p-Scan

Pscan finds over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes.
Just submit a list of gene or transcript identifiers: RefSeq (for human, mouse, and drosophila, e.g.

NM_000546) TAIR (e.g. AT1G08810) for Arabidopsis; SGD (e.g. YPL248C) for yeast and specify the source organism as well as the region you want to be analyzed.