Gene and Allele

By default only PI, technician and scientist have the authority to add genes and alleles.

Please add gene and allele records before adding mouse records.

Click on the toolbar or menu Lab->Genes and Alleles to add new genes and alleles.

Add gene records first, then click "Edit Alleles" to add alleles of a gene. For every new gene, the program will add a wild type allele "+" by default. The gene list is uneditable while editing alleles. Click "Edit Genes" to go back to gene list.

"Chr" is the field for gene locus.

The genotype of a mouse is shown as combination of short names of genes and their alleles. Whithin a genotype each gene locus has maximally two alleles. Gene loci are separated by ";". Allele names are separated by "/".

The length of gene shortname is best from 3-5 characters. The length of allele shortname is best from 1-3 characters.

The suggested rules to name alleles are listed in the "gene" window and below:

 

Genotype highlight

You can highlight selected genotypes by colors. Please follow the steps below to add new highlights:

You can change highlights on Gene&allele window or on "Display preference" window under menu->View->Display Preference:

Below are additional suggestions to name transgene and knockin:

Transgene is treated as new gene with unknown genomic locus. Please don't add transgene as an allele under the gene name. For example, Pdx1 cre is not an allele of Pdx1 if it is a transgene. It is recommended to create a new gene named Pdx1cre, and add an allele "i" as cre insertion.

Below are some examples for Cre transgenes:

The genomic location is unknown for these Cre transgenes. Add an insertion allele (i) under these genes so the mice carrying the cre transgene will have genotype i/+ or i/i. For example, the genotype of mice carrying Msxcre will be shown as Msxcrei/+ or Msxcrei/i (if homozygous).

Knockin is treated as an allele of the gene at the knockin locus. For example, cre knockin at Shh locus is an allele of Shh.

Any changes on the short name of genes or alleles will not be applied to the mouse records containing old names.