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transgene nomenclature

Luca Comai comai at U.WASHINGTON.EDU
Sat Sep 25 14:57:19 EST 1993


Dear Network,
I have discussed transgene nomenclature with Rich Jorgensen. As a result I am
posting an amended version of Rich's proposal. The modifications incorporated
were motivated by two needs: first, avoid confusion between native loci and
transgenic loci; second, avoid runaway proliferation of transgenic loci.
Luca Comai
UW, Seattle


Transgene nomenclature (a proposal)

1) Transgene loci are identified as such by the prefix "T" followed by an hyphen
and four upper case letters, corresponding to a specific T-DNA or plasmid used
in the transformation. Four letters are used instead of three to avoid confusion
with native loci and to provide more flexibility in making new symbols. Symbols
can be any four letter combination followed by one or more numerals. (Note:
symbols need not be related to genes carried by the transforming DNA)
 
Example:  a chalcone synthase transgene would be T-CHAS
 
2) Because transgenes can insert at many loci, each is distinguished
numerically
 
Example: T-CHAS1, T-CHAS2 - etc.
 
 3) Because one can construct an infinite number of chs transgene variations
(different promoters, different linked drug markers, etc.), any new one that
deserves it (see below) would be given a different four letter symbol. Thus,
symbols and blocks of numbers would be registered with the database (i.e.,
applied for and assigned).  
 
Example: a new construct with chalcone synthase, different from that in T-CHAS,
may be called T-CHLS

4) Transgene loci should be assigned symbols only when genetically characterized
as single Mendelian loci and when there is an obvious reason to do so

Example: suppose a transgenic construct was used to test an hypothesis such as
the function of a shortened protein. Because a negative answer was obtained, no,
future use is foreseen. In this case the laboratory may want to store the
transgenic material, but there is no need to go through the locus naming process
5) Transgene alleles can be designated by the same rules as for endogenous
genes. Epigenetic alleles are designated by the suffix ".epi" e.g.,
T-CHAS210-4.epi  




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