Subject: FlyBase query
Dear Dr. Posakony,
I am curating your paper for FlyBase:
Lai et al., 2000, Development 127(2): 291--306
and I have a question.
.
1. UAS-Bob
I need to make a record for this construct in FlyBase and an allele of
Bob to record the phenotypes caused by overexpression of Bob.
However, I need to know which Bob gene (A,B, C or D) to put the allele
under. In the materials and methods you state that you used 'PCR to
amplify the coding regions and 8-10nt of 5' UTR sequence' of Bob.
Since in the results it says that there are 'small differences in the
transcribed regions of the different Bob genomic loci' does this mean
that you can say which copy of Bob the coding region in UAS-Bob
corresponds to, or can you say that for example it could be A,B, or C
but definately isn't D.
If you do not know which Bob coding region it corresponds to, I will
probably put the allele for UAS-Bob under BobA, and include a note that
it could actually correspond to BobB, BobC or BobD (?) since the coding
regions are identical (at least for A-C).
I look forward to hearing from you,
Gillian
\--------------------------------------------------------------
Gillian Millburn.
FlyBase (Cambridge),
\--------------------------------------------------------------
>
Subject: Re: FlyBase query
>Dear Dr. Posakony,
>
>I am curating your paper for FlyBase:
>
>Lai et al., 2000, Development 127(2): 291--306
>
>and I have a question.
.
>
>1. UAS-Bob
>
>I need to make a record for this construct in FlyBase and an allele of
>Bob to record the phenotypes caused by overexpression of Bob.
>
>However, I need to know which Bob gene (A,B, C or D) to put the allele
>under. In the materials and methods you state that you used 'PCR to
>amplify the coding regions and 8-10nt of 5' UTR sequence' of Bob.
>
>Since in the results it says that there are 'small differences in the
>transcribed regions of the different Bob genomic loci' does this mean
>that you can say which copy of Bob the coding region in UAS-Bob
>corresponds to, or can you say that for example it could be A,B, or C
>but definately isn't D.
The UAS-Bob construct we used was made from a cDNA clone we recovered
called Bob2. In the coding region (used to make the UAS construct),
this clone matches our sequence of Bob A perfectly, and has a
one-base conservative substitution difference from our sequences of
Bob B and Bob C (i.e., the predicted protein product of the UAS
transgene is identical to that of Bob A, B, or C). It definitely does
not correspond to 'Bob D', which as we said in the paper just
reflects the sequence of the CK EST.
Best wishes,
Jim Posakony