Compressing .mov and keeping alpha without changing to .flv

Hello,

I am trying to run a .mov file with alpha through Adobe Media Encoder to get a compressed .mov file with alpha. 

I found that I could change the file type to .flv with On2 VP6 codec, but I cannot use that because my file type must be .mov.  I am bringing the compressed .mov into Unity as a movie texture and Unity will only accept .mov .mpg .mpeg .mp4 .avi .asf.

Is there a way that I can run a .mov with alpha through AME and get a compressed .mov with alpha?

Thank you

Jon