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Naming Genetically Engineered Mice (Part II): From Being Understandable to Being Written Correctly

Introduction

In the previous installment, we explained how to parse the names of genetically engineered mice, helping you understand their genetic backgrounds, types of genetic modifications, and laboratory codes. In this article, we address a practical question: How should the names of genetically engineered mice be formatted in scientific papers, grant applications, and experimental protocols? These designations involve not only letters and numbers but also the use of italics, roman type, superscripts, capitalization, as well as hyphens and slashes. Although the formatting may seem minor, it is crucial for accurately conveying genetic information. Drawing on the MGI naming guidelines, this article clarifies the most common pitfalls in scientific writing.

01 Italic and Roman typefaces: first, clearly identify the intended use.

Gene symbols, protein symbols, allele symbols, transgene symbols, and full strain names are not the same type of information and should not all be formatted with the same font style.

Special attention is required: Even if the gene name in a transgenic symbol appears within parentheses, it should not be taken as grounds for italicizing it. For randomly inserted transgenic symbols, the entire symbol must be written in upright type, in accordance with MGI’s transgenic nomenclature guidelines.

02 What content needs to be superscripted?

Superscripts are one of the most easily overlooked details in the nomenclature of genetically engineered mice. Take B6.129P2‑Trp53tm1Brn/J as an example: first, it is important to recognize that this is the full strain designation, not a standalone allele symbol.

The strain name can be broken down as follows:

How should superscripts in genotypes be handled? A genotype describes the combination of alleles carried by an individual, not the full strain name. Taking Trp53 as an example, common genotypes can be denoted as:

Remember: strain names, gene symbols, and allele symbols are information at different levels; superscripts are used only to denote the corresponding portion within an allele symbol and should not be applied to the entire strain name.

03 Case‑sensitivity conventions: distinguish between species and objects.

The capitalization of gene symbols is species‑dependent, and the conventions for writing genes and proteins should not be conflated.

| Common Errors

Write the mouse gene Trp53 as   TP53, which confounds species-naming conventions.

Gene symbols and protein symbols should both be formatted in italics.

Adopt the format of directly mapping mouse protein symbols to mouse gene symbols.

To standardize the format, the capitalization of letters in official strain names was altered without authorization.

Practical advice: For gene symbols, prioritize consulting authoritative databases such as MGI; protein symbols should follow established nomenclature guidelines and be tailored to the specific requirements of the target journal—do not rely solely on font style to distinguish them.

  04 Hyphen – Do not arbitrarily replace it with a slash /

In mouse strain nomenclature and genotypes, hyphens and slashes serve distinct functions and should not be interchanged merely for typographic aesthetics.

① Hyphen -: connects the different components of a strain name.

For example, B6.129P2‑Trp53tm1Brn/J: the hyphen is used to separate the genetic background from subsequent genetic modifications and is part of the official strain name; it should not be removed arbitrarily.

② Slash /: Its meaning depends on the context.

The forward slash may serve different functions in various naming conventions and cannot be uniformly interpreted as having the same meaning.

At the end of a complete strain name, a slash may be followed by a laboratory or source code, such as /J, /Mmjax;

In genotypes, a slash is typically used to separate two alleles at the same locus; for example, Trp53 tm1Brn/+ indicates that the individual carries the specified mutant allele and the wild-type allele.

In certain fusion transgenic nomenclatures, the forward slash may also be used to distinguish components derived from different genes within a construct; the officially registered nomenclature shall prevail.

Therefore, not all slashes should be interpreted as indicating hybridization, nor should it be assumed that slashes appear only at the end of strain names.

③ -/- does not necessarily correspond to a specific mutant allele.

-/- is a commonly used genotype abbreviation in the literature, but it cannot automatically replace all formal allele symbols. If the study subject carries a confirmed loss-of-function allele, researchers may use the knockout‑type abbreviation to describe its genotype; however, when it is necessary to trace the specific construct, mutation origin, or genetic background, explicit allele symbols should still be prioritized.

Similarly, flox/flox, f/f, and fl/fl are commonly used to denote homozygosity for conditional alleles, but they are standard abbreviations. In formal manuscripts or experimental protocols, the specific allele names and their meanings should be clearly specified upon first mention to avoid ambiguity between different constructs.

Principle: Abbreviations can enhance reading efficiency, but they must not compromise the accuracy of genetic information.  

05 How should one properly format papers and experimental protocols?

Once you’ve mastered the rules for individual symbols, you’ll also need to pay attention to how they are expressed in different writing contexts.

① Paper Title and Abstract

The title and abstract should prioritize clarity regarding the study subject, avoiding excessive abbreviations that might prevent readers from identifying the strain or genotype. For example, when a specific Trp53 allele is used in the study, its full, standardized strain name or allele designation should be provided upon first mention. If abbreviations are employed later in the text, care must be taken to ensure they do not conflict with other strains or genotypes.

