v5.5.3 (Database Updated 07/11/2019)

Database updated on 07/11/2019 with 66 changes
Gene annotation version 6.28
FlyBase ontology version 2019-03-28

Welcome to REDfly
Regulatory Element Database for Drosophila v5.5.3

About REDfly

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REDfly is a collaboration between the Halfon lab and the Center for Computational Research at the University at Buffalo.

Using REDfly:

Please see our User's Guide for more information.

Citing REDfly:

When referencing specific CRMs, please be sure to include a reference to the original discoverers (cited in the "cite" tab or under "PMID" in the GFF-formatted download).
  • Rivera, John, Keränen, Soile V. E., Gallo, Steven M. and Halfon, Marc S. (2018). REDfly: the transcriptional regulatory element database for Drosophila. Nucleic Acids Res.; doi:10.1093/nar/gky957

  • Gallo, S.M., Gerrard, D.T., Miner, D., Simich, M., Des Soye, B., Bergman, C.M. and Halfon, M.S. (2010). REDfly v3.0: Toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Res.; doi: 10.1093/nar/gkq999

  • Halfon, M.S., Gallo, S.M., and Bergman, C.M. (2008). REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila. Nucl Acids Res 36, D594-598; doi:10.1093/nar/gkm876

  • Gallo, S. M., Li, L., Hu, Z. and Halfon, M. S. (2006). REDfly: a regulatory element database for Drosophila. Bioinformatics, Vol. 22 no. 3 2006, pages 381-383; doi:10.1093/bioinformatics/bti794

  • Bergman, C. M., Carlson, J. W. and Celniker, S. E. (2005). Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster. Bioinformatics, Vol. 21 no. 5 2005, pages 1747-1749; doi:10.1093/bioinformatics/bti173

About our logo:

The REDfly logo was designed by Alex Read of alexreaddesign as part of the GMOD Spring 2010 Logo Program.

Funding Support:

REDfly is funded in part by National Science Foundation grant DBI-1758252 and National Institutes of Health grant R01 GM114067. Previous support was provided by NSF DBI-1355511.


REDfly utilizes the MySQL database. A schema diagram can be found here.

We would like to give special thanks to our student curators from the following classes:

Funded in part by the NSF and the NIGMS

Copyright © University at Buffalo—State University of New York. REDfly is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International license. The copyrights of all curated content belong to their respective owners.