same sequence is different in EMBL and GENBANK

Massimo Delledonne DELLE%IPCUCSC.earn at earn-relay.ac.uk
Wed May 4 11:06:48 EST 1994


Hello netters,
about 6 months ago we decide to amplify a protease inhibitor from soybean
bowman birk family. With the GCG program I found, in the italian EMBnet node, t
he sequence K01967 (GMBBI) with this title:
"Soybean bowman-birk protease inhibitor, complete coding region"
13-JUN-1985 (Rel 06, Created)
22-APR-1990 (Rel. 23, Last updated, Version 1)
looking at the electronic sequence and at the published sequence (Molecular clo
ning and analysis of a gene coding for the Bowman-Birk protease inhibitor in so
ybean. J. Biol. Chem. 259, 9883-9890 (1984)) cited in the record, I realized it
was the sequence I was looking for.
Then I designed the oligos to amplify the gene, but I was never able to amplify
it .... I decided to try another region, may be the problem was a sequence
error near the 3' of my 3' oligonucleotide (a little confusing as explanation,
but don't try to improve my english .. no way) so I changed region ... result:
 nothing .. still not able to find any band of this about 300 bp fragment.
PCR on the same DNA with primers for other protease inhibitors were ok, but Bow
man-Birk.....
 
Few months ago I've discovered the amazing world of internet, and the power of
gopher .. Discovered merlot.welch.jhu.edu I found a way to go everywhere in the
 world without knowing any internet address ... A couple of days ago, I tried t
o check for new bowman-birk sequences in genebank via gopher, and I discovered
this terrible thing:   8-I
 
Sequence number K01967 (the same of embl)  name SOYCIIPI (different from GMBBI)
definition: Soybean CII protease inhibitor gene, complete coding sequence
PLN 1986
interesting, same number but different definition and different name ...
I was sure to have found a different sequence ..... but ....never found this se
quence in EMBL ... why ?  ...
Authors ... the same
Title of the papers ...the same  ... funny ... never found this sequence on tha
t article .... mmmmhhhh .. interesting ...(same paper on the same volume at the
 same pages .... mumble mumble ...
and then I've discovered the thing that made me very nervous (and that was miss
ing in the EMBL sequence .... another paper:
ERRATUM. Molecular cloning and analysis of a gene coding for the Bowman-Birk pr
otease inhibitor in soybean. J. Biol. Chem. 260, 7806-7806 (1985)
 
mumble mumble ... what happen? Are these the same sequence or not ?
 
Ran to the library, got the erratum ... the original sequence was wrong  :-(
the gene is not a Bowman-birk gene anymore... and the sequence is very differen
t at the 3' terminus of the fragment I was trying to amplify| That was the reas
on|
 
Now my question is:
 
 
 
The GENEBANK sequence was uptade in 1986
The EMBL sequence was uptade in 1990
The GENBANK sequence is the correct one
 
Who made the mistake ? The autors who submitted the correct version to Genbank
and not to EMBL (but in this case why the EMBL sequence was updated in 1990)
or: GENBANK submitted to EMBL an incorrect update ...
or: EMBL made a mistake
 
In any case I think it is really bad to have to check both the databases to be
sure the sequence you are looking for is correct .... And .. how many sequences
in both the databases have the same problem?
 
Massimo Delledonne
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                                                  %%                     %%
Massimo Delledonne                              _%%%_____________________%%%_
Istituto di Genetica vegetale                    %%%  ()     %%      ()  %%%
Universita' Cattolica S.C. Piacenza -ITALY-       %%   ()   ("")    ()   %%
Bitnet    delle at ipcucsc                                ( )___%%___( )
Internet  delle at imicilea.cilea.it                        (        )
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