Subject: Re: FlyBase query
Dear Dr. Millburn,
..
Yes that is right.Some portion of Drosophila S 14 is embedded in the
N-terminus of CG12211 gene product with protein id AAF48956. However,
very beginning of the N-terminus, we found in genomic scaffold AE003512,
is missing, and the C-terminus of the sequence which is embedded in the
CG12211 is not correct.
If you take the complement of the sequences between 81476 and 81162 and
translate it, you would get the correct drosophila S14 protein. However,
the first methionine is still missing in this sequence, we were not able
to find it.
I am attaching the drosophila S14 protein sequence and also the alignment
of drosphila S14 with yeast,human,worm mitochondrial S14s.I hope this will
be helpful. If you have further question, please feel free to ask.
Emine
Mitochondrial S14 Homologs
drosop 1 ~~~~~~~~~~~~~~~~~~~~~~~QVRTKYADWKMIRDVKRRKCVKENAVERLRVNSLRKN
Human 1 MAAFMLGSLLRTFKQMVPSSASGQVRSHYVDWRMWRDVKRRKMAYEYADERLRINSLRKN
worm 1 ~~~~~~~~~~~~~~~~~~~~~~~~~MTFWASWRQLRDVKRREQIQEVGADRMRLKAIKFN
yeast 1 ~~~~~~~~~~~~~MGNFRFPIKTKLPPGFINARILRDNFKRQQFKENEILVKSLKFIARN
drosop 38 DILPPELREVADAEIAAFPRDSSLVRVRERCALTSRPRGVVHKYRLSRIVWRHLADYNKL
Human 61 TILPKILQDVADEEIAALPRDSCPVRIRNRCVMTSRPRGVKRRWRLSRIVFRHLADHGQL
worm 36 TILPQAIRDEAAEKMQKARKYDHPRLILNMCQFTGRQRGKIKPYRLSRHLFRRFADRSAL
yeast 48 MNLPTKLRLEAQLKLNALPNYMRSTQIKNRCVDSGHARFVLSDFRLCRYQFRENALKGNL
drosop 98 SGVQRAMW
Human 121 SGIQRATW
worm 96 SGVQRAMW
yeast 108 PGVKKGIW
> > 'Gillian Millburn (Genetics)' wrote:
> >
> > Dear Dr. Spremulli,
> >
> > I am curating your paper for FlyBase:
> >
> > Koc et al., 2000, J. Biol. Chem. 275(42): 32585--32591
> >
> > and I have a question about the 'MRP-S14' homolog in Drosophila you
> > describe in the paper.
> >
> > In your paper you say:
> >
> > 'The D. melanogaster genome also has a putative MRP-S14 homolog
> > (AE003512). However, due to a probable sequencing error, the D.
> > melanogaster homolog could not be obtained from the given coding
> > sequence. Instead, the partial putative S14 sequence is embedded in a
> > long open reading frame of unknown function (CG12211).'
> >
> > I think from this paragraph that you are saying that the CG12211 open
> > reading frame as it is currently annotated contains partial S14
> > sequence, and also (either side of the S14 sequence) unrelated exons,
> > so that CG12211 needs splitting in two \- to create an S14 gene and a
> > gene made of the surrounding unrelated exons. Is this interpretation
> > correct ?
> >
> > Also, I would be grateful if you could send me the part of the sequence
> > of CG12211 that you think corresponds to the S14 homolog. I would
> > curate this information as a personal communication from you to
> > FlyBase, and then it would be used by the molecular curators at FlyBase
> > when they reannotate this part of the genome (they are systematically
> > going to work through the genome to improve the 'CG' annotations based
> > on information from sequence databases, papers and personal
> > communications to FlyBase, so that the intron/exon structures of the
> > annotations are improved and the various splice forms are included in
> > the annotations). Any information you have on the likely sequence and
> > intron/exon structure of the Drosophila S14 homologue would be very
> > useful.
> >
> > I look forward to hearing from you,
> >
> > Gillian
> >
> > \--------------------------------------------------------------
> > Gillian Millburn.
> >
> > FlyBase (Cambridge),
> > Department of Genetics,
> > \--------------------------------------------------------------