Mausoleum

Naming loci and alleles

 

Kindly provided by Mikael Vestberg, Director Norsk Transgen Senter at University of Oslo

Depending on the cage card design you have chosen Mausoleum gives different amount of space to the information you need.

We have found that naming loci genes, transgenes and lines according to the nomenclature rules takes an inordinate amount of card space. Instead, write the complete locus name in the comment box for that particular locus and use an abbreviated version as name of the locus.

Using + or - as designation of allels could be very confusing when describing Insertional transgenes concurrently with homologous recombination events.

The correct designation for a locus flanked with loxP sites is lsn and after Cre mediated recombination lsn1, lsn2 etc.

Instead we propose that you could use the following genotypes in Mausoleum

"tg" for a insertional transgene.

"wt" for the wild type allele.

"un"  for undetermined, is a genotype we use after testing offspring that may be tg/wt or tg/tg owing to the wt being defined as the lack of transgene. Often we do not know the insertional site or have access/use quantitative methods for testing offspring.

 

Genotypes after homologous recombination

"ko" for a constitutive knock out

"ki" for a constitutive knock in/gene replacement

 

When the resistance cassette is still in the founder animals we use an extended designation

 

"neofl" for a loxP flanked Neomycinresistance cassette

After Cre recombination use the simplest possible designation for genotype

"ko, ki, wt even though there is a single loxP site left in the recombination procedure.

 

Quite often there are several recombination events taking place within a locus during the project. Such as a conditional knockout delivered with the neomycin resistance box. In those cases the FRT-flp system is commonly used for neo removal and loxP sites flank a crucial part of the gene.

 

"Frneo" would designate a FRT flanked Neomycin resistance cassette

"fl" would designate a floxed gene remaining after. There is little extra value to describing the original genotype as "Frneofl".

After Cre recombination the "fl" would be replaced by a "ko" to also give information on function.

 

Recombination is used to create continuously more complex loci.  With mutant recombination signals and recombination leading to reversal of genetic material rather than the deletion described above

Thus these genotype descriptions could be useful

"flm" mutant/variant loxP site. Detailed description in  the comments box

"flx" loxP sites oriented to cause a single recombination inverting the flanked sequence

"fmC" the above after inversion and fixation induced by Cre recombination

 

"Frm" mutant/variant FRT site

"Frx" sites oriented to cause a single recombination inverting the flanked sequence

"FmF" the above after inversion and fixation induced by flp recombination.

 

Certain genetrap constructs and possibly also other constructs use a combination of loxP and FRT sites and mutants such that the trap is inactivated by one recombination enzyme and reactivated by the other recombination enzyme. In this case designation may be very complex and should be described in detail and using a simple genotype designation.

 

Example a conditional knock out of the CD8 gene

 

Line:cKO-CD8

Locus: Cd8

 

Genotypes of first generation from breeding the chimera to a wildtype mouse:

Cd8wt/neofl or Cd8wt/wt

 

After breeding to Cre:

Cd8wt/neofl, CD8wt/fl or CD8wt/wt

 

Example a genetrap of the CD8 gene

 

Line: gt-CD8

Locus Cd8

 

Genotypes of first generation from breeding the chimera to a wildtype mouse:

Cd8wt/act or Cd8wt/wt

 

After breeding Cd8wt/act to Cre:

Cd8wt/Cin, CD8wt/act or CD8wt/wt

 

After breeding Cd8wt/act to Flp:

Cd8wt/Fin, CD8wt/act or CD8wt/wt

 

After breeding Cd8wt/Fin to Cre:

Cd8wt/CactF, CD8wt/ or CD8wt/wt