Riboformer: a deep learning framework for predicting context-dependent translation dynamics by Bin Shao, Jiawei Yan, Jing Zhang, Lili Liu, Ye Chen, Allen R. Buskirk

“…Riboformer leverages the transformer architecture to accurately predict ribosome densities at codon resolution. When trained on an unbiased dataset, Riboformer corrects experimental artifacts in previously unseen datasets, which reveals subtle differences in synonymous codon translation and uncovers a bottleneck in translation elongation. …”
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The complete mitochondrial genome and phylogenetic analysis of Omphalius rusticus (Gastropoda, Tegulidae) by Shuai Mao, Chengrui Yan, Jie Bai, Yingying Ye, Jiji Li, Yahong Guo, Jiantong Feng

“…The overall base composition is 33.48% (A), 33.52% (T), 15.58% (G) and 17.42% (C). The all start codon for 13 protein-coding genes is ATG and the most common termination codon is TAA. …”
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p53 immunocytochemistry and TP53 gene mutations in patients with chronic hepatitis C virus (HCV) infection. by Maciej Zabel, Wiesława Biczysko, Jacek Juszczyk, Karolina Olejniczak, Arkadiusz Czajka, Wiesława Przybyszewska, Agnieszka Adamek, Aldona Kasprzak

“…In the first patient, a substitution of C to T was demonstrated in position 1 of the codon 250, resulting in substitution of proline by serine. …”
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The complete mitochondrial genome of Wonwhang (Pyrus pyrifolia) by Ho Yong Chung, So Yun Won, Sang-Ho Kang, Seong-Han Sohn, Jung Sun Kim

“…The stop codon is also common in all mitochondrial genes. …”
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The complete mitochondrial genome of Ceriagrion fallax (Odonata: Zygoptera: Coenagrionidae) and phylogenetic analysis by Hainan Shao, Qiurong Li, Yunxiang Liu

“…Except for four PCGs (cox1, cox2, cox3, and nad5) end with the incomplete stop codon T––, all other PCGs terminated with the stop codon TAA. …”
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Molecular Characterization of the N-Acetylglucosamine Catabolic Genes in Candida africana, a Natural N-Acetylglucosamine Kinase (HXK1) Mutant. by Maria Rosa Felice, Megha Gulati, Letterio Giuffrè, Domenico Giosa, Luca Marco Di Bella, Giuseppe Criseo, Clarissa J Nobile, Orazio Romeo, Fabio Scordino

“…RESULTS:DNA sequence analysis of these genes revealed a number of characteristic nucleotide substitutions including a unique and distinctive guanine insertion that shifts the reading frame and generates a premature stop codon (TGA) 154 bp downstream of the ATG start codon of the HXK1 gene encoding the GlcNAc-kinase, a key enzyme of the GlcNAc catabolic pathway. …”
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Complete mitochondrial genome sequence of Abraximorpha davidii (Lepidoptera: Hesperiidae: Tagiadinae) by Yunxiang Liu, Wenrong Xian, Yongqiang Ma, Hong Zhou

“…Except for cox1 starting with CGA, all other PCGs start with the standard ATN codons (seven ATG and five ATT). Most of the PCGs terminate with the stop codon TAA, whereas cox1, cox2, nad5, and nad4 end with the incomplete codon T−. …”
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Complete mitochondrial genome of the freshwater monogonont rotifer Brachionus rubens (Rotifera, Brachionidae) by Beom-Soon Choi, Young Hwan Lee, Jin-Sol Lee, Erick O. Ogello, Hee-Jin Kim, Atsushi Hagiwara, Jae-Seong Lee

“…Of 12 protein-coding genes (PCGs), one gene (ND5) had incomplete stop codons. Furthermore, the start codon of ND4 and CO2 gene was ATT, while the start codon of other PCGs was ATG. …”
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Complete mitochondrial genome sequence of the Jayakar’s seahorse Hippocampus jayakari Boulenger, 1900 (Gasterosteiformes: Syngnathidae) by Rubin Cheng, Yun Fang, Yuqing Ge, Qiang Liu, Guangji Zhang

“…The protein-coding genes had ATG or GTG as the initiation codon and only 6 genes (COX1, ATP8, ATP6, ND4L, ND5 and ND6) terminated by the complete typical stop codon TAA. …”
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Homozygous deep intronic variant in SNX14 cause autosomal recessive Spinocerebellar ataxia 20: a case report by Olga Levchenko, Alexandra Filatova, Irina Mishina, Aleksey Antonenko, Mikhail Skoblov

