AMA Manual of Style (10th ed.) : A Guide for Authors and Editors

AMA Manual of Style Committee

Publisher:: Oxford University Press

Print Publication Date:: Mar 2007

Print ISBN-13:: 9780195176339

Published to AMA Manual of Style:: Apr 2009

DOI:: 10.1093/jama/9780195176339.001.0001

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Nonhuman Genetic Terms

Chapter:: Nomenclature
Author(s):: Harriet S. Meyer

15.6.5 Nonhuman Genetic Terms

[T]he word mouse … comes originally from the

Sanskrit mush derived from a verb meaning to

steal. … Mice and rats, through their voracious

activities in grain larders and as carriers of disease,

inflicted considerable losses in food and lives upon

ancient civilizations.
H. C. Morse III¹^(p6)

A very obvious gap in our understanding of human

genome evolution lies in the complete absence of any

mapping data from the eutherian orders most dis-

tantly related to man, particularly the edentates. We

would urge anyone with an interest in the genetics of

the aardvark and the armadillo to consider a unique

mapping project which will be at the forefront (al-

phabetically, at least) of the comparative mapping

effort.
J. A. Marshall Graves et al²^(p964)

Comparative genome analysis has shown that eukaryote species share genes to a great extent.³ Therefore, similar or identical names designate the same gene across species whenever possible. Italicization of gene symbols is uniformly observed.

Vertebrates.

Animal gene symbols resemble human gene symbols (see 15.6.2, Human Gene Nomenclature, and below).⁴^,⁵ However, unlike human gene symbols, animal gene symbols typically use or include lowercase letters and punctuation marks. Editors of medical publications may follow author style for animal gene symbols.

Gene terminology for the laboratory mouse (Mus musculus domesticus) and laboratory rat (Rattus norvegicus), often seen in medical publications because of the common use of those species in investigating diseases affecting humans, is prototypic of such style.

Mouse and Rat Gene Nomenclature. Mouse and rat gene nomenclature guidelines were unified in 2003 by the International Committee on Standardized Genetic Nomenclature for Mice and the Rat Genome and Nomenclature Committee.⁶

Mouse and rat gene symbols resemble human symbols in several respects.⁶^,⁷ They are descriptive, short (preferably 3 to 5 characters), and italicized. Symbols begin with letters, not numbers. They contain roman letters in place of Greek letters and arabic numerals in place of roman numerals.

Mouse and rat gene symbols differ from human symbols in using lowercase letters. Symbols usually contain an initial capital. Capital letters within a mouse gene symbol may indicate the laboratory code or code for another species/vector (see below). A symbol with all lowercase letters (ie, no initial capital) indicates a recessive trait. Mouse and rat gene symbols may contain hyphens and other punctuation.

The central source for mouse gene terms is the Mouse Genome Database (http://www.informatics.jax.org),⁸ and for rats, RatMap (http://ratmap.gen.gu.se) and the Rat Genome Database (http://rgd.mcw.edu).⁹ Gene names and symbols may be verified by means of the search features at those sites.

Style rules and conventions for mouse and rat gene symbols are shown in Tables 8 through 10. (Note: The gene descriptions in the tables that follow are based on but not identical to the approved gene names available in the Mouse Genome Informatics database, which are more complete and do not use Greek letters and other typographic variants. For instance, in searching for a term with a, one would type in “alpha.”) The Mammalian Orthology Query Form (http://www.informatics.jax.org/searches/homology_form.shtml) allows comparative searches of 20 vertebrate species. Note that a given letter or letter combination often but not always signifies a conventional usage. For instance, l at or near the end of a symbol often, but not always, indicates “like.”

