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An open reading frame (ORF) is a reading frame that has the potential to be transcribed into RNA and translated into protein. It requires a continuous sequence of DNA which may include a start codon, through a subsequent region which has a length that is a multiple of 3 nucleotides, to a stop codon in the same reading frame.
The ORF Finder (Open Reading Frame Finder) [16] is a graphical analysis tool which finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in the database. This tool identifies all open reading frames using the standard or alternative genetic codes.
It sets the frame for a run of successive, non-overlapping codons, which is known as an "open reading frame" (ORF). For example, the string 5'-AAATGAACG-3' (see figure), if read from the first position, contains the codons AAA, TGA, and ACG ; if read from the second position, it contains the codons AAT and GAA ; and if read from the third ...
An upstream open reading frame (uORF) is an open reading frame (ORF) within the 5' untranslated region (5'UTR) of an mRNA. uORFs can regulate eukaryotic gene expression. [1] [2] Translation of the uORF typically inhibits downstream expression of the primary ORF. However, in some genes such as yeast GCN4, translation of specific uORFs may ...
Repetitive regions may produce performance issues if they are not masked, and may even produce false evidence for gene annotation (for example, treating an open reading frame (ORF) in a transposon as an exon) [24] Depending on the letters used for replacement, masking can be classified as soft or hard: in soft masking, repetitive regions are ...
Ab Initio gene prediction is an intrinsic method based on gene content and signal detection. Because of the inherent expense and difficulty in obtaining extrinsic evidence for many genes, it is also necessary to resort to ab initio gene finding, in which the genomic DNA sequence alone is systematically searched for certain tell-tale signs of protein-coding genes.
This is known as the standard reading frame. However, in cases of frame shift mutations, an extra nucleotide (or more) is inserted into the DNA sequence, disrupting the typical reading frame and causing a shift in the sequence. This insertion prompts a shift in the reading frame due to the triplet nature of the genetic code.
Images of all localised proteins and their bioinformatic analysis can be viewed via the ‘Results Table’ or ‘Results Images’ buttons. In addition, use the search window on the entry site to find proteins containing features or motifs of particular interest to you that have been localised in this project.