“…Typically, these variants result in the formation of a premature stop codon, a shift in the reading frame or a variant in canonical splicing sites, as well as gross rearrangements. …”
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393 Harnessing the potential of transcriptional adaptation as a mechanism for rare Amyotrophic lateral sclerosis by Adriana Morales Gomez, Nathan Staff, Stephen C. Ekker

“…METHODS/STUDY POPULATION: The presence of a premature termination codon triggers transcriptional activation. Therefore, we utilized CRISPR-Cas9 tool to generate a premature termination codon in CHCHD10 gene in multiple types of cells, including induced pluripotent stem cells derived from patient samples with known CHCHD10 mutations causative for Amyotrophic lateral sclerosis. …”
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Analysis of Mesorhizobium loti Glycogen Operon: Effect of Phosphoglucomutase (pgm) and Glycogen Synthase (glgA) Null Mutants on Nodulation of Lotus tenuis by Viviana C. Lepek, Alejandra L. D'Antuono, Pablo E. Tomatis, Juan E. Ugalde, Susana Giambiagi, Rodolfo A. Ugalde

“…Primer extension experiments showed that transcription starts 19 bp upstream of the glgA start codon.…”
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Characterization of the complete mitochondrial genome sequence of Coilia brachygnathus (Clupeiformes, Engraulidae) from Huai River and its phylogenetic position by Yuan Tian, Tiezhu Yang, Shijie Yang, Leping Wang, Liangjie Zhao, Wenhao Sun

“…All PCGs employed a standard ATG as a start codon, except cytochrome c oxidase 1 (cox1) with GTG. …”
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The Complete Mitochondrial Genome of <i>Glischropus bucephalus</i> (Vespertilionidae; Chiroptera) Provides New Evidence for <i>Pipistrellus</i> Paraphyly by Svetlana S. Zhukova, Anna S. Speranskaya, Alexandra A. Lisenkova, Sergei V. Kruskop

“…The mitochondrial protein-coding genes use the standard start codon (ATN), one complete stop codon (TAA), and two incomplete stop codons (TA- and T-). …”
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The complete mitochondrial genome of Tropidothorax sinensis (Reuter, 1888) (Hemiptera: Lygaeidae) by Weidong Huang, Siyu Gong, Yunfei Wu, Fan Song, Hu Li

“…All protein-coding genes are initiated with ATN, except for COX1 and ND4L use TTG as the start codon, and terminate with TAA or TAG with the exception of COX2, COX3 and ND1 which use a single T residue as the stop codon. …”
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The mitochondrial genome of a leaf insect Phyllium westwoodii (Phasmatodea: Phylliidae) in Southeast Asia by Zhiwei Dong, Jun Li, Jinwu He, Guichun Liu, Chuyang Mao, Ruoping Zhao, Xueyan Li

“…All PCGs initiate with ‘ATN’ except for NAD4L that uses ‘TTG’ as the start codon, and terminate with ‘TAA’ except for COX2 that uses a single ‘T’ residue as the stop codon. …”
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The first mitochondrial genome of Calophyllum soulattri Burm.f. by Charles Anthon E. Cadorna, Dexter G. Pahayo, Jessica D. Rey

“…These RNA editing events created the start codon of nad1 and the stop codon of ccmFc. Most PCGs of the C. soulattri mitochondrial genome underwent negative selection, but atp4 and ccmB experienced positive selection. …”
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Case report: Novel mutations in the SPG11 gene in a case of autosomal recessive hereditary spastic paraplegia with a thin corpus callosum by Ji-Qing Duan, Hui Liu, Jia-Qiao Wu

“…The non-sense mutation (c.751C&gt;T) causes the conversion of codon 251st encoding the amino acid Gln into a stop codon (p. …”
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Functional studies of ring exported protein 1 (REX1) in Plasmodium falciparum by Pakiam, Jillian Ann

“…Transfection of these vectors into D10 parasites and subsequent immunofluorescence assays would show effects of the different regions on cleft architecture. Expression of codon-optimised REX1 in Escherichia coli (E.coli) was also performed. …”
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Ribosome occupancy profiles are conserved between structurally and evolutionarily related yeast domains by Nissley, D, Carbery, A, Chonofsky, M, Deane, C

“…The only evidence to date for such conservation of translation speed between homologous proteins has used codon rarity as a proxy for translation speed. There are, however, many other factors including mRNA structure and the chemistry of the amino acids in the A- and P-sites of the ribosome that influence the speed of amino acid addition.…”