You can create an mp4 via Adobe Media Encoder. Depending on your future plans for for re-using this project, that could be a wise choice or a bad choice. For example, if you plan to go to blu-ray, broadcast and some other distribution medium, you may want to render something a quicktime in Photo JPEG, using it in AME to transcode to the other distribution specs at the same time.
AE has some difficulties in rendering to MP4. You can make a MP4 file but it till have the .mov extension. I would suggest using the add to media encoder queue function in the composition menu. Once it's loaded in AME, you can select the H264 option in the format pulldown. Then you have all kinds of options in the preset pulldown based on what you need for the final output (iPhone, tablet, Youtube etc.). Your output will have the .mp4 extension.
Hope this helps.