When we (the Gene Disruption Project) submitted data to FlyBase for the P-element insertion EY12548, we mapped it to a site on 3R that corresponds to genome release 5 coordinate 3R:3175658 . This was based on the alignment of the flanking sequence (GenBank accession CL943536) against the release 3 genomic sequence. The flank is repetitive and aligns for most of its length with the consensus for the transposable element micropia. In reviewing a realignment we have done of the flanking sequences to the release 5 genomic sequence, I found that the flank of EY12548 has a better alignment with the 3RHet scaffold (784/787 matched bases) than the 3R scaffold (777/787). The alignment to the 3RHet scaffold maps to coordinate 3RHet:1860931 (plus strand). I would therefore suggest that FlyBase should revise the insertion site data accordingly.
When we (the Gene Disruption Project) submitted data to FlyBase for the P-element insertion EY20548, we mapped it to a site that corresponds to genome release 5 coordinate 2L:22185957 . This was based on the alignment of the flanking sequence (GenBank accession DX977644) against the release 3 genomic sequence. In reviewing a realignment we have done of the flanking sequence to the release 5 genomic sequence, I found that the flank of EY20548 has a better alignment to another segment of 2L that would map the insertion to release 5 coordinate 2L:20120504 (minus strand). I would therefore suggest that you revise the insertion site data in FlyBase accordingly.
I'm writing to provide a minor revision for the insertion site coordinate for the P element EY11224. The correct coordinate for release 5 is X:10635545 (minus strand), which is 48 bp away from the site currently recorded in FlyBase. The original insertion site data was based on an alignment to the release 3 genome sequence assembly. This insertion was in a gap in the release 3 sequence that was filled in the release 5 assembly, leading to the revised site coordinate.
I am writing on behalf of the Gene Disruption Project to correct an error with respect to the insertion site of PBac{3HPy+}C377 (FBti0037929). The insertion site we reported was based on the alignment of the 5prime flanking sequence (GenBank accession DX575622) with the reference genomic sequence. I discovered today that errors made in automated reading of a region of poor quality sequence near the insertion site caused a segment of the sequence to give a spurious alignment to the reference genomic sequence. We reported the insertion site based on this alignment. I've reread the sequence chromatogram and the corrected sequence aligns more convincingly to a different site in the release 5 genome assembly at 3R:17683905 (plus strand). We will submit the revised sequence to GenBank.