Table 8. Style Rules for Mouse Gene Symbols and Comparison With Human Gene Symbols (Examples)

Mouse Gene Symbol	Mouse Gene Description	Rule Illustrated	Human Gene Symbol (When Known)
a	nonagouti	lowercase initial capital because named for mutant recessive trait	ASIP
Afp	α-fetoprotein	initial capital, otherwise lowercase, Greek letter changed to roman	AFP
B2m	β₂-microglobulin	no subscript	B2M
Gla	α-galactosidase	Greek letter changed to roman and moved to end of symbol	GLA
Gt(ROSA)26Sor	gene trap, ROSA 26, Philippe Soriano	parentheses may be used
Rn4.5s	4.5S RNA	period permissible
Rn5s	5S RNA	symbol does not begin with number	RN5S1@ (@ signifies gene family; see 15.6.2, Human Gene Nomenclature)

Table 10. Conventions for Mouse Gene Symbols Identified in Collaborative Sequencing Efforts (Examples)^a

Mouse Gene Symbol	Mouse Gene Description	Convention Illustrated	Human Gene Symbol (When Available)
0610005C13Rik	RIKEN cDNA 0610005C13 gene	RIKEN symbol assigned to sequence that does not match known genes in other species; Rik: RIKEN Institute, Japan
Cdc42ep3	CDC42 effector protein (Rho GTPase binding) 3; formerly 3200001F04Rik	RIKEN symbol changed when gene identified in another organism	CDC42EP3
BC023055	cDNA sequence BC023055	BC indicates sequence from Mammalian Gene Collection of the National Institutes of Health	C10orf83
Aldob	aldolase 2, B isoform, formerly BC016435	Mammalian Gene Collection symbol changed when gene identified in another organism	ALDOB
AF179933	cDNA sequence AF179933	Genbank symbol for genes with no other information available in other organisms or sequencing efforts
Ppt2	palmitoyl-protein thioesterase 2, formerly AA672937 and 0610007M19Rik	Genbank sequence ID withdrawn when gene identified in other organism	PPT2

(a) See also Database Identifiers for Genomic Sequences in 15.6.1, Nucleic Acids and Amino Acids.

Mouse Alleles. A mouse allele symbol consists of a mouse gene symbol often with a superscript. As with mouse gene symbols, mouse allele symbols are italicized.

Allele symbols can be verified within the records of a mouse gene:

▪ Search for the gene symbol at http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=markerQF
▪ Click on link for the gene symbol that has been located
▪ Under Phenotypes, click on the numeric link after “all phenotypic alleles”

Allele searches are also available at http://www.informatics.jax.org/searches/allele_form.shtml.

Table 9. Conventions for Mouse Gene Symbols and Comparison With Human Gene Symbols (Examples)

Mouse Gene Symbol	Mouse Gene Description	Convention Illustrated	Human Gene Symbol (When Available)
Brca1	breast cancer 1	same as human symbol except for case	BRCA1
Cafq1	caffeine metabolism QTL 1	q: quantitative locus
C4bp-ps1	complement component 4 binding protein, pseudogene 1	-ps: pseudogene	C4BPB
D10Mit1	DNA segment, Chr 10, Massachusetts Institute of Technology 1	symbol for DNA segment identified only in the mouse; includes laboratory code (see “Laboratory Codes”)
D17H21S56	DNA segment, Chr 17, human D21S56	H21 indicates DNA segment resides on human chromosome 21	D21S56
G6pdx	glucose-6-phosphate dehydrogenase X-linked	similar but not identical to human gene symbol	G6PD
Gna-rs1	guanine binding protein, related sequence 1	-rs: related sequence	GNL1
Gtl10	gene trap locus 10	Gt: gene trap
Gt(ROSA)26Sor	gene trap ROSA 26, Philippe Soriano	vector in parentheses; laboratory code indicated (see “Laboratory Codes” section)
H2-Aa	histocompatibility 2, class II antigen A, α		HLA-DQA1
Hbb	hemoglobin β-chain complex	same as human symbol except for case	HBB
Hc9	heterochromatin, Chr 9	Hc: heterochromatin
Hras1	Harvey rat sarcoma virus oncogene 1	see also 15.6.3, Oncogenes and Tumor Suppressor Genes	HRAS
IGHMBP2 (formerly nmd)	immunoglobulin heavy chain μ binding protein 2 (formerly neuromuscular degeneration)	name change with new information about gene	Ighmbp2
l17Wis9	lethal, Chr 17, University of Wisconsin 9	initial l: lethal
Lamb1-1	β₁ laminin, subunit 1	hyphen separates 2 adjacent numbers	LAMB1
Lzp-s	P lysozyme structural	s: structural
mt-Rnr1	12S RNA, mitochondrial	mt: mitochondrial	MT-RNR1
Mcptl	mast cell protease-like	l: like
Nidd1, Nidd2, Nidd3, Nidd4	non-insulin-dependent diabetes mellitus 1, 2, 3, 4	same stem (root) for gene families
Nup160	nucleoporin 160	name change (formerly Gtl1-13)	NUP160
Rnr13	rRNA, chromosome 13 cluster
Tcrb	T-cell receptor β-chain		TRB@ (formerly TCRB; @ signifies gene family; see 15.6.2 Human Gene Nomenclature)
Tel10p	telomeric sequence, Chr 10, centromere end	Tel: telomere; 10: Chr 10; p: short arm
Tg(APOE)1Vln	transgene insertion 1, Fred Van Leuven	Tg: transgene; parenthetic material: inserted gene, in this case the human gene APOE; Vln: founder or “laboratory of” designation

