FlyBase annotated gene models in Drosophila melanogaster, we describe the many exceptional cases we have curated from the literature or identified in the course of FlyBase analysis. These range from atypical but common examples such as dicistronic and polycistronic transcripts, noncanonical splices, trans-spliced transcripts, noncanonical translation starts, and stop-codon readthroughs, to single exceptional cases such as ribosomal frameshifting and HAC1-type intron processing. In FlyBase, exceptional genes and transcripts are flagged with Sequence Ontology terms and/or standardized comments. Because some of the rule-benders create problems for handlers of high-throughput data, we discuss plans for flagging these cases in bulk data downloads.
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, crosby@morgan.harvard.edu.
authors.forename: Madeline A
authors.initials: MA
authors.lastname: Crosby
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138.
authors.forename: L Sian
authors.initials: LS
authors.lastname: Gramates
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138.
authors.forename: Gilberto
authors.initials: G
authors.lastname: Dos Santos
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138.
authors.forename: Beverley B
authors.initials: BB
authors.lastname: Matthews
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138.
authors.forename: Susan E
authors.initials: SE
authors.lastname: St Pierre
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138.
authors.forename: Pinglei
authors.initials: P
authors.lastname: Zhou
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Schroeder
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138.
authors.forename: Kathleen
authors.initials: K
authors.lastname: Falls
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138.
authors.forename: David B
authors.initials: DB
authors.lastname: Emmert
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138.
authors.forename: Susan M
authors.initials: SM
authors.lastname: Russo
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138.
authors.forename: William M
authors.initials: WM
authors.lastname: Gelbart
mesh_terms: D000818:Animals; D001483:Base Sequence; D018388:Codon, Terminator; D030541:Databases, Genetic; D004331:Drosophila melanogaster / Q000235:genetics*; D008928:Mitochondria / Q000235:genetics / Q000378:metabolism; D008957:Models, Genetic; D058977:Molecular Sequence Annotation; D014176:Protein Biosynthesis; D017393:RNA Editing; D022821:RNA Splice Sites
chemical_list: D018388:Codon, Terminator; D022821:RNA Splice Sites
keywords: bicistronic; multiphasic exon; non-AUG translation start; shared promoter; stop-codon suppression