Subject: P-insertion in Pdk missing from GeneSeen
The BDGP database contains a 100 nt flanking sequence for P-element
insertion EP(2)0547, which gives a BLAST hit to the gene CG8808 (=
Pdk).
>CG8808|FBgn0017558|CT3054|FBan0008808  last_updated:000321 
Length = 2560
Minus Strand HSPs:
Score = 348 (52.2 bits), Expect = 2.4e-13, Sum P(2) = 2.4e-13
Identities = 74/78 (94%), Positives = 74/78 (94%), Strand = Minus / Plus
Query: 77 TCGG-CGTTGGAGAATCCAGAGCCACCTGGAGTCGCATTCTCAATCCGAATTCCCAACCG 19
TCG C TTGGAGAATCCAGAGCCACCTGGAGTCGCATTCT AATCCGAATTCCCAACCG
Sbjct: 46 TCGAACATTGGAGAATCCAGAGCCACCTGGAGTCGCATTCTTAATCCGAATTCCCAACCG 105
Query: 18 TTCGCGTCAAAGTCGCGC 1
TTCGCGTCAAAGTCGCGC
Sbjct: 106 TTCGCGTCAAAGTCGCGC 123
Score = 155 (23.3 bits), Expect = 2.4e-13, Sum P(2) = 2.4e-13
Identities = 31/31 (100%), Positives = 31/31 (100%), Strand = Minus / Plus
Query: 100 GCGCTCGCAGCTTTTAGGTAAAATCGGCGTT 70
|||||||||||||||||||||||||||||||
Sbjct: 12 GCGCTCGCAGCTTTTAGGTAAAATCGGCGTT 42
However, this P insertion is not displayed on the GeneSeen map of
this region, which shows no P element insertions in the Pdk gene. My
suspicion is that it has not been mapped on GeneSeen because the
alignment of the flanking sequence with the genomic sequence has a
discontinuity. Further support for this insertion site is that
EP(2)0547 has been mapped by in situ hybridization to 45D8-9, which
is consistent with the cytogenetic location of Pdk.
Bob Levis
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Robert W. Levis, Ph.D.
Carnegie Institution of Washington
Department of Embryology
115 West University Parkway
Baltimore, MD 21210
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