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ZFIN Zebrafish Nomenclature Conventions ZFIN 斑马鱼命名规则

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ZFIN Zebrafish Nomenclature Conventions ZFIN 斑马鱼命名规则 ZFIN Zebrafish Nomenclature Conventions ZFIN 斑马鱼命名规则 翻译：张昀 审校：潘鲁湲 Based on Trends in Genetics Genetic Nomenclature Guide (1998) 本规则是基于 1998 年发表 Trends in Genetics 遗传学基因命名 指南（Genetic Nomenclature Guide）。 NOMENCLATURE INFORMATION 命名法来源 The current nomenclature guidelines are updates to rules established during a 此命名指导规则是在 1992 年 3 月德国 Ringberg 会议所讨论的 discussion session at a meeting in Ringberg, Germany, in March 1992, and are 规则基础上，修订更新，并广泛地被多数斑马鱼实验室认可的。 widely accepted by most zebrafish labs. Zebrafish Nomenclature Committee (ZNC) 斑马鱼命名委员会（Zebrafish Nomenclature Committee，ZNC） For questions and advice about appropriate nomenclature, contact us at 有关命名的问题和建议，请通过 [email protected] 与我们联系。 [email protected]. APPROVAL FOR GENE AND MUTANT NAMES 基因和突变名称的核验 申请基因名称或突变名称时，请填写下列相关申请表，并提供辅助 信息。 您的申请将由 ZFIN 命名协调员进行审核，申请信息在审核 Please use one of our submission forms to propose a new name for a gene or 期间将被保密。 mutant and to provide supporting information. Your submission will be sent to the 申请基因名称 ZFIN nomenclature coordinator for review and will be treated in confidence 申请位点/品系名称 Submit a Proposed GENE Name Submit a Proposed LOCUS/LINE Name ADDITIONAL RESOURCES 其他资源 A Tutorial for Proposing Zebrafish Gene Nomenclature 斑马鱼基因命名教程（A Tutorial for Proposing Zebrafish Gene Laboratory Line Designations Nomenclature） Other nomenclature guidelines: Human, Mouse, Fly (Drosophila), Yeast 基于机构的品系命名方法（Laboratory Line Designations） (Saccharomyces), Gene families 1. GENE NAMES AND SYMBOLS 1. 基因名称和符号（即缩写） Full gene names are lowercase italic, and gene symbols are three or more 完整基因名称的格式是英文字母小写、斜体。基因符号由三个 lowercase letters and are also italicized. The letters should be unique with respect 以上的小写字母构成，也需斜体。这些名称不可与已命名的斑马鱼 to other named zebrafish mutants and genes. Gene symbols should not be the 突变体或基因命名重复。当某基因确认为人类或小鼠直系同源基因 same as gene abbreviations in mouse or human, except in cases of established 的情况下，基因名称应与其保持一致，否则不应该使用相同的名称 orthology, where the gene symbol should match that of the orthologue. Zebrafish 或缩写。斑马鱼基因命名时不应包括任何涉及物种名称的字母，例 gene designations should not include any reference to species, for example d, dr, z 如 d，dr，z 或 zf。除特定情况外（见下文），不推荐使用标点符号， or zf. The use of punctuation such as period and hyphens in gene names or symbols 如句点和连字符等。 is discouraged, except under specific circumstances described below. 基因名称应在 ZFIN 注册。 Gene names should be registered at ZFIN. 1.1. Gene Nomenclature 1.1 基因命名规则 Genes should be named after the mammalian orthologue whenever possible. 基因应尽可能以哺乳动物的直系同源基因名称来命名。当该基 When mammalian orthologues are known, the same name and abbreviation 因的哺乳动物直系同源基因已确定时，应使用相同的名称和缩写， should be used, except all letters are italicized and lower case. Members of a gene 但是所有字母均为斜体和小写。统一基因家族的成员命名按顺序进 family are sequentially numbered. 行编号。 Examples: 例如： Names - engrailed 1a, engrailed 2b 基因名称： grailed 1a, engrailed 2b Symbols - eng1a, eng2b 基因符号： eng1a, eng2b In some cases when a zebrafish gene has been renamed to the mammalian orthologue from an older zebrafish name, it is still preferable within a publication 当某个斑马鱼基因被重新命名为哺乳动物直系同源基因的名称 to refer to the previous name. Refer to the previous name by appending the 时，在发表文章中最好也标记上基因的曾用名，比较好的方法是在 previous name in parentheses. Previous names are searchable at ZFIN. 