② Materials and Methods (Materials and Methods)

The Materials and Methods section should include the following information:   The official strain name or genotype of the mouse;   Animal source, supplier, and the corresponding catalog number or resource identifier;   Genetic background used in the study;   Methods for genotype confirmation related to the experiment;   When necessary, specify the exact names of the alleles used.

For example, B6.129P2‑Trp53tm1Brn/J can be verified against the official JAX website for its formal strain name and Stock No. 008462; the MGI database provides the corresponding strain record along with the MGI ID MGI:3790673. It should be noted that strain numbers, allele numbers, and database record numbers are not equivalent concepts. When citing these resources, the source must be clearly specified, and the actual procurement, breeding, and genotyping records shall prevail.

③ Results, Figures, and Figure Legends

The genotypes presented in the Results section, figure legends, and statistical graphs should be consistent. If the main text employs formal allele symbols while the figures use unexplained abbreviations such as KO, −/−, or f/f, readers may be unable to determine whether these designations refer to the same experimental subject. It is recommended to define the meanings of any abbreviations upon their first appearance and to maintain a uniform set of symbols throughout the manuscript. When multiple alleles, Cre systems, or reporter genes are involved, their respective genetic statuses should be clearly distinguished. At the final stage of preparation, verify that italics, superscripts, and special characters are displayed correctly in Word, PDF, statistical graphs, and supplementary materials. The plain‑text display on database pages may not fully reproduce the official typesetting format; therefore, one should not rely solely on copied strings to assess whether fonts and superscripts conform to standard conventions.

④ How should the Cre-loxP mouse genotype be written?

The Cre–loxP system is commonly used to generate conditional knockout models. When writing, it is necessary to specify both the conditional allele status of the target gene and the genetic status of the Cre system; the abbreviation “CKO” alone should not be used to represent the full genotype. Below, using the target gene Gene as an example, we present common abbreviations for genotypes:

In the formal manuscript, when a term is introduced for the first time, please provide detailed information on the target gene, the conditional allele, and the Cre strain; thereafter, use the established abbreviations, ensuring consistency across the text, figures, and figure legends.

⑤ Common Abbreviation Correspondence

Not all of these abbreviations are part of the official strain nomenclature. They are suitable for use in well-defined contexts but should not replace the necessary genetic information.  

06 Ultimate Quick Check: Review These Items After You Finish Writing

Before submitting your paper, grant application, experimental protocol, or product documentation, you can quickly verify the following:

① Is the gene symbol correct?

Does the case-sensitivity rule distinguish between mouse and human gene names?

② Are the italic and roman fonts correct?

Should genes, proteins, alleles, transgenic events, and strain names be distinguished?

③Is the superscript correct?

Should the allele designation be placed in the standard position, with the corresponding italicization preserved?

④ Should the hyphen be retained?

Was the hyphen and slash in the official name accidentally deleted or replaced?

⑤ Are strain names and allele symbols distinguished?

Have you mistaken a genetic background prefix or an origin code for part of the allele symbol?

⑥ Is the genotype clearly defined?

Are abbreviations such as KO, -/-, and flox/flox clearly defined?

⑦ Has the strain name been verified?

Has the official name been verified against the supplier’s or the official database?

⑧ Is the numbering correct?

Should strain numbers, allele numbers, and database record numbers be distinguished?

⑨Is the formatting of the entire text consistent?

Are the names consistent across the main text, figure captions, tables, and supplementary materials?

  Finally, it is worth emphasizing that the core of mouse nomenclature is not to create overly complex symbols, but rather to accurately convey information on genetic background, genetic modifications, and allele status. For strains or alleles that have already been officially registered, priority should be given to using the formal names provided in authoritative databases; any adjustments to font style or formatting should be made in accordance with the requirements of the manuscript or journal. Avoid arbitrarily altering names simply to achieve uniformity in format.  

Reference materials

1. Mouse Genome Informatics (MGI): Guidelines for Nomenclature of Genes, Genetic Markers, Alleles, and Mutations in Mouse and Rat
https://www.informatics.jax.org/mgihome/nomen/gene.shtml

2.MGI: Quick Guide to Nomenclature for Genes
https://informatics.jax.org/mgihome/nomen/short_gene.shtml

3.MGI: Names and Symbols for Mutant Alleles
https://informatics.jax.org/mgihome/nomen/allmut_help.shtml

4. MGI: Transgenes, see Section 4, “Transgenes,” and Section 4.1, “Symbols for transgenes,” in the official nomenclature guidelines.
https://www.informatics.jax.org/mgihome/nomen/gene.shtml

5. The Jackson Laboratory: B6.129P2-Trp53tm1Brn/J, Stock No. 008462
https://www.jax.org/strain/008462

6. MGI: B6.129P2-Trp53tm1Brn/J strain record, MGI:3790673
https://www.informatics.jax.org/strain/MGI%3A3790673

Note: This article is compiled based on the MGI Online Nomenclature Guidelines as of October 2026. The official database may be updated; for the definitive nomenclature of specific strains and alleles, please refer to the most recent registration records at the time of use.

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