I've been characterizing the cellular localization of an endogenous protein using an antibody directed against it and found that it is located in discreet round-shaped vesicle-like puncta that colocalize or are adjacent to the Golgi as detected with the Golgi marker GM130. Since I am new to the field I am having a hard time figuring out what type of structures these could be. They do not colocalize with the ER (Grp78), early endosome (EEA1) or the clathrin adaptor protein (AP2). I am confused by the fact that this protein partially colocalizes with the Golgi, but the shape of the structure is vesicular rather then elongated. Is it possible that some proteins are located only in distinct regions of the Golgi compartment? Or are these distinct vesicles that separate from the Golgi?
If anyone knows of markers that would be helpful in identifying the localization of my protein I would be incredibly grateful.