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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.
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1.1. Gene Nomenclature
Genes should be named after the mammalian orthologue whenever possible. When mammalian orthologues are known, the same name and abbreviation should be used, except all letters are italicized and lower case. Members of a gene family are sequentially numbered.
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Mutant names should be registered at ZFIN.
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1.4. Genes identified only by genomic sequencing projects
Large-scale genome sequencing projects use a variety of prediction methods to identify both open reading frames and genes. Some of these genes are already known, while others are new. Novel genes identified by these means often cannot be identified and are assigned a name comprised of a prefix, a clone name, and an integer. The prefix is used to specify the research institution that identified the gene (e.g., "si" for the Sanger Institute). A colon separates the prefix from the clone identifier. In many cases, there are multiple predicted reading frames in a single clone. These genes are distinguished with a full stop (period) between the clone name and an integer. Integers are assigned to genes in the clone as they are identified and do not indicate the order of genes. If part of a gene is found in more than one clone, the name of the first clone in which the 5' portion of the gene is found takes precedence.
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- Enhancer trap, promoter trap, gene trap constructs : These all use the same nomenclature conventions as described for transgenic constructs, substituting Et, Pt, Gt as necessary.
- Transgenes with transcripts in constructs: For those cases where a specific transcript or transcript promoter of a gene is used, the transcript number or name should be used. It should be noted that the use of hyphens here is distinct from the use of hyphens in regulatory or coding sequence fusions as discussed below. The hyphen in transcript names is an integral part of the transcript name and demarcates the transcript number for a gene.
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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.
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7. CONTRIBUTORS
Current Nomenclature Coordinator:
Amy Singer (asinger@zfin.org), ZFIN Database Team, Zebrafish Information Network, University of Oregon, USA
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