FuncPEP: A Database of Functional Peptides Encoded by Non-Coding RNAs by Mihnea P. Dragomir, Ganiraju C. Manyam, Leonie Florence Ott, Léa Berland, Erik Knutsen, Cristina Ivan, Leonard Lipovich, Bradley M. Broom, George A. Calin

“…The sequences encoding these peptides are known as small open reading frames (smORFs), many initiating with the traditional AUG start codon but terminating with atypical stop codons, suggesting a different biogenesis. …”
Get full text

Familial Medullary Thyroid Cancer: Five-year Review of the Most Frequent Mutations in the RET Gene: An Update by Blanca Estela Díaz Castañeda, Mariela Eulogio Vences, Brian Emmanuel Díaz Gordillo, Miriam Deyanira Rodríguez Piña, Hugo Mendieta Zerón

“…Patients with an inherited form of FMTC usually have a germline mutation in the RET proto-oncogene (10q11.2); these mutations generally occur in exons 10 (codons 618 and 620) and 11 (codons 630, 631, and 634). …”
Get full text

Expression of Anti-Lipopolysaccharide Factor Isoform 3 in <i>Chlamydomonas reinhardtii</i> Showing High Antimicrobial Activity by Anguo Li, Ruihao Huang, Chaogang Wang, Qunju Hu, Hui Li, Xiao Li

“…To construct the expression cluster, namely pH2A-Pm3, the codon optimized <i>ALFPm3</i> gene was fused with the <i>ble</i> reporter by 2A peptide and inserted into pH124 vector. …”
Get full text

Novel pathogenic NPR2 variants in short stature patients and the therapeutic response to rhGH by Hong Chen, Suping Zhang, Yunteng Sun, Jiao Chen, Ke Yuan, Ying Zhang, Xiaohong Yang, Xiangquan Lin, Ruimin Chen

“…Subsequently, a small gene model was constructed, and transcriptional analysis of the synonymous variant (c.2643G > A) was performed in patient 3, which revealed the deletion of exon 17 and the premature formation of a stop codon (p.His840Gln*). Functional studies showed that both NPR2 variants, His948Profs*5 and His840Gln*, failed to produce cGMP in the homozygous state. …”
Get full text

Characterization of a Chickpea Mutant Resistant to <i>Phelipanche aegyptiaca</i> Pers. and <i>Orobanche crenata</i> Forsk by Shmuel Galili, Joseph Hershenhorn, Evgeny Smirnov, Koichi Yoneyama, Xiaonan Xie, Orit Amir-Segev, Aharon Bellalou, Evgenia Dor

“…This nonsense mutation resulted in a CCD7 stop codon at position 70 of the protein. The influences of the CCD7M14 mutation on chickpea phenotype and chlorophyll, carotenoid, and anthocyanin content were characterized.…”
Get full text

Effective splicing restoration of a deep-intronic ABCA4 variant in cone photoreceptor precursor cells by CRISPR/SpCas9 approaches by Pietro De Angeli, Peggy Reuter, Stefan Hauser, Ludger Schöls, Katarina Stingl, Bernd Wissinger, Susanne Kohl

“…By strengthening a cryptic splice site, deep-intronic variant c.5197-557G>T induces the inclusion of a 188-bp intronic sequence in the mature mRNA, resulting in a premature termination codon. Here, we report the design and evaluation of three CRISPR-Cas9 approaches implementing Streptococcus pyogenes Cas9 (single and dual guide RNA) or Streptococcus pyogenes Cas9 nickase (dual guide RNA) for their potential to correct c.5197-557G>T-induced aberrant splicing in minigene splicing assays and patient-derived cone photoreceptor precursor cells. …”
Get full text

Comparative Plastome Analyses of <i>Ephedra</i> <i>przewalskii</i> and <i>E.</i> <i>monosperma</i> (Ephedraceae) by Shuang Han, Mingze Xia, Jingya Yu, Hao Xu, Yun Han, Faqi Zhang

