DNA samples from Df(3R)by10 (FBab0002713) heterozygotes were compared to samples from wild type flies by Comparative Genomic Hybridization microarrays at the Duke Model System Genomics Unit as described in Erickson and Spana, 2006 (http://flybase.org/reports/FBrf0193934.html ). Corning CGAP slides spotted with the AROS Drosophila V1.1.1 ~70 nucleotide oligo set from Eurofins MWG Operon (www.operon.com) were used for the analysis. Most annotated genes were represented by a single oligo (denoted by a DM number). Sequences present at one copy in deletion heterozygotes are detected by lower relative fluorescence when compared to sequences present in two copies in wild type flies.
The left Df(3R)by10 breakpoint lies within CG16779 or CG8147 or in the region between them, and lies in the range  3R:5294508..5321599  (R5) (predicted cytology: 85D17-18) based on the following evidence.
The gene order at the left Df(3R)by10 end is CG9363 (FBgn0037697), CG16779 (FBgn0037698), CG8147 (FBgn0043791). Sequences within CG8147 (DM00010603, 3R: 5321599.. 5321667 (R5)) were deleted. A sequence within CG16779 (DM00004217, 3R: 5294440..5294508 (R5)) was not deleted, but CG16779 may have been disrupted. A sequence within CG9363 (3R: 5284423..5284491 (R5)) was not deleted.
The right Df(3R)by10 breakpoint lies within CG9467 or CG8526 or in the region between them, and lies in the range 3R: 5623647..5629439 (R5) (predicted cytology: 85E9) based on the following evidence.
The gene order at the left Df(3R)by10 end is CG9467 (FBgn0037758), CG8526 (FBgn0037759), CG9461 (FBgn0037760). Sequences within CG9467 (DM00011681, 3R: 5623579..5623647 (R5)) were deleted. A sequence within CG8526 (DM00010926, 3R: 5629439..5629507 (R5)) was not deleted, but CG8526 may have been disrupted. A sequence within CG9461 (DM00011676, 3R: 5631180..5631248 (R5)) was not deleted.
The rest of the microarray data are consistent with genes between CG8147 and CG9467 being deleted in Df(3R)by10.
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Kevin Cook, Ph.D.               Bloomington Drosophila Stock Center
Department of Biology           Indiana University