Two tracks can be merged using the Merge Annotation Tracks tool:
Toolbox | Track Tools () | Merge Annotation Tracks ()
Select two or more tracks to be merged. The tracks have to be of the same type, e.g. gene tracks, and be based on the same genome.
Click Next and Finish to merge the tracks.
If the same annotation is found in both tracks, it is merged into one. If the two annotations share the same region (i.e. same coordinates), they are merged. Information from both annotations are retained in the output. Annotations are merged even when their names differ. Which name is being kept is entirely based on the order of the input tracks as the name being kept is derived from the track that was selected first in the Merge Read Mappings wizard. An extra column labeled Origin tracks is added to the resulting track indicating which track the annotation originates from. The Merge Annotation Tracks tool is useful when merging gene tracks from different sources using different naming conventions.
Please note that this tool is not well-suited for comparing tracks (see Comparing variants instead).