Conventions and rules for mouse allele symbols are shown in Table 11. In a phenotype expression, a superscript plus sign indicates wild-type, eg:

Nf1^tm1Fcr/Nf1⁺

Table 11. Rules and Conventions for Mouse Allele Terms (Examples)

Allele Symbol	Allele Name	Convention or Rule Illustrated
abn	abnormal	recessive trait, thus begins with lowercase; because there is no superscript indicating an allelic term, use context to clarify
Dbf	doublefoot	dominant trait, thus begins with capital; because there is no superscript indicating an allelic term, use context to clarify
Dnahc11^iv	situs inversus viscerum allele of dynein, axon, heavy chain 11 gene	allele superscript designation is lowercase (recessive)
Ins2^Akita	Akita allele of insulin 2 gene	allele superscript designation has initial capital (dominant)
Lama2^dy-2J	dystrophia muscularis allele, Jackson 2, of α₂-laminin gene (second allele discovered at the Jackson Laboratory)	laboratory code included in superscript (see “Laboratory Codes” section); hyphens used
Matp^Uw-dbr	underwhite dominant brown alleles of membrane-associated transporter protein gene	multiple alleles separated by hyphen in superscript

which indicates a phenotype with a mutant neurofibromatosis allele (targeted mutation 1, Fredrick Cancer Research and Development Center) and the wild-type neurofibromatosis allele.

Mouse Chromosomes.

Chromosome nomenclature is similar for mice and humans (see 15.6.4, Human Chromosomes). However, in mice, rearrangement terms are capitalized. The following listing and subsequent examples are from the International Committee on Standardized Genetic Nomenclature for Mice¹⁰:

Cen	centromere
Del	deletion
Df	deficiency
Dp	duplication
Hc	pericentric heterochromatin
Hsr	homogeneous staining region
In	inversion
Is	insertion
MatDf	maternal deficiency
MatDi	maternal disomy
MatDp	maternal duplication
Ms	monosomy
Ns	nullisomy
PatDf	paternal deficiency
PatDi	paternal disomy
PatDp	paternal duplication
Rb	robertsonian translocation
T	translocation
Tc	transchromosomal
Tel	telomere
Tet	tetrasomy
Tg	transgenic insertion
Tp	transposition
Ts	trisomy
UpDf	uniparental deficiency
UpDi	uniparental disomy
UpDp	uniparental duplication

As with human chromosomes, lowercase p represents the short arm and lowercase q the long arm. When specific mouse chromosomes are referred to, the word Chromosome is capitalized (and abbreviated Chr after first mention), eg:

Human chromosome 1 shows extensive homology to several mouse chromosomes, especially Chromosome (Chr) 4 and Chr 1.