现在的名称后使用括号标记曾用名。基因的曾用名可以在 ZFIN 上搜 Examples: shha (syu), bmp2b (swr) 索到。 例如：shha (syu), bmp2b (swr) 1.2. Duplicated genes 1.2 重复基因命名规则 The zebrafish genome contains duplicated segments that resulted from a 斑马鱼基因组包含许多重复片段。这些重复片段是辐鳍鱼纲从 genome-wide duplication in the ray fin fish lineage after it diverged from the lobe 总鳍纲（包括禽类和哺乳动物物种）中分化出来时，对整个基因组 fin lineage (that included avian and mammalian species). For this reason, zebrafish 进行了复制而产生的。因此，经常有哺乳动物中的单一基因，在斑 often have two copies of a gene that is present as a single copy in mammals. 马鱼中有两个基因拷贝的情况发生。 In these cases, symbols for the two zebrafish genes should be the same as the approved symbol of the human or mouse orthologue followed by "a" or "b" to 在这种情况下，斑马鱼的两个基因拷贝的名称应与人或小鼠直 indicate that they are duplicate copies. Before these symbols are assigned, it is 系同源基因的名称相同，并在其后添加“a”或“b”后缀，表明它 important to provide evidence by mapping that the two copies reside on 们是同一基因的重复拷贝。在分配后缀之前，需要通过基因定位来 duplicated chromosome segments. It is preferable that all copies in one of the 确认两个拷贝位于哪个重复染色体区段上。一个重复染色体区段中 duplicate chromosome segments use the same "a" or "b" suffix, although this will 的所有拷贝尽量使用的“a”或“b”后缀。然而由于历史原因，这 not always be possible for historical reasons. The a or b suffix does not indicate 样的命名方法不一定每次都可行。 “a”或“b”后缀并不代表被发 primacy of publication and will be assigned purely based on the suffix of the 表的先后次序，而纯粹基于基因所处的基因组环境。这一命名规则 surrounding genes. This terminology should not be used for duplicates that 不适用于辐鳍鱼类从总鳍鱼类分化之前产生的重复基因。对于这类 resulted prior to the divergence of ray fin and lobe fin fish. In these cases it is 情况，应优选使用与哺乳动物命名法最一致的规则。 preferable to use terminology that is most consistent with the mammalian 例如：hoxa13a，hoxa13b nomenclature. Examples: hoxa13a, hoxa13b In some cases when there is a unique mammalian orthologue, but addition of the 在另一些情况下，虽然在哺乳动物中有单一的直系同源基因命 a, b suffixes would conflict with a different mammalian gene symbol, then 名，但是在斑马鱼基因中添加“a”，“b”后缀之后会与哺乳动物中 numerical suffixes .1, .2 should be appended to the orthologous mammalian gene 的其他基因名称发生冲突。这种情况下，则通过在哺乳动物直系同 symbol instead of a, b. 源基因名称后添加数字后缀“.1”，“.2”的方法命名。 Tandem duplicate gene, with a single mammalian orthologue should have gene 对于单个哺乳动物同源基因，在斑马鱼中出现串联重复基因时， symbols appended with a .1, .2, using the same symbol as the mammalian 命名方法应该采用与哺乳动物同源基因相同的名称，并在后面添加 orthologue. The gene name should include the words, "tandem duplicate". “.1”，“.2”后缀的方法。此外，基因名称应含有“tandem duplicate”。 Examples: alkaline phosphatase, intestinal, tandem duplicate 1 (alpi.1) and 例如：alkaline phosphatase, intestinal, tandem duplicate 1 (alpi.1) alkaline phosphatase, intestinal, tandem duplicate 2 (alpi.2) and alkaline phosphatase, intestinal, tandem duplicate 2 (alpi.2) When mammalian gene duplications prevent identification of a unique 当哺乳动物的基因存在重复基因，导致无法确认其斑马鱼基因 mammalian orthologue, then an alternate gene symbol should be chosen. A 的直系同源关系时，应采用另一种命名方式。一种办法是选择是与 possible choice would be an approved gene symbol from a unique non- 非哺乳动物中唯一同源基因的名称。当一个基因与人类基因有同源 mammalian orthologue. When a gene is homologous to a human gene, but 性，但不确定是否直系同源时，该基因应以最接近的哺乳动物同源 orthology is ambiguous, the gene should be named after the closest mammalian 名称进行命名，并在同源名称后附加“like”后缀。