“…Among them, the <i>ndh</i> family genes were lost, which could be used to study the phylogeny and genetic diversity of the genus <i>Ephedra</i>, combined with multiple highly variable intergenic spacer (IGS) regions. Codon usage preference of <i>Ephedra</i> species was weak. …”
Get full text

Designing a T-cell epitope-based vaccine using in silico approaches against the Sal k 1 allergen of Salsola kali plant by Mohammad Hossein Shams, Seyyed Mohsen Sohrabi, Reza Jafari, Ali Sheikhian, Hossein Motedayyen, Peyman Amanolahi Baharvand, Amin Hasanvand, Ali Fouladvand, Mohammad-Ali Assarehzadegan

“…The molecular docking of the TEV with HLADRB1, and TLR4 showed TEV strong interactions and stable binding pose to these receptors. Moreover, the codon optimized TEV sequence was cloned between NcoI and XhoI restriction sites of pET-28a(+) expression plasmid. …”
Get full text

<i>JAK2</i> Variant Signaling: Genetic, Hematologic and Immune Implication in Chronic Myeloproliferative Neoplasms by Dania G. Torres, Jhemerson Paes, Allyson G. da Costa, Adriana Malheiro, George V. Silva, Lucivana P. de Souza Mourão, Andréa M. Tarragô

“…The <i>JAK2</i>V617F variant constitutes a genetic alteration of higher frequency in BCR/ABL1 negative chronic myeloproliferative neoplasms, which is caused by a substitution of a G ˃ T at position 1849 and results in the substitution of valine with phenylalanine at codon 617 of the polypeptide chain. Clinical, morphological and molecular genetic features define the diagnosis criteria of polycythemia vera, essential thrombocythemia and primary myelofibrosis. …”
Get full text

Genetic characterization of a novel picorna-like virus in Culex spp. mosquitoes from Mozambique by Harindranath Cholleti, Juliette Hayer, Jose Fafetine, Mikael Berg, Anne-Lie Blomström

“…Reads that are classified as Iflaviridae, Picornaviridae and Dicistroviridae were assembled by CodonCode Aligner and SPAdes. Gaps between the viral contigs were sequenced by PCR. …”
Get full text

A hypomorphic mutation in the mouse Csn1s1 gene generated by CRISPR/Cas9 pronuclear microinjection by A. V. Smirnov, T. A. Shnaider, A. N. Korablev, A. M. Yunusova, I. A. Serova, N. R. Battulin

“…Functionally most mutations led to gene knockout due to a frameshift or a start codon loss. Some of the mutations represented in-frame indels in the first coding exon. …”
Get full text

Complete mitochondrial genome sequence of Labriocimbex sinicus, a new genus and new species of Cimbicidae (Hymenoptera) from China by Yuchen Yan, Gengyun Niu, Yaoyao Zhang, Qianying Ren, Shiyu Du, Bocheng Lan, Meicai Wei

“…The results demonstrated that all PCGs were initiated by ATN codon, and ended with TAA or T stop codons. The study reveals that all tRNA genes have a typical clover-leaf secondary structure, except for trnS1. …”
Get full text

Evolution and Expression of the Expansin Genes in Emmer Wheat by Ming Li, Tao Liu, Rui Cao, Qibin Cao, Wei Tong, Weining Song

“…Phylogenetic analysis categorized the proteins into three subfamilies, namely EXPA, EXPB, and EXLA, in addition to the EXLB subfamily. Furthermore, codon preference analysis revealed an increased usage frequency of the nucleotide “T” in expansin proteins throughout the evolution of WEW and DW. …”
Get full text

An expanded RT-PCR melting temperature coding assay to rapidly identify all known SARS-CoV-2 variants and sub-variants of concern by Padmapriya P. Banada, Raquel Green, Deanna Streck, Rohini Kurvathi, Robert Reiss, Sukalyani Banik, Naranjargal Daivaa, Ibsen Montalvan, Robert Jones, Salvatore A. E. Marras, Soumitesh Chakravorty, David Alland

