E. coli gene names

Peter Rice pmr at sanger.ac.uk
Fri Dec 18 08:27:03 EST 1998

Liu M <lm11 at gpu.srv.ualberta.ca> writes:
> I wonder if anybody tell me what is the GAPA-RND intergenic region in E.
> coli genome, and what is yeaR gene. I found many people are using these
> terms and I just can't find their explanations.

Any E.coli gene name beginning with "y" is unidentified.

The logic goes that even after some 2000 E.coli genes were named there
were none that began with "y". The next two letters are both in the
range a-j and represent the genetic map position in minutes (from yaa
to yjj). The letter (R) is just to make the name unique and in this case
does not imply a regulatory function.

I believe Kenn Rudd was the inventor of this convention for naming
unidentified genes. They should be given real gene names later when
a function is found.

Kenn also seems to be the inventor of my favourite E.coli gene name:

lasT "hypothetical 25.3 kD protein in arcA-thrL intergenic region"

... lasT, at least when named, had no known function. All you need to
know is that the origin of the E.coli genetic map is defined as the
location of thrL. Nice one Kenn.

Peter Rice                | Informatics Division, The Sanger Centre,
E-mail: pmr at sanger.ac.uk  | Wellcome Trust Genome Campus,
Tel: (44) 1223 494967     | Hinxton, Cambridge, CB10 1SA, England
Fax: (44) 1223 494919     | URL: http://www.sanger.ac.uk/Users/pmr/

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