CDS sequences
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB36521 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Mature messenger RNAs (mRNAs) consist of coding sequence (CDS) and 5’ and 3’ untranslated regions, typically expected to show similar abundance within a given neuron. Examining mRNA from defined neurons we unexpectedly show extremely common unbalanced expression of cognate 3’ UTR and CDS sequences, observing many genes with high UTR relative to CDS, and others with high CDS to UTR. By in situ hybridization 19 of 19 genes examined show a broad range of UTR to CDS expression ratios in different neurons and other tissues. These ratios may be spatially graded or change with developmental age, but are consistent across animals. Further, for two genes examined, a UTR to CDS ratio above a particular threshold in any given neuron correlated with reduced or undetectable protein expression. Our findings raise questions about the role of isolated UTR sequences in regulation of protein expression, and highlight the importance of separately examining UTR and CDS sequences in gene expression analyses.
2016-03-04 | GSE75596 | GEO
Project description:The impact of RNA structures in coding sequences (CDS) within mRNAs is poorly understood. Here we identify a novel and highly conserved mechanism of translational control involving RNA structures within coding sequences and the DEAD-box helicase Dhh1. Using yeast genetics and genome-wide ribosome profiling analyses we show that this mechanism, initially derived from studies of the Brome Mosaic virus RNA genome, extends to yeast and human mRNAs highly enriched in membrane and secreted proteins. All Dhh1-dependent mRNAs, viral and cellular, share key common features. First, they contain long and highly structured CDSs, including a region located around nucleotide 70 after the translation initiation site, second, they are directly bound by Dhh1 with a specific binding distribution and third, complementary experimental approaches suggest that they are activated by Dhh1 at the translation initiation step. Our results show that ribosome translocation is not the only unwinding force of CDS and uncover a novel layer of translational control that involves RNA helicases and RNA folding within CDS providing novel opportunities for regulation of membrane and secretome proteins.
2016-11-04 | GSE87888 | GEO
Project description:Sphingomonas sp. CDS-1 Genome sequencing and assembly
| PRJNA387507 | ENA
Project description:Proteogenomics and ribosome profiling concurrently show that genes may code for both a large and one or more small proteins translated from annotated coding sequences (CDSs) and unannotated alternative open reading frames (named alternative ORFs or altORFs), respectively, but the stoichiometry between large and small proteins translated from the same gene is unknown. \textit{MIEF1}, a gene recently identified as a dual-coding gene, harbours a CDS and a newly annotated and actively translated altORF located in the 5’UTR . Here, we use absolute quantification with stable isotope-labeled peptides and parallel reaction monitoring to determine levels of both proteins in two human cells lines and in human colon. We report that the main \textit{MIEF1} translational product is not the canonical 463 amino acid MiD51 protein but the small 70 amino acid alternative MiD51 protein (altMiD51). These results demonstrate the inadequacy of the single CDS concept and provide a strong argument for modernizing functional annotations of genes.
2018-11-21 | PXD008147 | Pride
Project description:Paracentrotus lividus Msx-1 mRNA, complete CDS
| PRJEB21976 | ENA
Project description:Electrophorus sp. a CDS-2021 Genome sequencing and assembly
| PRJNA722843 | ENA
Project description:We constructed the electroautotrophic bacteria, i.e., Sporomusa ovata together with CdS for artificial photosynthesis that achieved the conversion of carbon dioxide to the acetate. The proteomic analysis in S.ovata-CdS biohybrids and S.ovata-only groups was conducted to propose the working mechanisms including carbon dioxide fixation, electron transfer, energy metabolism and redox oxygen damage repair.
2021-08-18 | PXD027986 | iProX
Project description: Not available
| S-EPMC1314900 | biostudies-literature