Reference Report

Reference
Citation	Spring, J. (2000.5.4). FlyBase error report for CG10497 on Thu May 4 05:27:21 2000. (Export to RIS)
FlyBase ID	FBrf0129035
Publication Type	Personal communication to FlyBase
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Text of Personal Communication	From FlyBase-error@XXXXXXXXXXXXXXX Thu May 04 13:22:37 2000 Envelope-to: gm119@XXXXXXXXXXXXXXX Delivery-date: Thu, 4 May 2000 13:22:37 \+0100 From: FlyBase-error@XXXXXXXXXXXXXXX Date: Thu, 4 May 2000 05:27:21 \-0700 (PDT) X-Authentication-Warning: hedgehog.lbl.gov: web set sender to FlyBase-error using \-f To: flybase-updates@XXXXXXXXXXXXXXX Cc: J.Spring@XXXXXXXXXXXXXXX Subject: FlyBase error report Content-Length: 1732 Error report from J. Spring (J.Spring@XXXXXXXXXXXXXXX) Gene or accession: CG10497 Gene annotation error Gene CG10497 has incorrect exon/intron structure. Comments: /gene='Sdc' AE003454 CT27296 CG10497 AAF46724 gi:7291294 The 85 aa Sdc gene product (gi:7291294) does not make sense. With few splice changes the genomic data can be adjusted to the published full length cDNA sequence and to 15 ests, so that a 399 aa protein product that is similar to other syndecan (Sdc) family members. The chages are marked with asterisks; the first (23078 instead of 23080) leads to a frame shift, the second is in the 5'untranslated and the last corresponds to the 5' end of the longest cDNA clone (U03282) and do not affect the protein. The new product of 299 aa still differs at 3 places from the published protein of 295 aa (sw:sdc_drome). But these changes are in repetitive regions and could be polymorphisms. Only the short cytoplasmic domain of syndecans is highly conserved (which is now missing in gi:7291294). Antibodies raised against recombinant protein also confirmed a larger protein than 85 aa (Spring et al. 1994). In a mRNA spliced according to the following corrected numbers: mRNA complement(join(4890..5502,5645..5812,8832..9350,9942..10080,23078..23185,908 59..91124,91782..91936)) the coding sequence would be: CDS complement(join(5330..5502,5645..5812,8832..9350,9942..10080,23078..23185,9 0859..90951)) Reference: Spring J, Paine-Saunders SE, Hynes RO, Bernfield M. Drosophila syndecan: conservation of a cell-surface heparan sulfate proteoglycan. Proc Natl Acad Sci U S A. 1994 Apr 12;91(8):3334-8. Yours sincerely, J. Spring Browser: Mozilla/4.5 ^en (WinNT; I) Accessed from: query.pl, /www/hedgehog_8000/htdocs
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Language of Publication	English
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