If you are anyways going to clone the genes into vectors and transfect cells, then you might as well clone the genes into vectors with a fusion to GFP, mCherry, etc. Just be sure the added size doesn't affect the function of the protein.

If a GFP is too big, then yes you can tag with a His, V5, myc etc but be careful because many of those antibodies are also unspecific in my experience.

If confocal is not the only way you want to detect, "Anti-His and Anti-V5 " works really fine in Western blotting. You can study interactions of two proteins (if the are interacting) with similar tags by Co-IP. It worked for me great!

Every antibody reacts differently in every cell line. Sometimes, they are very specific and bind only the tag. Other times, I have used cell lines expressing proteins with a His tag using a very popular His antibody from Abcam and had tons of staining all over the negative control. So, which tag and which antibody to use is specific to your situation and cell line.

Thank you all. May be this detail will help: The two closely related genes will be cloned each in one of the two MCs of pBUD4CE vector (invitrogen), then transformed in Top10 E.coli for subsequent plasmid DNA yield. The plasmid DNA will be transfected in primary chicken Embryo fibroblast /cos7 cells and monitored for evidence of individual gene expression. Method to be employed may include indirect immunoflourescent, or western blotting.

If I understood correctly Faruku, You are going to clone two CDs in a dual vector (in two MCS) and going to look for its expression. If it is the case, I would go with any of 2 different His/V5/myc/Flag epitope tagging with the protein of interest (I like His and V5 >myc) and check the level of proteins by western blotting with respective monoclonal antibodies.