Back right side of the cubby - couple of little foam fingers there to hold a pen vertical. Slightly too wide for an average pencil, but works fine for most pens. It is a nice touch 'cause otherwise, all pens end up on the bottom under everything.Where is the pen Clip
I have not found that yet.
But I think I am just going to drill a hole in the top of that wasted square protrubence in the left front of that box (where older models had a USB port). That will allow it to hold all sorts of pen or pencil shaped stuff, just like a pencil cup on a desk.