undergrads

I am currently working with a freshman undergraduate student who wants to graduate with a degree in pharmacy. Hopefully exposure to a molecular biology lab will steer her in the correct direction. Yesterday I walked her through the workings of a plant genomic DNA prep. It looks like the DNA we extracted is going to work. We will find out the answer today. We are testing whether or not the prep worked by PCR. She will be amplifying a region of DNA where I suspect there to be a transgene. I am asking her to help me with identifying the presence of 35S:NF-YB12:YFP:HA. I am a bit skeptical of this line because I have performed protein analysis and had odd results. Most of the proteins I am trying to detect are ~25 kDa, with a 27 kDa YFP marker. This should some to ~50 kDa. I am worried because I am getting bands on western blots that are only half that size. This tells me one of two things: either the protein of interest is being cleaved out, and I am detecting only YFP:HA, or the other scenario, which is that I have no idea.