Reference Report

Reference
Citation	Levis, R. (2009.8.13). Release 5 sequence localizations for HP and DP lines. (Export to RIS)
FlyBase ID	FBrf0208533
Publication Type	Personal communication to FlyBase
PubMed ID
PubMed Abstract
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
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Associated Files	File date: 2009.8.17 ; File size: 8000 ; File format: txt ; File name: Levis.2009.8.13.txt
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Language of Publication	English
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Data from Reference
Alleles (77)
	Alg10^HP37470 APP-BP1^HP32076 bon^HP32434 bun^DP00598 Cct1^HP35812 CG1737^HP11255 CG2556^HP10872 CG2926^DP01101 CG3500^HP20831 CG3773^DP01497 CG4061^HP10306 CG4169^HP30793 CG4199^HP10306 CG4729^DP01387 CG4825^HP31723 CG5073^HP36555 CG5196^HP30421 CG5715^HP35490 CG8195^HP20539 CG8319^HP35228 CG10306^HP25023 CG10898^HP30577 CG11095^HP10915 CG11414^HP25186 CG11590^HP10984 CG12746^HP37381 CG14054^HP10496 CG14304^HP30350 CG17618^HP37001 CG17928^DP00394 CG32262^DP00582 CG32277^HP36619 CG32373^HP35215 CG32626^HP10734 CG33275^HP30186 CG34104^HP10335 CG42321^HP26676 Cks30A^DP00300 CoVb^DP00597 Cp1^DP00318 Cpr^DP01397 cype^DP01427 dock^HP26308 fbl^HP30290 fwe^HP35545 Gclm^DP00242 glo^DP01368 gry^HP36619 Gγ1^HP20852 koko^DP00113 l(1)G0196^HP10784 lin19^HP25066 mei-217^HP10279 mei-218^HP10279 Mgat2^DP01278 Msh6^HP30192 MTA1-like^DP00445 mus210^HP25150 nito^HP25329 Nrx-1^HP35068 Pex10^DP01222 Pex19^DP00474 PNUTS^DP00473 ppl^DP00954 Prosβ5^DP00085 r^HP10945 Rab18^HP11051 raw^HP25259 ref(2)P^DP00665 sfl^DP01300 sima^HP36724 Slbp^HP36916 sll^DP01077 Spn55B^HP25975 ste24b^DP01043 vret^HP36220 wal^DP01159
Genes (127)
	Alg10 AlstR APP-BP1 bon bun Cct1 CG1737 CG2199 CG2556 CG2926 CG3500 CG3773 CG4061 CG4169 CG4199 CG4729 CG4825 CG5073 CG5167 CG5196 CG5250 CG5715 CG6136 CG6272 CG6791 CG7049 CG7326 CG7362 CG7950 CG8173 CG8195 CG8319 CG9636 CG10144 CG10289 CG10306 CG10898 CG11095 CG11414 CG11590 CG11752 CG12746 CG13380 CG13484 CG14054 CG14304 CG14671 CG17618 CG17928 CG31545 CG31729 CG32262 CG32267 CG32277 CG32373 CG32495 CG32626 CG32816 CG33275 CG34104 CG34139 CG34384 CG42321 CG42390 Cks30A Cng comm2 CoVb Cp1 Cpr Cpr65Ea cype dock E(spl)m7-HLH edl fbl FucTA fwe Gclm Glg1 glo gry GstD9 Gγ1 Hayan koko l(1)G0196 lin19 Lsm10 MED20 mei-217 mei-218 Mer Mgat2 MrgBP Msh6 MTA1-like mus210 nito Nrx-1 Or47a Pex10 Pex19 Pka-R2 PNUTS ppl Prosβ5 r Rab18 raw Rdl ref(2)P rev7 RpS28a Ser sfl sima Slbp sll Spn55B ste24b Su(var)3-3 synj tankyrase vret wal βTub85D
Insertions (311)
	All Insertions relating to this reference