Chromosome anomaly symbols usually include a unique laboratory code (see the “Laboratory Codes” section) and a series number, eg:

In5Rk	fifth inversion found by Roderick
T37H	37th translocation found at Harwell

Chromosome number appears in parentheses:

In(2)5Rk

inversion in Chr 2

Semicolons separate numbers of chromosomes involved in translocations:

T(4;X)37H

translocation involving Chr 4 and Chr X

Periods indicate the centromere in robertsonian translocations:

Rb(9.19)163H

robertsonian translocation involving Chr 9 and Chr 19

In insertions, the donor chromosome number comes first:

Is(7;1)40H

insertion from Chr 7 to Chr 1

For further rules and conventions for chromosomes, see the chromosome nomenclature section of the Mouse Genome Informatics website.¹⁰

Laboratory Codes. Laboratory registration codes appear as 1- to 4-letter symbols in animal genetic terminology, including chromosomal, DNA locus, and mouse strain nomenclature (see below). Such codes help identify specific colonies, useful in genetic studies that can extend over many generations. Laboratory codes are registered with the Institute of Laboratory Animal Resources at the National Academy of Sciences in Washington, DC, and may be located at http://dels.nas.edu/ilar_n/ilarhome.¹¹ These codes uniquely identify an investigator, laboratory, or institution that breeds rodents or rabbits. Laboratory codes have initial capitals and appear without expansion. Examples are as follows:

Arb: Arthritis and Rheumatism Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases

Ddd: University of Durham, Drug Dependence Group

J: The Jackson Laboratory

N: National Institutes of Health

Ty: Benjamin A. Taylor, The Jackson Laboratory

Wil: Jean Wilson, University of Texas

Mouse Strains. Mouse strain names¹² are registered at the Mouse Genome Informatics website (http://www.informatics.jax.org/mgihome/submissions/submissions_menu.shtml). Mouse strain names are available at http://www.informatics.jax.org/external/festing/search_form.cgi. (Rat strain names are registered at the Rat Genome Database.⁹)

Mouse strain names consist of capital letters or combinations of capital letters and numbers:

A

BXH

CBA

C57BL

FVB

HDA32

A few earlier strains have names that are entirely numeric, eg:

129

A substrain is indicated by a term following the strain name after a virgule, usually the laboratory registration codes (see above), eg:

129/J

A/J

atherosclerosis in CBA/J mice

FVB/N mice used as controls

A serial number may precede the laboratory code, eg, the 10 before the J in this example:

C57BL/10J

Exceptions to the initial capital after the virgule exist in the case of 2 well-known strains (not substrains) of mouse:

BALB/c

C57BR/cd

Many standard laboratory mouse strains are derived from crosses dating back to the early 20th century or even older lines, and the names reflect abbreviations for characteristics:

A	albino
BALB	Bagg, albino
DBA	dilute, brown, nonagouti

However, mouse strain names are not expanded.

Strain names may be abbreviated using approved abbreviations, eg:

B	C57BL
C	BALB/c

Note that some abbreviations are the same as some names of different strains (eg, the strain C and the abbreviation C), so context must clarify. Additional abbreviations are available at http://www.informatics.jax.org/mgihome/nomen/strains.shtml.

Abbreviations and the letter X are used to indicate recombinant inbred strains (female parental strain first), eg:

CXB	BALB/c x C57BL

Capital F followed by a number in parentheses may appear after a strain designation to indicate the number of inbred generations:

F(20)

20 inbred generations

For further guidelines on mouse strain nomenclature, see the Mouse Genome Informatics website at http://www.informatics.jax.org/mgihome/nomen/strains.shtml.¹²

Invertebrates

Drosophila melanogaster. Gene symbols for the fruitfly Drosophila melanogaster are generally capital and lowercase or all lowercase for recessive phenotypes. This convention is also observed for gene names. Gene symbols may include punctuation.¹³^,¹⁴ A source for background on Drosophila gene names is FlyNome.¹⁵ Nomenclature rules and symbol search are available at FlyBase.¹³

