Currently, GREAT supports recent assemblies of the well-annotated human (UCSC hg19 and UCSC hg18), mouse (UCSC mm9) and zebrafish (UCSC danRer6) genomes. GREAT will be available for the new zebrafish Zv9/danRer7 assembly soon. GREAT can be expanded to include additional well-annotated genomes and can also be expanded into poorly-characterized genomes by carefully projecting annotations from well-annotated genomes. 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.