Splice site consensus for A.T (?)

nigel at codon3.berkeley.edu nigel at codon3.berkeley.edu
Tue Apr 14 11:12:16 EST 1992


>From: sam at weeds.mgh.harvard.edu (Sam Cartinhour)
>Subject: splice sites in arabidopsis

The following information was obtained for Arabidopsis by asking AATDB for the
"splice concensus", based on 123 introns:

     5' concensus          --------intron---------->

A    34    47    80    12  |   0    1    73    68    31    37    42
C    33    42    15     1  |   1    0     8    15    10    20    16
G    30    21     9   101  | 119    3    15     8    58    10    20
T    26    13    19     9  |   3  119    27    32    24    56    45
X     0     0     0     0  |   0    0     0     0     0     0     0


     3' concensus  ----------intron--------->

A    22    22    26    46     7   118     2  |   30    35    31    33
C    17    18     9     9    74     0     1  |   18    20    22    20
G    21    25     8    42     2     3   118  |   62    18    23    39
T    63    58    80    26    40     2     2  |   13    50    47    31
X     0     0     0     0     0     0     0  |    0     0     0     0

Sam Cartinhour
cartinhour at frodo.mgh.harvard.edu


************************************************************************

Don't pester Sam about the DB just yet:

>Subject: The weed DB
>Status: R


Hi Nigel

Mike Cherry and I are the developers of AATDB. Right now the database
is in "beta" test, meaning that we have distributed it to a handful of
sites so that they can bang away at it. The major purpose of this
phase is to catch data errors, inconsistencies, and omissions.  The
software itself has already been tested extensively (it has been in
use for nine months as the program that runs the worm database,
ACEDB). 

In one or two weeks we are going to open up distribution to basically
any site that is "unix-ready", i.e., has the appropriate hardware and
can set up and run the database right away. We will be making an
announcement about it to our aatdb-info list. Again, the focus will be
on getting user feedback on data quality, but also we will want to
begin setting up a system whereby users can contribute data if they
want.

sam

*************************************************************

-nigel


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       Nigel Walker              \  Mu  /   nigel at enzyme.berkeley.edu   
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