Classification and function of small open reading frames [PDF]
Nature Reviews Molecular Cell Biology, 2017 Small open reading frames (smORFs) of 100 codons or fewer are usually - if arbitrarily - excluded from proteome annotations. Despite this, the genomes of many metazoans, including humans, contain millions of smORFs, some of which fulfil key physiological functions. Recently, the transcriptome of Drosophila melanogaster was shown to contain thousands of
Pedro Patraquim
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Translational buffering by ribosome stalling in upstream open reading frames. [PDF]
PLoS Genetics, 2022 Upstream open reading frames (uORFs) are present in over half of all human mRNAs. uORFs can potently regulate the translation of downstream open reading frames through several mechanisms: siphoning away scanning ribosomes, regulating re-initiation, and ...
Ty A Bottorff +3 more
doaj +2 more sources
Translational regulation of PKD1 by evolutionarily conserved upstream open reading frames [PDF]
RNA BiologyMutations in PKD1 coding sequence and abnormal PKD1 expression levels contribute to the development of autosomal-dominant polycystic kidney disease, the most common genetic disorder. Regulation of PKD1 expression by factors located in the promoter and 3´
Lei Chen +4 more
doaj +2 more sources
ORFer – retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files [PDF]
BMC Bioinformatics, 2002 Background Functional genomics involves the parallel experimentation with large sets of proteins. This requires management of large sets of open reading frames as a prerequisite of the cloning and recombinant expression of these proteins.
Sievert Volker +2 more
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Upstream open reading frames repress the translation from the iab-8 RNA. [PDF]
PLoS GeneticsAlthough originally classified as a non-coding RNA, the male-specific abdominal (MSA) RNA from the Drosophila melanogaster bithorax complex has recently been shown to code for a micropeptide that plays a vital role in determining how mated females use ...
Yohan Frei +4 more
doaj +2 more sources
Upstream open reading frames may contain hundreds of novel human exons. [PDF]
PLoS Computational BiologySeveral recent studies have presented evidence that the human gene catalogue should be expanded to include thousands of short open reading frames (ORFs) appearing upstream or downstream of existing protein-coding genes, each of which might create an ...
Hyun Joo Ji, Steven L Salzberg
doaj +2 more sources
Noise reduction by upstream open reading frames [PDF]
Nature Plants, 2022 AbstractGene expression is prone to burst production, making it a highly noisy process that requires additional controls. Upstream open reading frames (uORFs) are widely present in the 5′ leader sequences of 30–50% of eukaryotic messenger RNAs1–3. The translation of uORFs can repress the translation efficiency of the downstream main coding sequences ...
Ho-Wei Wu +5 more
openaire +3 more sources
Pervasiveness of Microprotein Function Amongst Drosophila Small Open Reading Frames (SMORFS) [PDF]
CellsSmall Open Reading Frames (smORFs) of less than 100 codons remain mostly uncharacterised. About a thousand smORFs per genome encode peptides and microproteins about 70–80 aa long, often containing recognisable protein structures and markers of ...
Ana Isabel Platero +4 more
doaj +2 more sources
Mutational constraint analysis workflow for overlapping short open reading frames and genomic neighbors [PDF]
BMC GenomicsUnderstanding the dark genome is a priority task following the complete sequencing of the human genome. Short open reading frames (sORFs) are a group of largely unexplored elements of the dark genome with the potential for being translated into ...
Martin Danner +5 more
doaj +2 more sources
Open Reading Frame Phylogenetic Analysis on the Cloud [PDF]
International Journal of Genomics, 2013 Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity.
Che-Lun Hung, Chun-Yuan Lin
doaj +3 more sources