在另一些情况下， homologue with the word 'like' appended to the name of the homologue. In some 如果斑马鱼中的某一基因家族存在同源的哺乳动物基因家族，但基 cases, a gene family described in zebrafish is homologous to a mammalian gene 因家族对应的进化关系不清，那么斑马鱼基因家族应使用哺乳动物 family but the evolution of the gene family is ambiguous. Under these 基因家族的名称命名，其基因编号延续使用哺乳动物已有的基因编 circumstances the zebrafish gene family should be named with the same stem as 号，在其后依次进行编号。如果此基因家族的成员位于同一染色体 the mammalian gene family with the gene number beginning after the end of the 上，相邻基因应依次顺序编号。 mammalian numbering and continuing sequentially throughout the gene family. If the members of the gene family are on the same chromosome, the adjacent genes should be given sequential numbers. 1.3. Mutant loci with unidentified genes 1.3 突变位点位于未识别的基因的情况 Mutant loci for which the gene has not yet been identified are given placeholder 当某突变位于尚未识别为基因的位点时，则给予该基因一个暂 gene names. When the gene is identified, it is renamed following standard 用名。此后如该基因被识别，则按照上述的标准命名方法重新命名。 nomenclature guidelines as described above. Genes identified by mutation are 通过突变识别出的基因，通常以突变表型来命名。基因符号（简写） typically named to reflect the mutant phenotype. The symbol should be derived 应该从完整基因名称中提取而来。由突变而来的名称通常不使用数 from the full name. Numbers should generally not be used in naming a mutant. 字。 Example: touchy feely, tuf 例如：touchy feely，tuf Mutant names should be registered at ZFIN. 突变名称应在 ZFIN 注册。 1.4. Genes identified only by genomic sequencing projects 1.4 由基因组测序项目识别的基因的命名 Large-scale genome sequencing projects use a variety of prediction methods to 大规模基因组测序项目使用各种预测方法来解析开放阅读框和 identify both open reading frames and genes. Some of these genes are already 基因。有些基因是已知的，有些则是新基因。通过这些方法解析的 known, while others are new. Novel genes identified by these means often cannot 新基因常常不能被识别，其名称由前缀，克隆名称和整数组成。前 be identified and are assigned a name comprised of a prefix, a clone name, and an 缀表明识别该基因的研究机构（例如，“si”指 桑格研究所），之后以 integer. The prefix is used to specify the research institution that identified the 冒号将前缀与克隆名称分开。在许多情况下，单个克隆中存在多个 gene (e.g., "si" for the Sanger Institute). A colon separates the prefix from the 预测的开放阅读框，则用句点（英文句号）来隔开克隆名称和其整 clone identifier. In many cases, there are multiple predicted reading frames in a 数编号。其后的整数编号表征该克隆基因被解析的次序，并不表征 single clone. These genes are distinguished with a full stop (period) between the 其在克隆中的顺序。如果一个基因的多个片段在多个克隆中被发现， clone name and an integer. Integers are assigned to genes in the clone as they are 则命名时优先采用发现该基因的 5'端的第一个克隆的名称。 identified and do not indicate the order of genes. If part of a gene is found in more 例如：si:bz3c13.1, si:bz3c13.2, si:bz3c13.3 than one clone, the name of the first clone in which the 5' portion of the gene is 最初由基因组测序项目解析和命名的基因，在获得更多相关信 found takes precedence. 息之后，将依照标准命名规则（如上所述）重新命名。 Examples: si:bz3c13.1, si:bz3c13.2, si:bz3c13.3 Genes initially identified by genomic sequencing projects are renamed using standard nomenclature guidelines (described above) as more information about them becomes available. 1.5. Genes identified only by other large scale projects 1.5 仅由其他大规模研究项目识别的基因的命名 Large-scale sequencing of ESTs or full length cDNA clone sets often result in large
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