Discovery of Human sORF-Encoded Polypeptides (SEPs) in Cell Lines and Tissue by Ma, Jiao, Ward, Carl C., Jungreis, Irwin, Slavoff, Sarah A., Schwaid, Adam G., Neveu, John, Budnik, Bogdan A., Kellis, Manolis, Saghatelian, Alan

“…The discovery of novel SEPs increases the size of the genome and the proteome and provides insights into the molecular biology of mammalian cells, such as the prevalent usage of non-AUG start codons. Through modifications of the existing SEP-discovery workflow, we discover an additional 195 SEPs in K562 cells and extend this methodology to identify novel human SEPs in additional cell lines and human tissue for a final tally of 237 new SEPs. …”
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Characterisation of influenza A viruses with mutations in segment 5 packaging signals. by Hutchinson, E, Wise, H, Kudryavtseva, K, Curran, MD, Digard, P

“…Most mutations tested were well-tolerated, but a virus with alterations to NP codons 464-466, near the 5'-end of the vRNA, produced small plaques and replicated to around one-tenth of the level of wild type virus. …”

Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes by Vaishali P. Waman, Pandurang Kolekar, Mukund R. Ramtirthkar, Mohan M. Kale, Urmila Kulkarni-Kale

“…Selection on codons of non-structural genes was observed to impact diversification of lineages in Asian I, cosmopolitan and sylvatic genotypes. …”
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Systematic pattern analyses of Vδ2+ TCRs reveal that shared “public” Vδ2+ γδ T cell clones are a consequence of rearrangement bias and a higher expansion status by Lihua Deng, Anna Harms, Sarina Ravens, Immo Prinz, Immo Prinz, Likai Tan

“…Public Vδ2+ TCRs result from germline-like rearrangement and synonymous codons, associated with a higher expansion status.…”
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Chloroplast Genome Structure and Phylogenetic Analysis of 13 Lamiaceae Plants in Tibet by Yiming Niu, Qian Qin, Yanjing Dong, Xiaoyun Wang, Shouwen Zhang, Zejing Mu

“…A total of 26,328–26,887 codons were detected in 13 cp genomes. According to the RSCU value analysis, the codons mostly ended with A/T. …”
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Correlated evolution of nucleotide substitution rates and allelic variation in <it>Mhc-DRB </it>lineages of primates by de Groot Natasja G, Garamszegi László Z, Bontrop Ronald E

“…Selection pressure by pathogens or other microevolutionary forces may result in a high rate of non-synonymous substitutions at the codons specifying the contact residues of the antigen binding sites (ABS), and the maintenance of extreme MHC allelic variation at the population/species level. …”
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Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes. by Mann, J, Byakwaga, H, Kuang, X, Le, A, Brumme, C, Mwimanzi, P, Omarjee, S, Martin, E, Lee, G, Baraki, B, Danroth, R, McCloskey, R, Muzoora, C, Bangsberg, DR, Hunt, P, Goulder, P, Walker, B, Harrigan, P, Martin, J, Ndung'u, T, Brockman, M, Brumme, Z

“…Nef clones exhibited substantial inter-subtype diversity: cohort consensus residues differed at 25% of codons, while a similar proportion of codons exhibited substantial inter-subtype differences in major variant frequency. …”

Pfcrt and pfmdr1 alleles associated with chloroquine resistance in Plasmodium falciparum from Guyana, South America by Wallis Best Plummer, Lexley M Pinto Pereira, Christine VF Carrington

“…Results indicate that the pfcrt K76T is ubiquitous in this environment, and confirmatory sequencing of codons 72 and 76 revealed two novel allelic sequences SVMIT and RVMNT in addition to the previously identified CVMNT and SVMNT haplotypes. …”
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The complete mitochondrial genome of Uca lactea (Ocypodidae, Brachyura) and phylogenetic relationship in Brachyura by Ting-Ting Yang, Yu Liu, Zhao-Zhe Xin, Qiu-Ning Liu, Dai-Zhen Zhang, Bo-Ping Tang

“…All PCGs were initiated by ATN codons. The nucleotide composition was also biased toward A + T nucleotides (69.48%). …”
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Structure, Activity and Function of the Dual Protein Lysine and Protein N-Terminal Methyltransferase METTL13 by Magnus E. Jakobsson

