Microarray analysis of Df(3R)p-XT103
Kim Cook, Eric Spana and Kevin Cook
DNA samples from Df(3R)p-XT103 (FBab0002842) 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)p-XT103 breakpoint lies within CG31369 either within the intronic gene Or85b or to its left in the range  3R:4245820..4336007  (R5) (predicted cytology: 85A1-2) based on the following evidence.
The gene order at the left Df(3R)p-XT103 end is CG31369 (FBgn0250829) with CG31462 (FBgn0051462) and Obp85a (FBgn0037589) lying within its introns, Or85b (FBgn0037590). A sequence within Or85b (DM00015657,  3R:4336007..4336068  (R5)) was deleted. A sequence within Obp85a (DM00000502,  3R:4245752..4245820  (R5)) was not deleted, but Obp85a and CG31369 may have been disrupted. A sequence within CG31369 to the right of CG31462 (DM00016089,  3R:4224231..4224299  (R5)) was not deleted.
The right Df(3R)p-XT103 breakpoint lies within CG11966, CG11967 or RagA or in a region between them, and lies in the range  3R:4778677..4809191  (R5) (predicted cytology: 85B8-C1) based on the following evidence.
The gene order at the left Df(3R)p-XT103 end is CG11966 (FBgn0037645), CG11967 (FBgn0037647), RagA (FBgn0037647), CG11970 (FBgn0027503). A sequence within CG11966 (DM00000676,  3R:4778609..4778677  (R5)) was deleted. A sequence within RagA (DM00000678,  3R:4809191..4809259  (R5)) was not deleted, but RagA may have been disrupted. A sequence within CG11970 (DM00000679,  3R:4815638..4815706  (R5)) was not deleted. There was no microarray sequence representing CG11967. These mapping results agree with those of Kim-Ha et al. (http://flybase.org/reports/FBrf0053359.html), who placed the distal endpoint of Df(3R)p-XT103 30 to 40 kb distal to osk.
The rest of the microarray data are consistent with genes between Or85b and CG11966 being deleted in Df(3R)p-XT103.