|Citation||Levis, R. (2009.8.13). Release 5 sequence localizations for HP and DP lines. (Export to RIS)|
|Publication Type||Personal communication to FlyBase|
|Text of Personal Communication||
On 8/13/2009 3:37 PM, Robert Levis wrote:
I am attaching a table of sequence locations for the collection at the Bloomington Stock Center of P-element insertions described by Staudt et al. (2005) (FBrf0191391). These locations are based on the flanking sequence tags deposited by the authors in GenBank. The sequences were retrieved from GenBank by Joseph Carlson, who aligned them with the D. melanogaster reference genomic sequence (Release 5) using software he developed for his work on the Gene Disruption Project. In some cases, I selected the best alignment from a table of several alternative alignments in his database.
For almost all of the lines in the table, the flanking sequence clearly aligned at a single site in the genomic sequence. There is a "1" in the right column of the table for these unique alignments. However, there are three lines for which the flanking sequence aligned equally well at two genomic sites a few kilobases apart. There is one line for which the flanking sequence aligned equally well at two genomic sites on different chromosomes. For these four lines for which the flanking sequence maps to two sites, each site is listed on a separate line in the table and there is a "2" in the right column.
The GenBank records do not specify the position of the insertion within the flanking sequence. However, the flanking sequences are relatively short (approximately 50 bp or less) and so the ambiguity in the insertion position is fairly small. The location specified in the attached table is that of the nucleotide of the genomic sequence that aligns with the 5' end of the flanking sequence.
In addition, I was not able to determine a map location from the GenBank sequence for the following lines. Either the sequence was never submitted to GenBank, the sequence aligns equally well to multiple sites in the genome, or I can't find any credible alignment of the flanking sequence to genomic sequence.
DP00384 45/47 match to TE 1360 consensus
HP36889 aligns at multiple sites
HP35104 no credible alignment
HP32367 no credible alignment
HP31858 no credible alignment
HP21974 nts 16-50 align with TE hobo
HP20255 no credible alignment
HP11042 no credible alignment
HP10995 no credible alignment
HP10973 no credible alignment
DP01487 46/47 match to TE 1360 consensus, 47/47 match to multiple sites
DP01433 46/47 match to multiple sites
DP01393 19 bp flank, no 19/19 hits
DP00102 no credible alignment
What does this section display?
This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms).
What does this section not display?
This section does not currently display links that were removed or gene model changes.
Click the icon below to subscribe to this FlyBase record and receive updates automatically through your feed reader.
|All updates||Click here to see a list of all updates to this record from FB2010_08 and on.|
|Associated Files||File date: 2009.8.17 ; File size: 8000 ; File format: txt ; File name: Levis.2009.8.13.txt|
|Language of Publication||English|
|Additional Languages of Abstract|
|Also Published As|
|Data from Reference|