IUBio Biosequences .. Software .. Molbio soft .. Network News .. FTP


rajorgensen at UCDAVIS.EDU rajorgensen at UCDAVIS.EDU
Sun Sep 19 18:30:04 EST 1993

David Smyth pointed out that because transgenes are (meant to be) functional 
genes, they could be considered as wild type and if so should be upper case.  

At the risk of confusing this discussion with the one on dominance, the 
proposal could be amended as follows:

1) Transgene loci are identified as such by the prefix "t" (or "T"?) (by 
analogy to the bacterial plasmid "p" designation).

Example:  a chalcone synthase transgene would be T-CHS (or TCHS or 

2) Because transgenes can insert at many loci, each is distinguished 
numerically as T-CHS1 through T-CHS1000 - and beyond.

3) Because one can construct an infinite number of chs transgene variations 
(different promoters, different linked drug markers, etc), there has to be a 
mechanism to avoid two labs using the same designation.  Thus, symbols and 
blocks of numbers would be registered with the database (i.e., applied for 
and assigned).  Thus, Fred Ausebel might be assigned T-CHS1-100 and Joe 
Schmo, T-CHS101-110.  (Note: This is exactly what was adopted by bacterial 
geneticists in 1976 for plasmid nomenclature.  Unfortunately, e-mail was not 
available to "spread the word" and to make the process of registering symbols 
painless. As the field exploded, the system was overrun; hence many 
constructs were called things such as, p12X/lac-4bnptII#1, and that sort of 
nonsense (which looks a lot like many transgene designations in plants).)

4) Transgene loci should be assigned symbols only when genetically 
characterized as single Mendelian loci. 

5) Transgene alleles can be designated by the same rules as for endogenous 
genes, e.g., T-CHS210-4.  

6) Symbols can be any three letter combination followed by one or more
numerals. (Note: symbols would not have to have any relationship to genes 
carried by the transferred insert, and often should not.  For instance, a 
T-DNA might carry a nos/npt gene and a 35S-driven AGAMOUS cDNA, as well as a 
2'/GUS gene. Perhaps the construct is called pNAG101.  At first thought, the 
researcher might want to register the name T-NAG101 for a transgene locus 
carrying this T-DNA.  But what of the next ten loci?  T-NAG102, etc might 
appear to correspond to plasmids pNAG102, etc, but would in reality be 
different loci with the pNAG101 T-DNA.  For this reason, it would be less 
confusing to choose three letter codes that are different than the T-DNA 
plasmid's symbol.)


Rich Jorgensen

More information about the Arab-gen mailing list

Send comments to us at biosci-help [At] net.bio.net