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Levis, R.W. (2000.11.20). Unannotated gap in genomic sequence and error in cn gene sequence. 
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From levis@XXXX Mon Nov 20  22:47:56  2000
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Date: Mon, 20 Nov 2000  17:48:20  \-0500
To: Gillian Millburn (Genetics) <gm119@XXXX>
From: Robert Levis <levis@XXXX>
Subject: Re: Unannotated gap in genomic sequence and error in cn gene
sequence
Gillian,
.
In the course of mapping the flanking sequence of a P insertion line
on the genomic sequence, I found evidence for a 1.8 kb deletion
disrupting the cinnabar (cn) gene in the BDGP/Celera sequence,
relative to a previously published sequence of the same region
(GenBank accession U56245). When I asked Dr. Susan Celniker of the
BDGP about this discrepancy, she replied that she is confident that
the BDGP/Celera sequence in this region is correct. She noted that
the genomic DNA sequenced by BDGP/Celera was from a strain with a
mutant cn allele (genotype y; cn bw sp). One may therefore infer
that this deletion is responsible for the mutant cn phenotype.
Here are the details of the putative cn1 lesion. U56245 is a 12.3
kb genomic sequence that includes the cn gene from a strain with a
wildtype cn allele. The U56245 sequence partially overlaps the
BDGP/Celera scaffold segment AE003839. A dot plot of U56245 (reverse
complement) (Y axis) vs AE003839 nts 1-10000 (X-axis) (see attached
Picture File of the output window) shows a deletion of ~1.8 kb in
AE003839 between nucleotides 1863 and 1864. I also did a BLAST of
the entire AE003839 vs U56245 (see attached html file of the output).
The deletion occurs at position 457 of the cn gene predicted amino
acid sequence. The deletion fuses the truncated cn ORF to an
unrelated ORF. The cn protein predicted by the wild-type U56245
sequence (GenPept locus AAC47351) is 524 aa, while that predicted by
the cn1 allele of the AE003839 sequence (GenPept locus AAF59196) is
504 aa. These two predicted proteins are nearly identical from 1-457
but then have no significant similarity beyond this point.
Bob Levis
\--
\------------------------------------
Robert W. Levis, Ph.D.
Carnegie Institution of Washington
Department of Embryology
115 West University Parkway
Baltimore, MD 21210
phone: (410) 554-1238
fax: (410) 467-1147
email: levis@XXXX
\------------------------------------
[FlyBase curator comment: attached Picture File and html file are archived.]
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