Based on Trends in Genetics Genetic Nomenclature Guide (1998)
1. GENE NAMES AND SYMBOLS
Full gene names are lowercase italic, and gene symbols are three or more lowercase letters and are also italicized. The letters should be unique with respect to other named zebrafish mutants and genes. Gene symbols should not be the same as gene abbreviations in mouse or human, except in cases of established orthology, where the gene symbol should match that of the orthologue. Zebrafish gene designations should not include any reference to species, for example d, dr, z or zf. The use of punctuation such as period and hyphens in gene names or symbols is discouraged, except under specific circumstances described below.
Gene names should be registered at ZFIN.
Pseudogenes are sequences that are generally untranscribed and untranslated and which have high homology to identified genes . However, it has recently been shown that in different organisms or tissues functional activation may occur. Pseudogenes will be assigned the next number in the relevant symbol series, suffixed by a "p" for pseudogene e.g. prf1.9p is the symbol for "perforin 1.9, pseudogene".
The protein symbol is the same as the gene symbol, but non-italic and the first letter is uppercase.
Examples: Shha (Syu), Bmp2b (Swr)
3. ALLELES and GENOTYPES
3.1 Line designations
Due to technical constraints, genotypes at ZFIN are shown in alphabetical order by gene, and then by allele designation. See below for display of complex genotypes involving transgenic or chromosomal rearrangements.
4. CHROMOSOMES AND ABERRATIONS
The chromosome numbering system corresponds to the old Linkage Group designations with what was LG1 now named Chr1. Chromosomes are designated by non-italic numerals, 1 to 25. Reminder: cytogenetically identified chromosome numbers differ from the ‘Chr’ designations used for linkage groups and the reference genome sequence. Chromosome differences have not been observed between males and females in laboratory strains.
Df indicates deficiency. The term xxx should describe the salient features of the deficiency, as determined by the investigator. In cases where the deficiency removes sequences from named genes, the name should contain the standard symbols for those genes. The deleted genes should be listed in order, when known, separated by commas. The line designation should follow standard nomenclature conventions (institution designation followed by line number).
The term xxx should describe some salient feature of the translocation, as determined by the investigator. In cases where the translocation moves a named gene primarily studied by the investigator, xxx would usually be the standard symbol for that gene. Alternatively, xxx could just be an experimental series number.
The line designation should follow standard nomenclature conventions (institution designation followed by line number). After the line designation comes a comma, and then a phrase that indicates the new order of the chromosomes, starting from the top of the chromosome as displayed by convention. The first number (##) is the Chr number, followed by upper case U to indicate the upper arm of a chromosome or by upper case L to indicate the lower arm of a chromosome. The location of the centromere is indicated by a period. No spaces. Translocations are written as an allele of a gene when the gene is disrupted at one of the breakpoints of the translocation. There can be as many as four alleles of a translocation.
5. PRIORITY IN NAMES
As described above, zebrafish genes are named based on orthology to a human or mouse gene. If an ortholog cannot be identified, then the name that appears first in the literature will be given priority assuming it follows other nomenclature guidelines. ZFIN recommends submission of proposed gene names via the ZFIN form or consultation with the zebrafish nomenclature committee (firstname.lastname@example.org) for nomenclature assignment.
When a mutation is found in a previously cloned zebrafish gene, then the mutant will be referred to as an allele of the gene. If both the cloned gene and the mutation are known by different names and later found to be the same gene, then the name of the gene usually takes priority. The exception to this rule is when the mammalian gene has a gene symbol that is less than two characters such as the mouse gene brachyury which has the symbol T. In this case the zebrafish gene retained the original name no tail, ntl.
6. MAPPING AND SEQUENCING INFORMATION
The genome project began in 1994, and by 1996 the genetic map was closed. NIH funded major programs to develop a doubled haploid meiotic mapping panel, deficiency strains and expressed sequence tags (ESTs), The ESTs and anonymous markers have been mapped on two radiation-hybrid panels. The Sanger Institute began full genome sequencing in 2001. A physical map is being constructed from the BAC libraries used for sequencing. Genomic information is updated regularly on ZFIN.
Current Nomenclature Coordinator:
Amy Singer (email@example.com), ZFIN Database Team, Zebrafish Information Network, University of Oregon, USA
Erik Segerdell, XenBase, University of Calgary, Canada
Melissa Haendel (firstname.lastname@example.org)), Oregon Health and Sciences University, USA
Ceri Van Slyke (email@example.com), Zebrafish Information Network, University of Oregon, USA
Yvonne Bradford (firstname.lastname@example.org), Zebrafish Information Network, University of Oregon, USA
- The Zebrafish Science Monitor (1992) Sept. 21.
- Mullins, M. (1995) Genetic methods: conventions for naming zebrafish genes in The Zebrafish Book (3rd edition, Westerfield, M., ed.), pp 7.1-7.4, University of Oregon Press.
- Genetic Nomenclature Guide, Trends in Genetics (1998).