Gene Symbol	Name
Ppi	Preproinsulinlike
SerT	Serotonin transporter
su(Hw)	suppressor of Hairy wing
tRNA:S7:23Ea	transfer RNA:ser7:23Ea (ser7: seventh isoform of serine; 23E: map position)

As with mouse alleles, Drosophila alleles are indicated with superscripts:

Hn^r, Hn^r2 (Henna gene, eye color-defective alleles)

Caenorhabditis elegans. The gene symbols for this nematode (roundworm) consist of 3 lowercase letters, hyphen, arabic numeral (sometimes a decimal), and, sometimes, a roman numeral after a space¹⁴^,¹⁶:

dpy-1

dpy-5 I

let-37 X

sir-2.1

Parentheses indicate mutation in the gene:

let-37(mn138)

Mutation symbols consist of 1- or 2-letter terms plus a number:

mn138

A characteristic of a mutation may be indicated by a 2-letter ending set in roman type:

hc17ts (ts: temperature sensitive)

OMIA.

Online Mendelian Inheritance in Animals is the counterpart to Online Mendelian Inheritance in Man (OMIM; see 15.6.2, Human Gene Nomenclature).¹⁷^,¹⁸

Microorganism Gene Nomenclature

Yeasts. Gene symbols for the fungus Saccharomyces cerevisiae consist of 3 capital letters plus a number (or, occasionally, a number-letter) ending¹⁹:

Gene Symbol	Name
ACT1	actin
CDC25	adenylate cyclase regulatory protein
COX5A	cytochrome c oxidase chain Va

This represents a change from earlier style in which all-lowercase symbols were used for loci named for recessive mutations (the preponderance of symbols) and all-capital symbols for loci named for dominant mutations. Allele symbols still follow the case convention (ie, capital for dominant, lowercase for recessive).

Bacterial Gene Nomenclature. Gene terms typically consist of an italicized lowercase 3-letter abbreviation often with an uppercase locus designator. The phenotype or encoded entity (eg, enzyme) is in all roman letters with an initial capital.¹⁴^,²⁰^,²¹

Gene Symbol	Phenotype (Explanation)
araA	AraA (L-arabinose isomerase)
asr	Asr (acid shock protein)
imp (formerly ostA)	OstA (organic solvent intolerance; imp: increased membrane permeability)
katE	KatE (catalase)
sodA	SodA (superoxide dismutase, manganese)
sodB	SodB (superoxide dismutase, iron)

A number of bacterial genome databases are available on the Internet. The National Center for Biotechnology Information sponsors Entrez Genome (http://www.ncbi.nlm.nih.gov/entrez: under Search, select Gene, then search for the gene in question).

Alleles are designated with a number after the uppercase letter or following a hyphen, when not assigned to a locus. Wild-type alleles are designated with a superscript plus sign:

ara⁺

araA1

ara-23

sodA1

Retroviral Gene Nomenclature. Human immunodeficiency virus and other retro-viruses contain 3 main structural genes and a number of regulatory genes²² (see also 15.6.3, Oncogenes and Tumor Suppressor Genes):

Structural:
env	envelope gene
gag	group-specific core antigen gene
pol	polymerase gene

Regulatory:
nef	negative factor
rev	regulator of viral protein expression
tat	transactivator of viral transcription
vif	viral infectivity
vpr	viral protein R
vpu	viral protein U
vpx	viral protein X

Compare typographic style of gene names and their products (p stands for protein, gp for glycoprotein):

Gene	Gene Product (Protein or Polypeptide)	Protein Products (Examples)
env	Env	gp41, gp120
gag	Gag	p6, p7, p17, p24
pol	Pol	p12, p32, p66/51
nef	Nef	p27
rev	Rev	p19
tat	Tat	p14
vif	Vif	p24
vpr	Vpr	p15
vpu	Vpu	p16
vpx	Vpx	p14

References

1. Morse HC III. The laboratory mouse—a historical perspective. In: Foster HL, Fox F, eds. The Mouse in Biomedical Research. Vol 1. Orlando, FL: Academic Press Inc; 1981:6-10.
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2. Marshall Graves JA, Wakefield MJ, Peters J, Searle AG, Womack JE, O'Brien SJ. Report of the Committee on Comparative Gene Mapping. In: Cuticchia AJ, ed. Human Gene Mapping 1994: A Compendium. Baltimore, MD: Johns Hopkins University Press; 1995:962-1016.
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3. Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nat Genet. 2000; 25(1):25-29. Also available at http://www.geneontology.org/GO_nature_genetics_2000.pdf. Accessed April 21, 2006.
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4. ARKdb. http://www.thearkdb.org. Accessed April 21, 2006.

