Database updated on 26-Jan-2017 with 423 changes

REDfly version 5.2.2 released!
REDfly now has the latest FlyBase anatomy ontology.
Regulatory Element Database for Drosophila v5.2.2


About REDfly

Sign up to receive announcements about important REDfly news.

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

User's Guide

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).

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.

Support REDfly is funded in part by National Science Foundation grant DBI-1355511 and by National Institutes of Health grant R01 GM114067.

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

We would like to give special thanks to the students of BCH502 "Genome Annotation and Analysis" (2013).

  • Michael Campbell
  • James Schuler
  • Jonathan Sipior
  • Cassandra Whitford



Funded in part by the NSF and the NIGMS