Messenger RNAs (mRNAs) consist of a coding region (open reading frame (ORF)) and two untranslated regions (UTRs), 5'UTR and 3'UTR. Ribosomes travel along the coding region, translating nucleotide triplets (called codons) to a chain of amino acids. The coding region was long believed to mainly encode the amino acid content of proteins, whereas regulatory signals reside in the UTRs and in other genomic regions. However, in recent years we have learned that the ORF is expansively populated with various regulatory signals, or codes, which are related to all gene expression steps and additional intracellular aspects. In this paper, we review the current knowledge related to overlapping codes inside the coding regions, such as the influence of synonymous codon usage on translation speed (and, in turn, the effect of translation speed on protein folding), ribosomal frameshifting, mRNA stability, methylation, splicing, transcription and more. All these codes come together and overlap in the ORF sequence, ensuring production of the right protein at the right time.

中文翻译：

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编码区域中广泛存在的非模块化重叠码。

信使 RNA (mRNA) 由一个编码区 (开放阅读框 (ORF)) 和两个非翻译区 (UTR) 5'UTR 和 3'UTR 组成。核糖体沿着编码区移动，将核苷酸三联体（称为密码子）翻译成氨基酸链。长期以来，人们认为编码区主要编码蛋白质的氨基酸含量，而调节信号则位于 UTR 和其他基因组区域。然而，近年来我们了解到，ORF 广泛分布着各种调节信号或代码，这些信号或代码与所有基因表达步骤和其他细胞内方面有关。在本文中，我们回顾了与编码区域内重叠代码相关的当前知识，例如同义密码子使用对翻译速度的影响（以及反过来，翻译速度对蛋白质折叠的影响）、核糖体移码、mRNA 稳定性、甲基化、剪接、转录等。所有这些代码汇集在一起​​，并在 ORF 序列中重叠，确保在正确的时间生产正确的蛋白质。