AE - Render Supers with Alpha

These render settings in After Effects will allow you to export a stand alone super with the alpha (transparent) channel embedded in the final file.

With the composition you want to render selected, go to:

Composition > Add to Render Queue

By default AE will export as Lossless.

Select Output Module > Lossless with Alpha

Select Output To to save to an appropriate location

Select Render to export the final composition