can potentially be translated into a seven amino acid peptide.
Based on uORF
theory within 5'-UTR of mRNAs which translate to small peptides and can regulate eukaryotic gene expression), deleted sequences of OCT4 5'UTRs were translated using expasy translate tool.
During cellular stress induced by cancer, noncanonical translation utilizing uORF elements or IRES elements drives translation of specific stress response and adaptation proteins.
Schier, "Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish," Nature Communications, vol.
In this review, we will first discuss the mechanism of canonical translation initiation, followed by noncanonical mechanisms that utilize RNA sequence features including upstream open reading frames (uORFs) and internal ribosome entry site- (IRES-) mediated translation mechanisms, the role of eukaryotic initiation factors in noncanonical translation, and their significance in cancer progression.
Another category of novel peptides is peptides mapping to known protein-coding regions, including to their untranslated regions (UTRs), but in an alternative frame [e.g., peptides derived from upstream open reading frames (uORFs)].
So one can start using proteogenomics, in a more meaningful way than before, to look for evidence of protein-level expression of transcripts currently annotated as noncoding RNAs or pseudogenes, to search for short ORFs and uORFs. The number of transcripts observed in any RNA-Seq data for any sample is astonishing.
Different types of cis-acting elements encoded in mRNA 5' untranslated region (57 UTR) sequences can mediate regulation of translational initiation; such elements include (1) secondary structure that can block a scanning ribosome and thereby inhibit recognition of an AUG initiation codon, (2) IRESs that stimulate cap-independent translation, (3) protein binding sites that either repress or promote translation in response via transacting factors, and (4) upstream AUG codons, in some cases, associated with upstream open reading frames (uORFs