Subject: Help FlyBase please
Greg
So FB can properly curate yr Gibson et al., 1999, Genetics 151(3): 1081--1091
can you tell me was Amy.2.6 from Amy-d or Amy-p ?
Thanks
Michael
Subject: amy-p nor amy-d
Michael,
The short answer, regrettably, is neither. The microsat. we list as 2.6 was
initially reported in Schlotterer, Vogl and Tautz (1997: Genetics
 146:309-320 ) as a subclone derived from DS00062, which maps to 54AB in the
Amy region. When I got your message on Saturday, I ran a BLAST search
against FB, and the sequence actually maps to the complete sequence of
DS00058, which has been localized to 31AB according to FB.
So then I went back to my recombination map, which was assembled by
MapMaker, but based on individual pairwise distances, marker 2.6 could lie
close to marker 2.3 at 35B. There isn't a lot of recombination near the
centromere, but there were several double recombinants in the data set.
Since there were no significant QTLs in the region, the conclusions of the
paper aren't altered, but I will send a corrigendum off to Genetics once I
hear back from Christian Schlotterer.
On a similar matter, we have just discovered that an ASO marker against a
SNP in the Dopamine receptor that is supposedly localized at 35EF is
genetically at cytological interval 88 or 89 (this time there is no
ambiguity in the map - the recombination frequencies are perfectly in
agreement with published data). There is no picture of the in situ in the
original paper, and when you do a BLAST search, there is no match of DopR to
a P1 even though 35EF is shown as almost finished sequence.
Roger Hoskins and I found a few inconsistencies between mapped positions of
STSs and ESTs as reported on FB while assembling our SNP map of 10 strains -
which should be submitted in a few weeks. After 10 years in the business I
should be more wary of published data, but given the volume of data I guess
this is to be expected. Fly Base is a truly great resource, so thanks for
all of your care and effort.
Greg