The Mouse Genome Informatics at the Jackson Laboratories is helping to support the Resource Identification Initiative (#rrid), by showing how to obtain your proper identifiers for knockout mice that can be used in the scientific literature. They hope that authors / scientists using mice will properly identify their organism so that information can be easily accessed by other scientists.

1. Finding an Resource Identification
Initiative(RII) ID for a mouse strain
RII: http://scicrunch.com/resources
Mouse Genome Informatics (MGI): http://www.informatics.jax.org/

2. Background
• Many researchers work at the level of the gene, but to accurately identify your
research organism requires identification at the level of genotype, which is the
complete description of the allele composition (specific allele(s), zygosity) and
the strain background.
– Different alleles are important because of
• Different generation methods (targeted, transgenic, ENU induced, spontaneous, etc)
• Different attributes (null/knockout, conditional-ready, modified isoform, inducible, etc)
• Underlying biologically-relevant differences in construction (specific domain modification,
whole gene, etc)
• Differences relevant to researcher protocols (how to genotype, etc)
– Different strain backgrounds are important because of
• Modifier effects from the background
• Altered phenotypic expression (ex. 5 tumors vs. 50 tumors, age of onset, etc)
• Appropriate choice of control animals
• Disclaimer: MGI is working with RII to improve the content and clarity of
information available on their site. This doc describes how to navigate right
now, there are still bugs and “missing” info/capabilities

3. Starting from RII:
1. Begin here. Search for organism.
You can also begin by typing your
gene into the search bar in the upper
right, then filtering for organism
2. Notice tabs are now
highlighted with “ORGANISMS”
selected as default. Click on
ANTIBODIES or TOOLS to
change if desired.
3. Begin typing your gene name
and select from the dropdown
list (here, Pax2)

4. 4. Expand sidebar filters by clicking on [+] symbols. All available options/filters are displayed
5. Narrow by selecting database and/or species. For mice, use MGI or IMSR (International
Mouse Strain Resource) from “Database”. This walk through will use MGI, apply the filter by
clicking “MGI”. The grey number indicates how many records there are in each, for MGI,
each unique genotype is a record.
ZFIN = zebrafish; CGC = Caenorhabditis Genetics Center

5. 6. If complex genotypes
have been reported (i.e.
Pax2 mutant and another
gene mutation within the
same animal) these will
appear with multiple genes
in “Affected Gene”. Click
“Pax2” to filter for single
marker genotypes
7. Select the specific mutant allele from “Genomic Alteration”. If
you are not sure which allele, go to MGI and search “Pax2” or
“Pax2tm1Pgr” for more details.
Attributes, links and more will (hopefully) be added soon to make this
step easier.
Allele IDs use standardized nomenclature with “tm” = targeted
mutation and last 3~5 digits being the lab code for the researcher or
project that generated the mice. See
http://www.informatics.jax.org/mgihome/nomen/allmut_quickhelp.sht
ml
Note that filters applied now
appear on top. Click the X to
remove

6. Finding your allele in MGI: Option 1. From
a reference using MGI Reference Query

7. Finding your allele in MGI: Option 2. Using
a gene search
Pax2
See next page…

8. Finding your allele in MGI: Option2. Using
a gene search
Use “Category” column, and others to find alleles
matching the description of your allele.
Click allele hyperlinks to go to allele detail page.
See next page…

9. Confirm mutation description,
locate original reference describing
mutation generation
Carrying this Mutation: Mouse Strains: 1 strain
available
This strain is commercially available through
one of the repositories indexed by the IMSR, so
you may have purchased it.
See other references using this specific allele

10. 8. Select specific allele
Resuming in RII:
9. Select strain
background
10. Identify RII record that
corresponds to your mouse
Describes zygosity: homozygous mutant
Describes strain genetic background
Goes to MGI genoview page

11. Compare RII with MGI
(from MGI’s Allele Detail page for Pax2tm1Pgr)
Homozygous for Pax2tm1Pgr/Pax2tm1Pgr
Genetic background: involves
129S1/Sv*129X1/SvJ*C57BL/6
See three genotypes homozygous for
Pax2tm1Pgr/Pax2tm1Pgr
Row hm2 describes the genotype
consistent with:
Pax2tm1Pgr/Pax2tm1Pgr on a background
that involves
129S1/Sv*129X1/SvJ*C57BL/6
Column hm2 describes phenotypes
annotated to this specific genotype

12. Compare RII with MGI
(from MGI’s Allele Detail page for Pax2tm1Pgr)
Click catalog # in RII or
row/column labels in MGI to go
to the genoview popup
Find unique genotype ID in the url

13. Obtain RII ID
This is the RII ID code to include in your manuscript.
If a genotype does not already exist that matches your mouse, please contact MGI at
http://www.informatics.jax.org/mgihome/submissions/amsp_submission.cgi so we can
create a (confidential) genotype prior to submission.