How do you export an animation with video file in timeline?

Hello,

I've got an animation I've done over the top of a video clip. The video is on one layer and the animation on the one above. Is there a way I can export the clip with the video included?

I've tried exporting as a png sequence and then in Premiere adding that over the video clip but it's out of sync (even with correct frame rates)

See above but with an animated gif and exporting as a video.

Can anyone help? Cheers!