Databases and repositories currently included in footprintDB:

		If you want to search for an specific entry use the Search Entry Form. 
			
If you want to search for a protein sequence or a DNA motif use the Sequence Search Form.
			
If you want to download motifs or sites for another databases different from 3D-footprint, please visit the original sources or ask permission to the authors.		

		

			A new feature in footprintDB is the possibility to refer any Transcription factor, DNA motif or site with the following URL format:


			https://footprintdb.eead.csic.es/index.php?db=DATABASENAME:VERSION&[motif|tf|site]=ACCESSION


			You must specify the database name followed by colon and the version, then ampersand, the data type (motif, tf or site) equals sign and the accession name (be careful it is case sensitive).

			Like in this example.
			The resulting URL will be automatically redirected to the footprintDB entry.
		

		

		

		
DatabaseVersionTFsMotifsSitesDescriptionAuthorsData

		
JASPAR 120242513634757601Open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six taxonomic groupsRauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, et al.
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					DNA Binding Motifs

DNA Binding Sites

CISBP 21.02187818920Subset of directly determined DNA motifs within the CIS-BP Database.Weirauch MT, Yang A, Albu M et al.
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					DNA Binding Motifs

3D-footprint 320231221186815572059DNA-binding proteins from the Protein Data Bank with annotated interface residues and structure-based DNA motifsContreras-Moreira,B.
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HT-SELEX2 4May201753317610SELEX motifs of human TFs bound to methylated and unmethylated ligandsYin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schubeler D, Vinson C and Taipale J
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					DNA Binding Motifs

UniPROBE 52016060169710424503Repository of experimental data from universal protein binding microarray (PBM) experimentsHume MA, Barrera LA, Gisselbrecht SS, Bulyk ML
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					DNA Binding Motifs

DNA Binding Sites

HOCOMOCO 61053510660Homo sapiens comprehensive model collection containing carefully hand-curated TFBS models constructed by integration of binding sequences obtained by both low and high-throughput methodsKulakovskiy I.V., Vorontsov I.E., Yevshin I.S., Soboleva A.V., Kasianov A.S., Ashoor H., Ba-Alawi W., Bajic V.B., Medvedeva Y.A., Kolpakov F.A., Makeev V.J.
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					DNA Binding Motifs

AthalianaCistrome 7v4_May20165328610Raw and unmethylated genomic DNA DAP-seq motifs for Arabidopsis thaliana in-vitro-expressed TFs. OMalley RC, Huang SC, Song L et al.
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					DNA Binding Motifs

HumanTF 81.05328180Sequence-specific binding preferences of human TFs obtained by high-throughput SELEX and ChIP sequencing. A total of 830 binding profiles were obtained, describing 239 distinctly different binding specificitiesJolma A., Yan J., Whitington T., Toivonen J., Nitta K.R., Rastas P., Morgunova E., Enge M., Taipale M., Wei G., Palin K., Vaquerizas J.M., Vincentelli R., Luscombe N.M., Hughes T.R., Lemaire P., Ukkonen E., Kivioja T., Taipale J.
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					DNA Binding Motifs

HumanTF2 91.01396630Sequence-specific binding preferences of human TF pairs that bind cooperatively to DNA obtained by CAP-SELEX analysis of 9,400 TF-TF-DNA interactions. This analysis revealed 315 TF-TF interactions recognizing 618 heterodimeric motifs, most of which have nJolma A., Yin Y., Nitta K. R., Dave K., Popov A., Taipale M., Enge M., Kivioja T., Morgunova E., Taipale J.
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					DNA Binding Motifs

