To identify motifs downstream of TSSs potentially differing between the structurally related bidirectionally transcribed enhancer TSSs and nonCGI-associated promoter TSSs, we extracted 600bp regions downstream of each TSS and performed comparative de novo motif searches using HOMER. Here, we analyzed one set using the other set as background (corrected for region size, matched for GC content and autonormalized) to calculate motif enrichment only on the given strand. The top motif enriched downstream of nCGI promoters was the 5’-splice site motif. Genomic distributions of the enriched splice site motif, as well as the AATAAA termination signal were generated using HOMER.