“…METTL13-mediated methylation of eEF1A has functional consequences related to translation dynamics and include altered rate of global protein synthesis and translation of specific codons. Aberrant regulation of METTL13 has been linked to several types of cancer but the precise mechanisms are not yet fully understood. …”
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VSG mRNA levels are regulated by the production of functional VSG protein by Maudlin, IE, Kelly, SB, Schwede, A, Carrington, M

“…Here, the regulation of VSG mRNA levels has been investigated by first measuring VSG mRNA copy number, and second using ectopic expression of VSG transgenes containing premature termination codons. The findings are that (i) VSG mRNA copy number varies with the identity of the VSG and (ii) a pathway detects synthesis of non-functional VSG protein and results in an increase in VSG mRNA levels.…”

A nonsense exon in the Tpm1 gene is silenced by hnRNP H and F. by Coles, J, Hallegger, M, Smith, C

“…As well as generating protein isoform diversity, in some cases alternative splicing generates RNAs that harbor premature termination codons and that are subject to nonsense-mediated decay (NMD). …”

The amount of nitrogen used for photosynthesis modulates molecular evolution in plants by Kelly, S

“…Specifically, plants that require more nitrogen to conduct photosynthesis experience stronger selection on transcript sequences to use synonymous codons that cost less nitrogen to biosynthesise. It is further shown that the strength of selection acting on transcript nitrogen cost constrains molecular sequence evolution such that genes experiencing stronger selection evolve at a slower rate. …”

Molecular analysis of APC mutations in familial adenomatous polyposis and sporadic colon carcinomas. by Cottrell, S, Bicknell, D, Kaklamanis, L, Bodmer, W

“…These mutations were either point mutations or small deletions or insertions causing frameshifts, and all generated stop codons. One 5 base-pair deletion was found in a sporadic colon tumour, a colorectal cancer cell line derived from a sporadic colon tumour, and in four unrelated FAP patients. …”

The complete mitochondrial genome of the hybrid of Leiocassis longirostris (♂)×Pelteobagrus fulvidraco (♀) by Guosong Zhang, Xia Liang, Jiajia Zhang, Jie Li, Shaowu Yin

“…All the protein initiation codons are ATG, except for COX1 that begins with GTG. …”
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Thousands of human non-AUG extended proteoforms lack evidence of evolutionary selection among mammals by Alla D. Fedorova, Stephen J. Kiniry, Dmitry E. Andreev, Jonathan M. Mudge, Pavel V. Baranov

“…Abstract The synthesis of most proteins begins at AUG codons, yet a small number of non-AUG initiated proteoforms are also known. …”
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On cyclic DNA codes over the rings Z4 + wZ4 and Z4 + wZ4 + vZ4 + wvZ4 by Abdullah Dertli, Yasemin Cengellenmis

“…The links between the elements of the rings R, S and 16 and 256 codons are established, respectively. The cyclic codes of odd length over the finite ring R satisfy reverse complement constraint and the cyclic codes of odd length over the finite ring S satisfy reverse constraint and reverse complement constraint are studied. …”
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The complete mitochondrial genome of Encyrtus infelix (Hymenoptera: Encyrtidae) by Mei Xiong, Qing-Song Zhou, Yan-Zhou Zhang

“…All the 13 PCGs begin with typical ATN codons. Among them, seven genes terminate with TAA, one with TA– and five with T––. …”
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Annotated plastome of the temperate woody vine Muehlenbeckia australis (G.Forst.) Meisn. (Polygonaceae) by Tanja M. Schuster, Moreland D. Gibbs, Michael J. Bayly

“…The plastome includes 131 genes comprising 83 protein-coding genes, 37 transfer RNA genes, eight ribosomal RNA genes, two possible pseudogenes, psbL and rpl23 with internal stop codons, and truncated repeats of ndhF and rps19 at IR boundaries.…”
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Recent Developments of Engineered Translational Machineries for the Incorporation of Non-Canonical Amino Acids into Polypeptides by Naohiro Terasaka, Yoshihiko Iwane, Anna-Skrollan Geiermann, Yuki Goto, Hiroaki Suga

“…In order to efficiently incorporate a wide range of ncAAs, several methodologies have been developed, such as orthogonal aminoacyl-tRNA-synthetase (AARS)–tRNA pairs, aminoacylation ribozymes, frame-shift suppression of quadruplet codons, and engineered ribosomes. More recently, it has been reported that an engineered translation system specifically utilizes an artificially built genetic code and functions orthogonally to naturally occurring counterpart. …”
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