AthaMYB 101.011622416Analysis of the DNA-Binding Activities of the Arabidopsis R2R3-MYB Transcription Factor Family by One-Hybrid Experiments in Yeast.Kelemen Z., Sebastian A., Xu W., Grain D., Salsac F., Avon A., Berger N., Tran J., Dubrecq B., Lurin C., Lepiniec L., Contreras-Moreira B., Dubos C.
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EEADannot 112023-12-228314426Manual curation of selected DNA motifs and cis regulatory sites, mostly from plantsContreras-Moreira B, Sebastian A.
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FlyZincFinger 121.0 691410Global analysis of Drosophila Cys2-His2 zinc finger proteinsEnuameh MS et al (Wolfe Lab)
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					DNA Binding Motifs

SMILE-seq 131.0711030Validated DNA-binding data from a set of full-length human, mouse and Drosophila TFs, including some heterodimers and distinct structural classes. This data has been obtained by semiautomated protein-DNA interaction characterization technology (SMiLEseq)Isakova A., Groux R., Imbeault M., Rainer P., Alpern D., Dainese R., Ambrosini G., Trono D., Bucher P., Deplancke B.
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ArabidopsisPBM 1420140210641080Collection of 63 plant TFs representing 25 families, using protein-binding microarrays. Almost half of these TFs recognize secondary motifs, which in some cases were completely unrelated to the primary element. Analyses of coregulated genes and transcriptFranco-Zorrilla JM
Lopez-Vidriero I
Carrasco JL
Godoy M
Vera P
Solano R
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					DNA Binding Motifs

Athamap 15200910287491144AthaMap provides a genome-wide map of potential transcription factor binding sites (TFBS) in Arabidopsis thalianaBulow L, Engelmann, S., Schindler, M., Hehl R.
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					DNA Binding Motifs

DNA Binding Sites

DBTBS 161.071901261A database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation informationSierro N., Makita Y., de Hoon M.J.L. and Nakai K.
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					DNA Binding Motifs

DNA Binding Sites

RegulonDB 177.582821862Curated data of the transcriptional regulatory network of Escherichia coli K12Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muniz-Rascado L, Martinez-Flores I, Salgado H, Bonavides-Martinez C, Abreu-Goodger C, Rodriguez-Penagos C, Miranda-Rios J, Morett E, Merino E, Huerta AM, Trevino-Quintanilla L, Collado-Vides J.
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					DNA Binding Motifs

DNA Binding Sites

DrosophilaTF 181.16062886Motif models reported in 51 primary references in the form of position PWMs for 56 Drosophila melanogaster transcription factorsDown TA, Bergman CM, Su J, Hubbard TJ
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					DNA Binding Motifs

DNA Binding Sites

humanC2H2ZF-ChIP 19Feb201539390HS Najafabadi, S Mnaimneh, FW Schmitges, M Garton, KN Lam, A Yang, M Albu,
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					DNA Binding Motifs

		

		

		

		


1Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Cheneby J, Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard B, Sandelin A, Wasserman WW, Parcy F, Mathelier A. JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles. Nucleic Acids Res : (2023). [Pubmed]


2Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K, Zheng H, Goity A, van Bakel H, Lozano JC, Galli M, Lewsey MG, Huang E, Mukherjee T, Chen X, Reece-Hoyes JS, Govindarajan S, Shaulsky G, et al. Determination and inference of eukaryotic transcription factor sequence specificity. Cell. 2014 Sep 11;158(6):1431-43. doi: 10.1016/j.cell.2014.08.009. [Pubmed]


3Contreras-Moreira B. 3D-footprint: a database for the structural analysis of protein-DNA complexes. Nucleic acids research 38:D91-7 (2010). [Pubmed]


4Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schübeler D, Vinson C, Taipale J. Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science : (2017). [Pubmed]


5Hume MA, Barrera LA, Gisselbrecht SS, Bulyk ML. UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions. Nucleic Acids Res : (2015). [Pubmed]


6Kulakovskiy IV, Vorontsov IE, Yevshin IS, Soboleva AV, Kasianov AS, Ashoor H, Ba-Alawi W, Bajic VB, Medvedeva YA, Kolpakov FA, Makeev VJ. HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. Nucleic Acids Res : (2016). [Pubmed]


