I second Frank´s and Artem´s answers: experiments will show you where
your protein is!
A good starting point is to perform subcellular fractionation to
separate as many different organelles, and trace your protein by western
blotting those. For all organelles I know there exist typical marker
proteins (for many of which antibodies are commercially available) that
you can (and should!) use as controls for the fractionation.
In vivo localization of a protein can be visualized by gfp fusions just
as you did, but you should consider that GFP is quite big and might
interfere with your protein's function and/or localization.
deleonardis at farmbiol.uniba.it wrote:
>> I'm a Ph d sudent and I'm working for an ipotetical mitochondrial or
>> peroxisome carrier protein (human) (maybe Aprille's carrier) and I just
>> work with my protein fused with GFP, but I dont'have any evidence of
>> mitochondrial localization for my protein (i used CHO cell). So, the best
>> software for alignment give an high omology with Ca2+ binding solute carrier
>> protein of rabbit.....but other softwares say that my protein is
>> cytosolic(Prosite, ecc) . I study in vitro (ricostituited into
>> proteoliposome) the transport of my protein cloned and overexpressed in
>> Does anyone help me, such as say me the best software for subcellular
>> loclization ....ecc.