In order, I would start using the projected GO Terms from Danio rerio, then straight to human and mouse. A large proportion of GO terms are applicable across all vertebrates, but the Cellular Component section is where most differences lie. GO used to have a list of curated terms that couldn't be projected taxonomically, so that when you would try to project from, say, Medaka to Human, it would not include those terms.
In Biomart, you can cross Medaka-Zebrafish genes by orthology, then get the GO terms for Zebrafish:
Repeat for Medaka-Human and Medaka-Mouse.
You can see all the GO annotations for medaka in the QuickGO browser www.ebi.ac.uk/QuickGO)
Click on the 'Search and Filter GO annotation sets' link on the front page and this will bring you all of the annotation in the GOA database. To filter for just medaka annotation, click on the 'Filter' button in the top-right hand Annotation Toolbar, select the 'Taxon' tab and type the taxon identifier(s) into the text box, then click on 'Refresh' at the bottom of the page. This will result in a table containing all of the annotations to the taxon you requested.
You can change the default UniProt accessions to Ensembl IDs by clicking on 'ID mapping' in the Annotation Toolbar and select the type of Ensembl ID you want, then click 'Refresh'.
You can look at various statistics for this annotation set by using the 'Statistics' button in the Annotation Toolbar.
You can also download the annotation set, but please ensure that you increase the download limit to the number of annotations in the set - this value can be found in the 'Summary' tab of the 'Statistics' section.