Annotation tracks, as well as annotations on sequences (individual elements or in sequence lists), can be exported to a GFF3 format file using the dedicated GFF3 exporter.
A subset of annotations on a sequence or sequence list can be exported from the Annotation Table () view: select the annotations to export in the table, right-click, and choose Export Selection to GFF3 File from the menu (figure 15.20). Further information about sequence annotations is in Working with annotations.
When relationships between annotations should be maintained, for example the relationship of transcripts to genes, all the tracks containing related annotations must exported together, with the "Output as single file" option selected.
Relationships are represented in GFF3 using Parent and ID tags, as described in the GFF3 documentation (http://gmod.org/wiki/GFF3). See also GFF3 format. Parent tags cannot be preserved if relevant tracks are not included or if different annotation types are output to separate files.
For example, annotations in transcript tracks typically contain a Parent linking the transcript to a gene. If the transcript and gene tracks are exported together, the Parent tags are preserved. If this GFF3 file is later imported, the relationships between transcripts and genes will be intact in the resulting tracks.