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Small open reading frames: a comparative genetics approach to validation
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...
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Investigating open reading frames in known and novel transcripts using ORFanage
ORFanage is a system designed to assign open reading frames (ORFs) to known and novel gene transcripts while maximizing similarity to annotated...
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CRISPR–Cas9-based functional interrogation of unconventional translatome reveals human cancer dependency on cryptic non-canonical open reading frames
Emerging evidence suggests that cryptic translation beyond the annotated translatome produces proteins with developmental or physiological functions....
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OpenVar: functional annotation of variants in non-canonical open reading frames
BackgroundRecent technological advances have revealed thousands of functional open reading frames (ORF) that have eluded reference genome...
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Methods for Analysis of Interactome of Microproteins Encoded by Short Open Reading Frames
Abstract—Recent studies demonstrated that short open reading frames (sORFs, <100 codons) can encode the peptides or microproteins that perform...
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PRPF19 mRNA Encodes a Small Open Reading Frame That Is Important for Viability of Human Cells
AbstractHigh-throughput ribosome profiling demonstrates the translation of thousands of small open reading frames located in the 5′ untranslated...
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Moonlighting genes harbor antisense ORFs that encode potential membrane proteins
Moonlighting genes encode for single polypeptide molecules that perform multiple and often unrelated functions. These genes occur across all domains...
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Alternative Reading Frames are an Underappreciated Source of Protein Sequence Novelty
Protein-coding DNA sequences can be translated into completely different amino acid sequences if the nucleotide triplets used are shifted by a...
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Small open reading frames in plant research: from prediction to functional characterization
Gene prediction is a laborious and time-consuming task. The advancement of sequencing technologies and bioinformatics tools, coupled with accelerated...
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ProTInSeq: transposon insertion tracking by ultra-deep DNA sequencing to identify translated large and small ORFs
Identifying open reading frames (ORFs) being translated is not a trivial task. ProTInSeq is a technique designed to characterize proteomes by...
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Short open reading frames (sORFs) and microproteins: an update on their identification and validation measures
A short open reading frame (sORFs) constitutes ≤ 300 bases, encoding a microprotein or sORF-encoded protein (SEP) which comprises ≤ 100 amino acids....
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Upstream open reading frames regulate translation of cancer-associated transcripts and encode HLA-presented immunogenic tumor antigens
BackgroundUpstream open reading frames (uORFs) represent translational control elements within eukaryotic transcript leader sequences. Recent data...
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Upstream open reading frame-introducing variants in patients with primary familial brain calcification
More than 50% of patients with primary familial brain calcification (PFBC), a rare neurological disorder, remain genetically unexplained. While some...
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Novel open reading frames in human accelerated regions and transposable elements reveal new leads to understand schizophrenia and bipolar disorder
Schizophrenia (SCZ) and bipolar disorder are debilitating neuropsychiatric disorders arising from a combination of environmental and genetic factors....
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Noncanonical open reading frames encode functional proteins essential for cancer cell survival
Although genomic analyses predict many noncanonical open reading frames (ORFs) in the human genome, it is unclear whether they encode biologically...
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Analysis of codon usage patterns in open reading frame 4 of hepatitis E viruses
BackgroundHepatitis E virus (HEV) is a member of the family Hepeviridae and causes acute HEV infections resulting in thousands of deaths worldwide....
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Pan-cancer analysis of transcripts encoding novel open-reading frames (nORFs) and their potential biological functions
Uncharacterized and unannotated open-reading frames, which we refer to as novel open reading frames (nORFs), may sometimes encode peptides that...
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Little but Loud. The Diversity of Functions of Small Proteins and Peptides – Translational Products of Short Reading Frames
AbstractCell functioning is tightly regulated process. For many years, research in the fields of proteomics and functional genomics has been focused...
