International Knockout Mouse Consortium

The search box offers many methods of searching the IKMC database.

You can specify multiple search terms separated by spaces or commas. Each of these terms will be used to match genes in the database. The search terms are case insensitive, so "PAX6" is treated the same as "Pax6" by the search.

The search box makes assumptions about the terms. These assumptions are:

• The term is an MGI ID if it starts with the letters MGI
• The term is an Ensembl ID if it starts with the letters ENSMUSG
• The term is a Vega ID if it starts with the letters OTTMUSG
• The term is an NCBI ID if it is a number
• The term is a genomic region if it fits the pattern "chrX:####-####" where X is a valid chromosome, and #### are valid start and stop coordinates
• Otherwise, the term is assumed to be a gene symbol or a gene name

Searching symbols

If you enter a gene symbol or a gene name, the system will perform a "begins with" match against all current gene symbols. It will also perform a "begins with" match against current names, old symbols, old names and synonyms. All matches will be displayed in alphabetical order by gene symbol. You may also search for multi-word terms by grouping the term in quotes. See the exact usage in the examples section.

Wildcard searches

You may include asterisk (*) wildcards anywhere in your search term to indicate you want partial matches.

For example, if you wanted to find all genes that contained the term skeletal you could search for "*skeletal*" and it would return all genes that contained the word "skeletal" in the gene name (or old name or symbol or synonym).

Search genomic coordinates

Searching by genomic coordinates will return all genes that are entirely within the region specified. If a partial overlap on either end is made, the gene will be excluded. When searching by coordinates, the results will be in coordinate order.

Example Searches:

zfp

ENSMUSG00000031633

You can browse the IKMC database by selecting the "Browse" tab in the upper right of the screen. You are presented two options

• Browse by gene symbol
• Browse by chromosome

Browsing by symbol separates the genes in the database by the first letter of the gene's official symbol. The genes are presented 50 genes at a time. Clicking on "Browse by gene symbol" brings you to the first page of genes that start with the letter "A" (case insensitive).

You are presented with navigation to go to the first page, the last page, or the previous/next page. You can jump to each letter of the alphabet (along with 0-9) by selecting the letter from the list.

Enter the gene symbol into the search box on the upper right and search. The resulting query summary lists one record (row) for each gene that matches your query.

The Gene column displays the gene symbol, chromosome, and location.

The Knockout Project Status column displays the current status of the gene in the following knockout project pipelines: KOMP-CSD, KOMP-Regeneron, EUCOMM, NorCOMM. The "Details" link leads to a page that provides more information about knockout attempts for the gene.

The Other Resources column displays information about mutant ES cells and mice for the gene that are available through the International Mouse Strain Resource (IMSR) or the International Gene Trap Consortium (IGTC). Also listed are targeted mutations and other mutations recorded in MGI.

The gene status details page (reached by following the "Details" link from the results summary) includes status information about all knockout attempts for the selected gene. If knockout attempts have lead to the generation of a targeting vector, or to more advanced stages, links to graphics detailing targeting vector and allele designs are provided. If IKMC products are available, order links to the corresponding repositories are provided.

The Regeneron pipeline comprises the following statuses:

• Regeneron Selected
• Parental BAC Obtained
• Design Finished/Oligos Ordered
• Targeting Vector QC Completed
• Vector Electroporated into ES Cells
• ES cell colonies picked
• ES cell colonies screened / QC no positives
• ES cell colonies screened / QC one positive
• ES cell colonies screened / QC positives
• ES Cell Clone Microinjected
• Germline Transmission Achieved

A detailed description of the EUCOMM and CSD pipeline statuses is available here.

Mutant ES cells or mice for your gene generated by other projects (i.e. outside the IKMC effort) might already be publicly available from the International Gene Trap Consortium (IGTC) or through the International Mouse Strain Resource (IMSR). Please check the Other Resources column for this information.

The answer to both questions is yes. IKMC welcomes gene nomination and prioritization requests from the research community. Please complete and submit the online gene nomination form. All submissions will be forwarded to and considered by the IKMC administrators.

Due to the high-throughput nature of the IKMC efforts, no special efforts for individual genes can be pursued if there are experimental problems with the targeting effort for that gene. Therefore, it is currently difficult to provide production timelines . If successful, there is a 60% chance that targeting will be completed after 6 month, and an 80% chance that it will be completed after 9 month. There will be instances where the targeting effort will take longer or not succeed at all. Once the mutant ES cells are ready they will be transferred from the production centers to the corresponding KOMP, EUCOMM, and NorCOMM Repositories which are responsible for distributing KOMP products.

Yes. For KOMP products go to the KOMP Repository website and search for your gene of interest using the Product Search box. For genes for which KOMP targeting is in progress, there will be a Register Interest link. Follow that link to register interest. You will receive email notification as soon as KOMP products for your gene are available. Similar functionality will be implemented for the EUCOMM and NorCOMM projects as well.

The main emphasis of IKMC (as currently funded) is to generate targeting vectors and mutant ES cells. Only for a limited number of genes, mutant mice, embryos or sperm will be generated by the production centers. However, for KOMP, the KOMP Repository offers additional services, on a cost recovery basis, to obtain mice, embryos, or sperm from mutant ES cells.

To order IKMC products you can search the IKMC database and follow the order links on the gene status details page (see above).

You can also access the different IKMC Repositories directly.

• To order KOMP products go to the KOMP Repository website and search for your gene of interest using the Product Search box. If the search results show "Available for Distribution" follow that link to the ordering page. More information on ordering KOMP products and services is available at the KOMP Repository home page.
• To order EUCOMM products, go to the EUCOMM Ordering Site. You can contact EUCOMM at eucomm@sanger.ac.uk.
• To order NorCOMM products go to the NorCOMM Services
• To order TIGM products go to the TIGM Repository.