Changes affecting gene model number or type in releases 3.0 and 3.1 of the annotated D.melanogaster genome. - FlyBase Genome Annotators (2002)
For each genome release, there are generally a number of changes that affect the total number or type of gene models (annotations) for that annotated genome. FlyBase curates standard comments indicating the nature of the change to the gene model in each of the affected gene reports. These comments are attributed to a "FlyBase analysis" type reference for that genome release. The type of changes and the comments that may be found on the gene reports are listed here. The list contains all the different types of changes that may be commented for any genome release, a particular genome release may not contain all the different types of changes. This particular reference is the "FlyBase analysis" reference for release 3 of the annotated D.melanogaster genome. A. Changes affecting gene model number. There are 4 main types of changes. 1. New Gene Models. When a gene model is made where previously there was none annotated on the genome, a comment of the following type is listed in the "OTHER COMMENTS" subsection of the "OTHER INFORMATION" section of the relevant gene report, attributed to this reference. "New annotation (CGxxxxx) in release 3 of the genome annotation." where CGxxxxx is the annotation symbol. 2. Restored Gene Models. A gene model that had previously been deleted in an earlier release of the genome (due to lack of sufficient supporting evidence) may be restored in a later release of the genome if new evidence for the gene model becomes available. In this case, a comment of the following type is listed in the "OTHER COMMENTS" subsection of the "OTHER INFORMATION" section of the relevant gene report, attributed to this reference. "Annotation CGxxxxx restored in release 3 of the genome annotation." where CGxxxxx is the annotation symbol. 3. Deleted Gene Models. A gene model may be deleted due to lack of sufficient supporting evidence. In this case, although there will no longer be a gene model on gbrowse, the gene report is not deleted, so that data about the gene from the literature is still available on FlyBase, and a comment of the following type is listed in the "OTHER COMMENTS" subsection of the "OTHER INFORMATION" section of the relevant gene report, attributed to this reference. "Annotation CGxxxxx eliminated in release 3 of the genome annotation." where CGxxxxx is the annotation symbol. 4. Merged Gene Models. Gene models that were previously separate may be merged, due to new supporting evidence. In this case, a comment of the following type is listed in the "RELATIONSHIP TO OTHER GENES" subsection of the "OTHER INFORMATION" section of the gene report representing the new merged gene model, attributed to this reference. "Annotations CGxxxxx and CGyyyyy merged as CGzzzzz in release 3 of the genome annotation." where CGzzzzz is the annotation symbol of the new merged gene model. 5. Split Gene Models A gene model may be split into two or more separate gene models, due to new supporting evidence. In this case, a comment of the following type is listed in the "RELATIONSHIP TO OTHER GENES" subsection of the "OTHER INFORMATION" section of the gene report representing each new separate gene model, attributed to this reference. "Annotation CGxxxxx split into CGyyyyy and CGzzzzz in release 3 of the genome annotation." where CGyyyyy and CGzzzzz are the annotation symbols of the new separate gene models. B. Changes affecting gene model type. If a gene model is changed from protein coding (annotation symbol begins with "CG") to non-protein coding (annotation symbol begins with "CR") or vice versa, a comment of the following type is listed in the "OTHER COMMENTS" subsection of the "OTHER INFORMATION" section of the relevant gene report, attributed to this reference. "Annotation CGxxxxx renamed CRxxxxx in release 3 of the genome annotation." or "Annotation CRxxxxx renamed CGxxxxx in release 3 of the genome annotation." C. Additional comments. The following types of additional comments may also be attributed to this reference. 1. Dicistronic gene models. If a new dicistronic gene model is created, a comment of the following type is listed in the "RELATIONSHIP TO OTHER GENES" subsection of the "OTHER INFORMATION" section of the gene reports representing each open reading frame, attributed to this reference. "One or more of the processed transcripts for this gene contain(s) two non-overlapping open reading frames (ORFs). The non-overlapping ORFs are represented by X, Y." Where X and Y are the gene symbols representing each open reading frame. 2. Gene models sharing untranslated sequences. If two separate gene models are newly identified to share untranslated sequences but have non-overlapping open reading frames, a comment of the following type is listed in the "RELATIONSHIP TO OTHER GENES" subsection of the "OTHER INFORMATION" section of the gene reports representing each open reading frame, attributed to this reference. "One or more of the processed transcripts for this gene share(s) untranslated sequences with a transcript of an adjacent gene, but encode(s) a single open reading frame (ORF). The non-overlapping ORFs that share untranslated sequences are represented by X, Y." Where X and Y are the gene symbols representing each non-overlapping open reading frame. 3. Known mutations in the sequenced strain. If a mutation in the sequence strain is newly identified in a genome release, an allele representing this mutation is created and a comment of the following type is listed in the "COMMENTS" section of the allele report, attributed to this reference. "Mutation found during genome annotation of the strain used in the genome sequencing project."