7O'Malley RC, Huang SS, Song L, Lewsey MG, Bartlett A, Nery JR, Galli M, Gallavotti A, Ecker JR. Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape. Cell 165:1280-92 (2016). [Pubmed]


8Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, Palin K, Vaquerizas JM, Vincentelli R, Luscombe NM, Hughes TR, Lemaire P, Ukkonen E, Kivioja T, Taipale J. DNA-Binding Specificities of Human Transcription Factors. Cell. 2013 Jan 17;152(1-2):327-39. [Pubmed]


9Jolma A, Yin Y, Nitta KR, Dave K, Popov A, Taipale M, Enge M, Kivioja T, Morgunova E, Taipale J. DNA-dependent formation of transcription factor pairs alters their binding specificity. Nature 527:384-8 (2015). [Pubmed]


10Kelemen Z., Sebastian A., Xu W., Grain D., Salsac F., Avon A., Berger N., Tran J., Dubrecq B., Lurin C., Lepiniec L., Contreras-Moreira B., Dubos C. Analysis of the DNA-Binding Activities of the Arabidopsis R2R3-MYB Transcription Factor Family by One-Hybrid Experiments in Yeast. PLoS One 10, e0141044 (2015). [Pubmed]


11Contreras-Moreira B, Sebastian A. FootprintDB: Analysis of Plant Cis-Regulatory Elements, Transcription Factors, and Binding Interfaces. Methods Mol Biol 1482:259-77 (2016) [Pubmed]


12Enuameh MS et al (2013) Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. Genome Res. 23(6):928-40. doi: 10.1101/gr.151472.112 [Pubmed]


13Isakova A, Groux R, Imbeault M, Rainer P, Alpern D, Dainese R, Ambrosini G, Trono D, Bucher P, Deplancke B. SMiLE-seq identifies binding motifs of single and dimeric transcription factors. Nat Methods 14:316-322 (2017). [Pubmed]


14Franco-Zorrilla J.M, López-Vidriero I, Carrasco J.L, Godoy M, Vera P, Solano R. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proceedings of the National Academy of Sciences of the United States of America : (2014). [Pubmed]


15Bulow L, Engelmann S, Schindler M, Hehl R. AthaMap, integrating transcriptional and post-transcriptional data. Nucleic acids research 37:D983-6 (2009).  [Pubmed]


16Sierro N, Makita Y, de Hoon M, Nakai K. DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic acids research 36:D93-6 (2008). [Pubmed]


17Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muniz-Rascado L, Garcia-Sotelo JS, Weiss V, Solano-Lira H, Martinez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernandez S, Alquicira-Hernandez K, Lopez-Fuentes A, Porron-Sotelo L, Huerta AM, Bonavides-Martinez C, Balderas-Martinez YI, Pannier L, Olvera M, Labastida A, Jimenez-Jacinto V, Vega-Alvarado L, Del Moral-Chavez V, Hernandez-Alvarez A, Morett E, Collado-Vides J. RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res. 2013 Jan 1;41(D1):D203-D213. [Pubmed]


18Down T.A, Bergman C.M, Su J, Hubbard T.J. Large-scale discovery of promoter motifs in Drosophila melanogaster. PLoS computational biology 3:e7 (2007). [Pubmed]


19Najafabadi HS, Mnaimneh S, Schmitges FW, Garton M, Lam KN, Yang A, Albu M, Weirauch MT, Radovani E, Kim PM, Greenblatt J, Frey BJ, Hughes TR. C2H2 zinc finger proteins greatly expand the human regulatory lexicon. Nat Biotechnol 33:555-62 (2015). [Pubmed]



		

	

			
		
				

	
Disclaimer and license


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. Downloaded data have CC-BY-NC-SA license. FootprintDB is also available at RSAT::Plants, part of the INB/ELIXIR-ES resources portfolio.