After Effects hasn't been able to directly export GIFs for some time now. There are plugins available that'll do it or you should be able to use the Media Encoder if you're on Windows (I don't use Windows so I'm just going on what the documentation says).
See How to export a GIF from After Effects?
Otherwise you'll have to export something that supports transparency from After Effects then import in to Photoshop and export as a GIF from there. I usually export a PNG sequence but you could export a lossless MOV too. Most of the following applies regardless of the output format..
From the render queue, choose the format from the Output Module Settings dialog and make sure the video output channels are set to "RGB + Alpha" (otherwise it will output without the transparency). Also make sure "Resize" isn't checked.
From the Render Settings dialog, make sure the resolution is set to "Full" (and the corresponding "size" is correct). You can change your frame rate here too (you generally don't want a GIF at ~30 fps or whatever your video is).
After outputting your PNG sequence, open them in Photoshop by selecting the first in the sequence in the file open dialog (clicking "Options" if needs be) and making sure "Image Sequence" is checked. Set the frame rate in the dialog that pops up next to the same as you set in the output from After Effects.
Use Photoshop's "Save For Web" to export the GIF. Make sure "Transparency" is checked (you'll see the transparency grid in the preview) and make sure your image size is set to 100%.
You should now have a transparent GIF at the correct size.