5. RatMapGroup. RATMAP: the Rat Genome Database. http://ratmap.gen.gu.se/. Accessed April 21, 2006.

6. International Committee on Standardized Genetic Nomenclature for Mice and Rat Genome and Nomenclature Committee. Rules for nomenclature of genes, genetic markers, alleles, and mutations in mouse and rat. http://www.informatics.jax.org/mgihome/nomen/gene.shtml#genenom. Updated January 2005. Accessed April 21, 2006.

7. Maltais LJ, Blake JA, Chu T, Lutz CM, Eppig JT, Jackson I. Rules and guidelines for mouse gene, allele, and mutation nomenclature: a condensed version. Genomics. 2002;79(4):471-474. Also available at http://www.informatics.jax.org/mgihome/nomen/short_gene.shtml. Accessed April 21, 2006.
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8. Jackson Laboratory. MGI: Mouse Genome Informatics. http://www.informatics.jax.org. Updated April 20, 2006. Accessed April 21, 2006.

9. RGD: Rat Genome Database. http://rgd.mcw.edu. Updated April 17, 2006. Accessed April 21, 2006.

10. International Committee on Standardized Genetic Nomenclature for Mice. Rules for nomenclature of chromosome aberrations. http://www.informatics.jax.org/mgihome/nomen/anomalies.shtml. Accessed April 21, 2006.

11. ILAR: Institute for Laboratory Animal Research. Laboratory Code Registry. http://dels.nas.edu/ilar_n/ilarhome. Accessed April 21, 2006.

12. International Committee on Standardized Genetic Nomenclature for Mice and Rat Genome and Nomenclature Committee. Rules for nomenclature of mouse and rat strains. http://www.informatics.jax.org/mgihome/nomen/strains.shtml. Updated January 2005. Accessed April 21, 2006.

13. FlyBase: a database of the Drosophila genome. http://flybase.net. Accessed April 21, 2006.

14. Stewart A, ed. TIG Genetic Nomenclature Guide. Tarrytown, NY: Elsevier Trends Journals; 1995.
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15. FlyNome: a database of Drosophila nomenclature. http://www.flynome.com. Accessed April 21, 2006.

16. Hodgkin J. Recommended genetic nomenclature for Caenorhabditis elegans. http://elegans.swmed.edu/Genome/nomen.html.01_10_25. Accessed April 21, 2006.

17. Nicholas FW. Online Mendelian Inheritance in Animals (OMIA). http://www.angis.org.au/omia. Updated October 16, 2003. Accessed April 21, 2006.

18. Rangel P, Giovannetti J. Genomes and Databases on the Internet: A Practical Guide to Functions and Applications. Norfolk, England: Horizon Scientific Press; 2002.
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19. SGD gene naming guidelines. http://www.yeastgenome.org/gene_guidelines.shtml. Accessed April 21, 2006.

20. Demerec M, Adelberg EA, Clark AJ, Hartman PE. A proposal for a uniform nomenclature in bacterial genetics. Genetics. 1966;54(1):61-76.
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21. Journal of Bacteriology 2006 instructions to authors. http://jb.asm.org/misc/itoa.pdf. Accessed April 21, 2006.

22. Guatelli JC, Siliciano RF, Kuritzkes DR, Richman DD. Human immunodeficiency virus. In: Richman DD, Whitley RJ, Hayden FD, eds. Clinical Virology. 2nd ed. Washington, DC: ASM Press; 2002:685-729.
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