“…The SMB-VOC assay targets the signature codons 501, 484 and 452 in the SARS-CoV-2 spike protein which we show can specifically detect and differentiate all known VOCs including the Omicron subvariants (BA.1, BA.2, BA.2.12.1, BA.4/BA.5). …”
Get full text

Identification of a novel splice site mutation in the SERAC1 gene responsible for the MEGDHEL syndrome by Sarah Snanoudj, Patrick Mordel, Quentin Dupas, Cécile Schanen, Alina Arion, Marion Gérard, Marie‐Hélène Read, Djamel Nait Rabah, Didier Goux, Françoise Chapon, Mickael Jokic, Stéphane Allouche

“…Results Analysis of nuclear genes using an ampliSeq™ targeted custom panel disclosed two compound heterozygous variants in the SERAC1 gene: a nonsense substitution in exon 4, c.202C>T, resulting in a premature stop codon (p.Arg68*), and a novel variant at a canonical splicing site upstream exon 4 (c.129‐1G>C). mRNAs sequencing from the fibroblasts of the patient showed that the splice site variant resulted in exon 3 skipping without frameshift while Western blot experiments showed the absence of SERAC1 expression compared to controls and abnormal filipin staining. …”
Get full text

Comparison of Multiple Strategies for Precision Transgene Knock-In in <i>Gallus gallus</i> Genome via Microhomology-Mediated End Joining by Lijuan Wang, Jiaxin Sun, Zhipeng Liu, Qiang Zheng, Guojun Wang

“…We designed three targeted sgRNAs for the all-in-one plasmid at the 3′UTR of <i>GAPDH</i> near the stop codon. The donor-plasmid-carrying microhomology arms correspond to sgRNA and EGFP fragments in the forward and reverse directions. …”
Get full text

Natural variation in HvAT10 underlies grain cell wall-esterified phenolic acid content in cultivated barley by Kelly Houston, Amy Learmonth, Ali Saleh Hassan, Jelle Lahnstein, Mark Looseley, Alan Little, Robbie Waugh, Robbie Waugh, Robbie Waugh, Rachel A. Burton, Claire Halpin

“…We show that HvAT10 is rendered non-functional by a premature stop codon mutation in half of the genotypes in our mapping panel. …”
Get full text

Hypoprolactinemia as a Clue to Diagnosis of Mild Central Hypothyroidism due to IGSF1 Deficiency by Anastasios Papadimitriou, Anna Papadopoulou, Kleanthis Kleanthous, Dimitrios T. Papadimitriou, Vassiliki Papaevangelou

“…Sequencing of IGSF1 gene revealed a novel genetic change c.3805C>T in exon 19; substitution of amino acid Arginine at position 1269 with a premature «stop» codon resulting in an altered protein product. The patient additionally presented delayed adrenarche, low height velocity that resolved spontaneously and normal pubertal onset associated with increased FSH levels. …”
Get full text

Comparative Analysis of Mitochondrial Genomes in Two Subspecies of the Sunwatcher Toad-Headed Agama (<i>Phrynocephalus helioscopus</i>): Prevalent Intraspecific Gene Rearrangements... by Na Wu, Jinlong Liu, Song Wang, Xianguang Guo

“…The nucleotide composition and the codon usage are similar to those previously published from toad-headed agamas. …”
Get full text

Expression of Modified Snowdrop Lectin (<i>Galanthus nivalis</i> Agglutinin) Protein Confers Aphids and <i>Plutella xylostella</i> Resistance in <i>Arabidopsis</i> and Cotton by Peng He, Huanhuan Jia, Hui Xue, Yuechen Zeng, Lili Tian, Xiaoli Hu, Shufen Chang, Yanli Jiang, Jianing Yu

“…We report a modified <i>GNA</i> gene (<i>ASGNA</i>) via codon optimization, its insertion into <i>Arabidopsis thaliana</i>, and transient expression in cotton to test its efficacy as an insect-resistance gene against cotton aphids and <i>Plutella xylostella</i>. …”
Get full text