Gene or accession: CG9610
Gene annotation error
Gene CG9610 has incorrect exon/intron structure.
Comments: Probably neither of the annotated forms for this gene (CG9610/poxm)
are correct. The original publication (Bopp et al. 1989,  <up>FBrf0049627</up>) shows
the same 3' splice junction shown in FlyBase for poxm-RA, but the 5' splice
junction is very far upstream. We have confirmed that this is correct by
rt-pcr and 5'RACE. The first exon of the gene corresponds to the EST RE72571
plus the genescan prediction mapping at 4158837-4158973 (rel.4). The
translation will give MDPE (first nt. of the E codon only) from this first
exon, splicing to SQCPQY at the currently annotated 3' splice junction at
~4146620. In addition to the evidence of (1) the original publication, (2) our
RACE results, and (3) the presence of the ESTs and predicted splice site at
the right location, the translated product makes much more sense: the protein
picks up ~25 amino acids of homology with its vertebrate orthologs pax1 and
pax9. There may be alternate 5' starts--we did not do a cap-dependent RACE and
cannot be certain if some shorter products we got are real or are RACE
artifacts--but we are confident in the existence of the isoform described
above. None of our products were consistent with the current annotation.