TRANSFAC

The TRANSFAC database contains experimentally determined transcription factor binding sites, and is a rich source of information for those interested in promoters and gene regulation.

You can create a free account on their website, and get transcription factor binding sites for a transcription factor by searching.

Finding binding sites of muscle-specific transcription factors in TRANSFAC
For example, I am interested in muscle-specific transcription factors such as MyoD. I searched for them in TRANSFAC like this: (at the search page)

1. Once you log in, you can then click on 'Search the TRANSFAC Public database', and on the search page you can choose to search in the 'Factor' table, and then you can choose search term 'muscle', and select 'Cell specificity (positive)' in the 'Table field to search in' menu:

2. and this will bring up a list of muscle-specific transcription factors. If you click on a particular transcription factor (e.g. MyoD, or hlh1 (the C.elegans ortholog of MyoD)), it will give you details such as 'BS' (binding site) which tells you the binding site sequence. )

(I can't show the MyoD entry here as it's copyright info, but make yourself a free account and you can view it too!)

Searching for binding sites in a sequence using TRANSFAC
You can also use the TRANSFAC website to search for binding sites in your sequence of interest. Go to MATCH webpage, and paste in your sequence there, and press 'Submit' to search.

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