Welcome to footprintDB

20/06/2017 Updated interface annotations
04/05/2017 Added SMILE-seq motifs
25/04/2017 FASTA files of transcription factors available for download (see blog)
22/03/2017 Updated UniPROBE
21/12/2016 Updated 3D-footprint
19/10/2016 Check our new tutorial
28/06/2016 Added Athaliana cistrome motifs
27/05/2016 Added HumanTF2 with 663 motifs from TF heterodimers from Jolma et al
04/01/2016 Updated JASPAR to 2016 version

Current version of footprintDB includes:

  • 7553 Transcription Factors (TFs, 5837 unique)
  • 9817 Position Specific Scoring Matrices (PSSMs, PWMs or DBMs, 9217 unique)
  • 24714 DNA Binding Sites (DBSs, 21389 unique)
extracted from the literature and other repositories.

The binding interfaces of (most) proteins in the database are inferred from the collection of protein-DNA complexes described in 3D-footprint.

footprintDB predicts:

  1. Transcription factors which bind a specific DNA site or motif
  2. DNA motifs or sites likely to be recognized by a specific DNA-binding protein

As summarized in the schema:
footprintDB working schema
footprintDB Search footprintDB Tutorial


These data are available AS IS and at your own risk. The EEAD/CSIC do not give any representation or warranty nor assume any liability or responsibility for the data nor the results posted (whether as to their accuracy, completeness, quality or otherwise). Access to these data is available free of charge for ordinary use in the course of research.