Ensembl provides annotations indicating regions in the genome that are experimentally verified to be bound by transcription factors (from ChIP-Seq experiments). Within these regions, we now also provide precise transcription factor binding sites. To generate these binding sites, we make use of publicly available Position Weight Matrices (PWM) from Jaspar.
Transcription factor binding sites can be seen as black boxes in the Regulatory Features track. If you click on a Regulatory Feature you can see information regarding the binding sites contained within that regulatory feature. This includes the binding matrix used and a binding score representing how well a particular site matches the binding matrix. Clicking on a specific black box within the regulatory feature will highlight the corresponding information on the menu (the darker blue line in the figure showing information for a CTCF binding site). Transcription factor binding sites are also displayed as evidence for a regulatory feature (as ‘Core PWM’ entries).
To generate these PWM matches we take Jaspar matrices and find matches throughout the genome. Then, we use experimental binding data to stringently choose high confidence binding sites that fall within regions enriched in ChIP-Seq experiments for the corresponding factor. More details on this process can be found here.