Background: The coronavirus disease has led to an exhaustive exploration of the SARSCoV- 2 genome. Despite the amount of information accumulated, the prediction of short RNA motifs encoding peptides mediating protein-protein or protein-drug interactions has received limited attention. Objective: The study aims to predict short RNA motifs that are interspersed in the SARS-CoV-2 genome. Methods: A method in which 14 trinucleotide families, each characterized by being composed of triplets with identical nucleotides in all possible configurations, was used to find short peptides with biological relevance. The novelty of the approach lies in using these families to search how they are distributed across genomes of different CoV genera and then to compare the distributions of these families with each other. Results: We identified distributions of trinucleotide families in different CoV genera and also how they are related, using a selection criterion that identified short RNA motifs. The motifs were reported to be conserved in SARS-CoVs; in the remaining CoV genomes analysed, motifs contained, exclusively, different configurations of the trinucleotides A, T, G and A, C, G. Eighty-eight short RNA motifs, ranging in length from 12 to 49 nucleotides, were found: 50 motifs in the 1a polyprotein-encoding orf, 27 in the 1b polyprotein-encoding orf, 5 in the spike-encoding orf, and 6 in the nucleocapsidencoding orf. Although some motifs (~27%) were found to be intercalated or attached to functional peptides, most of them have not yet been associated with any known functions. Conclusion: Some of the trinucleotide family distributions in different CoV genera are not random; they are present in short peptides that, in many cases, are intercalated or attached to functional sites of the proteome.

中文翻译：

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新的短 RNA 基序可能与 SARS-CoV-2 基因组相关

背景：冠状病毒疾病引发了对 SARSCoV-2 基因组的详尽探索。尽管积累了大量信息，但编码介导蛋白质-蛋白质或蛋白质-药物相互作用的肽的短RNA基序的预测受到的关注有限。目的：该研究旨在预测散布在 SARS-CoV-2 基因组中的短 RNA 基序。方法：该方法使用 14 个三核苷酸家族来寻找具有生物学相关性的短肽，每个三核苷酸家族的特征是由在所有可能的构型中具有相同核苷酸的三联体组成。该方法的新颖之处在于使用这些家族来搜索它们在不同 CoV 属的基因组中的分布情况，然后比较这些家族的分布。结果：我们使用识别短 RNA 基序的选择标准，确定了不同 CoV 属中三核苷酸家族的分布以及它们之间的关系。据报道，这些基序在 SARS-CoV 中是保守的；在分析的其余 CoV 基因组中，基序仅包含三核苷酸 A、T、G 和 A、C、G 的不同配置。发现了 88 个短 RNA 基序，长度从 12 到 49 个核苷酸不等：50 个基序在1a多蛋白编码orf中，27在1b多蛋白编码orf中，5在刺突编码orf中，6在核衣壳编码orf中。尽管发现一些基序 (~27%) 插入或附着在功能肽上，但其中大多数尚未与任何已知功能相关联。结论：一些三核苷酸家族在不同冠状病毒属中的分布不是随机的；它们存在于短肽中，在许多情况下，短肽插入或附着在蛋白质组的功能位点上。