There is some confusion regarding Df(2L)Exel6011 and one of its progenitor insertions, P{XP}SP2637d02085, in FlyBase (FB2016_05).
Df(2L)Exel6011 was made using P{XP}SP2637d02085 (FBti0057390) and P{XP}vrid01873 (FBti0054652).  FlyBase lists the following coordinates for the Df and the XP's:
The Df goes from  2L:5147258  to  2L:5305646 
P{XP}SP2637d02085 is at  2R:18652815  (this one does not make sense)
P{XP}vrid01873 is at  2L:5305646  (this one does make sense)
It turns out Exelixis thought there were multiple insertions in the P{XP}SP2637d02085 line (so presumably Exel originally had flanking sequences that blasted two places). When the GDP analyzed the sequence Exel provided, it looks like they only analyzed the one flank that puts the insertion on 2R (it is not unlikely that there was only one unambiguous flank to analyze).  So, that's the coordinate FlyBase attached to d02085. (I re-did the blast and it does indeed blast to  2R:18652815 .)
I looked up the Df in Parks et al 2004 (FBrf0175003) and it lists d02085 at  2L:5139829  (  2L:5147258  in R6 coordinates).  The current ends of the Df in FlyBase are based on Kevin Cook's analysis of the data in 2008 (FBrf0205061) and he based the lower coordinate on the Exel-provided coordinate for d02085.  Available genetic analysis of the Df suggests it is okay so, in the absence of progenitor flanking sequence that makes sense, this seems like the right thing to do.
The d02085 stock no longer exists and was never published except for the Df paper (FBrf0175003) and the Bellen paper describing the pipeline for the re-analysis. Still, it would make sense to update the information about d02085 in FlyBase.
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Annette Parks
Bloomington Drosophila Stock Center
Dept of Biology
Indiana University