Small open reading frames: a comparative genetics approach to validation [PDF]
BMC Genomics, 2023 Open reading frames (ORFs) with fewer than 100 codons are generally not annotated in genomes, although bona fide genes of that size are known. Newer biochemical studies have suggested that thousands of small protein-coding ORFs (smORFs) may exist in the ...
Niyati Jain +4 more
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Evidence for conservation and selection of upstream open reading frames suggests probable encoding of bioactive peptides [PDF]
BMC Genomics, 2006 Background Approximately 40% of mammalian mRNA sequences contain AUG trinucleotides upstream of the main coding sequence, with a quarter of these AUGs demarcating open reading frames of 20 or more codons.
Wang Xue-Qing +2 more
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Predicting statistical properties of open reading frames in bacterial genomes. [PDF]
PLoS ONE, 2012 An analytical model based on the statistical properties of Open Reading Frames (ORFs) of eubacterial genomes such as codon composition and sequence length of all reading frames was developed.
Katharina Mir +4 more
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Identification of short open reading frames in plant genomes [PDF]
Frontiers in Plant Science, 2023 The roles of short/small open reading frames (sORFs) have been increasingly recognized in recent years due to the rapidly growing number of sORFs identified in various organisms due to the development and application of the Ribo-Seq technique, which ...
Yong Feng +5 more
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Conserved elements within open reading frames of mammalian Hox genes [PDF]
Journal of Biology, 2009 A recent study in BMC Evolutionary Biology shows that many of the open reading frames in mammalian Hox genes are more conserved than expected on the basis of their protein sequence.
Woltering Joost M, Duboule Denis
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Integrated workflow for discovery of microprotein-coding small open reading frames [PDF]
STAR Protocols, 2023 Summary: Small open reading frame (smORF)-encoded microproteins, proteins containing less than 100–150 amino acids, are an emerging class of functional biomolecules.
Kevin Cao +3 more
doaj +2 more sources
AlterORF: a database of alternate open reading frames [PDF]
Nucleic Acids Research, 2007 AlterORF is a searchable database that contains information regarding alternate open reading frames (ORFs) for over 1.5 million genes in 481 prokaryotic genomes. The objective of the database is to provide a platform for improving genome annotation and to serve as an aid for the identification of prokaryotic genes that potentially encode proteins in ...
Inti Pedroso +6 more
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Evolutionary divergence of novel open reading frames in cichlids speciation [PDF]
Scientific Reports, 2020 Novel open reading frames (nORFs) with coding potential may arise from noncoding DNA. Not much is known about their emergence, functional role, fixation in a population or contribution to adaptive radiation.
Shraddha Puntambekar +9 more
doaj +3 more sources
Standardized annotation of translated open reading frames [PDF]
Nature Biotechnology, 2022 Ribosome profiling (Ribo-seq) has extended our understanding of the translational ‘vocabulary’ of the human genome, uncovering thousands of open reading frames (ORFs) within long noncoding RNAs (lncRNAs) and presumed untranslated regions (UTRs) of protein-coding genes.
Jonathan M. Mudge +34 more
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Conserved upstream open reading frames in higher plants [PDF]
BMC Genomics, 2008 Background Upstream open reading frames (uORFs) can down-regulate the translation of the main open reading frame (mORF) through two broad mechanisms: ribosomal stalling and reducing reinitiation efficiency.
Schultz Carolyn J +2 more
doaj +3 more sources