Hi fredoagudelo,
QuickTime is a name for a huge collection of codecs, with very different features.
Most QT based results are in no need for anything but RGB values. So, you need either to chose a format that can work with alpha channels or render out the channel in a separate version.
I tested QT Animation here, and it works. Make certain to interpreted the file correctly in Ae.
I have send you an upload link to your Private Messages here on Cineversity. If you could just render this clip with 12 frames or so?
Formats with alpha options: “Animation [M+]”, or “ProRes4444”
Formats typically used as end-delivery (e.g. web publishing) format have no alpha channel. For those formats (if you must, not advice to use such formats at all!), use the “Separate Alpha” option in the Render Settings.
Typically, it is not advised to use QT for rendering. Any interruption requires a new restart of the whole rendering, etc. Especially any compression that is not lossless has to be avoided during production, certainly with any wish to use alpha information during the post-work. Many QT formats switch occasionally Gamma, if not told otherwise, which is an old problem that carries on, based on old gamma based times. Most formats only support 8bit/channel, which seems very dated – to say the least. Not even to talk about color management.
Image sequences are way more common and industry standard, but also here, avoid 8bit/channel, and for high quality work, use Open EXR.
All the best
