Currently, GREAT supports one recent assembly each of the well-annotated human (UCSC hg18) and mouse (UCSC mm9) genomes. GREAT can be expanded to include additional well annotated genomes (such as Zebrafish), and can also be expanded into less characterized genomes by carefully projecting annotations from well annotated ones. We hope to gradually expand the set of species we support.
If you have genomic regions defined for a different species or assembly from the ones we currently support, you can use the UCSC LiftOver utility to convert to a supported assembly. The LiftOver typically works very well for within-species coordinate conversion (e.g. from one human assembly to another), but it can also be used as a best approximation of mapping regions in one genome to the orthologous regions of a genome for a different species (e.g., from chimpanzee to human), although more caution is obviously advised in these cases.