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<title>Open reading frame</title>

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Open reading frame

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In <a href="Molecular_biology" title="Molecular biology">molecular biology</a>, reading frames are defined as spans of <a href="DNA" title="DNA">DNA</a> sequence between the start and stop <a href="Codon" class="mw-redirect" title="Codon">codons</a>. Usually, this is considered within a studied region of a <a href="Prokaryote" title="Prokaryote">prokaryotic</a> DNA sequence, where only one of the <a href="#Six-frame_translation">six possible reading frames</a> will be "open" (the "reading", however, refers to the RNA produced by <a href="Transcription_(biology)" title="Transcription (biology)">transcription</a> of the DNA and its subsequent interaction with the <a href="Ribosome" title="Ribosome">ribosome</a> in <a href="Translation_(biology)" title="Translation (biology)">translation</a>). Such an open reading frame (ORF) may<a href="#cite_note-Sieber_2018-1">[1]</a> contain a <a href="Start_codon" title="Start codon">start codon</a> (usually AUG in terms of <a href="RNA" title="RNA">RNA</a>) and by definition cannot extend beyond a <a href="Stop_codon" title="Stop codon">stop codon</a> (usually UAA, UAG or UGA in RNA).<a href="#cite_note-2">[2]</a> That start codon (not necessarily the first) indicates where translation may start. The <a href="Transcription_terminator" class="mw-redirect" title="Transcription terminator">transcription termination</a> site is located after the ORF, beyond the translation stop codon. If transcription were to cease before the stop codon, an incomplete <a href="Protein" title="Protein">protein</a> would be made during translation.<a href="#cite_note-3">[3]</a>

In <a href="Eukaryote" title="Eukaryote">eukaryotic</a> <a href="Gene" title="Gene">genes</a> with multiple <a href="Exon" title="Exon">exons</a>, <a href="Intron" title="Intron">introns</a> are removed and exons are then joined together after transcription to yield the final <a href="MRNA" class="mw-redirect" title="MRNA">mRNA</a> for protein translation. In the context of <a href="Gene_prediction" title="Gene prediction">gene finding</a>, the start-stop <a href="Definition" title="Definition">definition</a> of an ORF therefore only applies to spliced <a href="Messenger_RNA" title="Messenger RNA">mRNAs</a>, not genomic DNA, since introns may contain stop codons and/or cause shifts between reading frames. An alternative definition says that an ORF is a sequence that has a length divisible by three and is bounded by stop codons.<a href="#cite_note-Sieber_2018-1">[1]</a><a href="#cite_note-Claverie_1997a-4">[4]</a> This more general definition can be useful in the context of <a href="Transcriptomics_technologies" title="Transcriptomics technologies">transcriptomics</a> and <a href="Metagenomics" title="Metagenomics">metagenomics</a>, where a start or stop codon may not be present in the obtained sequences. Such an ORF corresponds to parts of a gene rather than the complete gene.

<div class="mw-heading mw-heading2"><h2 id="Biological_significance">Biological significance</h2></div>

One common use of open reading frames (ORFs) is as one piece of evidence to assist in <a href="Gene_prediction" title="Gene prediction">gene prediction</a>. Long ORFs are often used, along with other evidence, to initially identify candidate <a href="Genetic_code" title="Genetic code">protein-coding</a> regions or <a href="Non-coding_RNA" title="Non-coding RNA">functional RNA</a>-coding regions in a <a href="DNA" title="DNA">DNA</a> sequence.<a href="#cite_note-deonier2005p25-5">[5]</a> The presence of an ORF does not necessarily mean that the region is always <a href="Translation_(genetics)" class="mw-redirect" title="Translation (genetics)">translated</a>. For example, in a randomly generated DNA sequence with an equal percentage of each <a href="Nucleotide" title="Nucleotide">nucleotide</a>, a <a href="Stop-codon" class="mw-redirect" title="Stop-codon">stop-codon</a> would be expected once every 21 <a href="Codon" class="mw-redirect" title="Codon">codons</a>.<a href="#cite_note-deonier2005p25-5">[5]</a> A simple gene prediction algorithm for <a href="Prokaryotes" class="mw-redirect" title="Prokaryotes">prokaryotes</a> might look for a <a href="Start_codon" title="Start codon">start codon</a> followed by an open reading frame that is long enough to encode a typical protein, where the <a href="Codon_usage_bias" title="Codon usage bias">codon usage</a> of that region matches the frequency characteristic for the given organism's coding regions.<a href="#cite_note-deonier2005p25-5">[5]</a> Therefore, some authors say that an ORF should have a minimal length, e.g. 100 codons<a href="#cite_note-Claverie_1997-6">[6]</a> or 150 codons.<a href="#cite_note-deonier2005p25-5">[5]</a> By itself even a long open reading frame is not conclusive evidence for the presence of a <a href="Gene" title="Gene">gene</a>.<a href="#cite_note-deonier2005p25-5">[5]</a>

<div class="mw-heading mw-heading3"><h3 id="Short_open_reading_frames">Short open reading frames</h3></div>

Some short open reading frames,<a href="#cite_note-7">[7]</a> also named small open reading frames,<a href="#cite_note-8">[8]</a> abbreviated as sORFs or smORFs, usually < 100 codons in length,<a href="#cite_note-9">[9]</a> that lack the classical hallmarks of protein-coding genes (both from ncRNAs and mRNAs) can produce functional <a href="Peptide" title="Peptide">peptides</a>.<a href="#cite_note-ZanetBenrabah2015-10">[10]</a> They encode <a href="Microprotein" title="Microprotein">microproteins</a> or sORF‐encoded proteins (SEPs). The <a href="Five_prime_untranslated_region" title="Five prime untranslated region">5’-UTR</a> of about 50% of mammal mRNAs are known to contain one or several sORFs,<a href="#cite_note-11">[11]</a> also called <a href="Upstream_ORF" class="mw-redirect" title="Upstream ORF">upstream ORFs</a> or uORFs. However, less than 10% of the vertebrate mRNAs surveyed in an older study contained AUG codons in front of the major ORF. Interestingly, uORFs were found in two thirds of proto-oncogenes and related proteins.<a href="#cite_note-12">[12]</a> 64–75% of experimentally found translation initiation sites of sORFs are conserved in the genomes of human and mouse and may indicate that these elements have function.<a href="#cite_note-13">[13]</a> However, sORFs can often be found only in the minor forms of mRNAs and avoid selection; the high conservation of initiation sites may be connected with their location inside promoters of the relevant genes. This is characteristic of <a href="SLAMF1" title="SLAMF1">SLAMF1</a> gene, for example.<a href="#cite_note-14">[14]</a>

<div class="mw-heading mw-heading2"><h2 id="Six-frame_translation">Six-frame translation</h2></div>

Since DNA is interpreted in groups of three nucleotides (codons), a DNA strand has three distinct reading frames.<a href="#cite_note-:0-15">[15]</a> The double helix of a DNA molecule has two anti-parallel strands; with the two strands having three reading frames each, there are six possible frame translations.<a href="#cite_note-:0-15">[15]</a>

<div class="mw-heading mw-heading2"><h2 id="Software">Software</h2></div>

<div class="mw-heading mw-heading3"><h3 id="Finder">Finder</h3></div>

The ORF Finder (Open Reading Frame Finder)<a href="#cite_note-16">[16]</a> 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. The deduced amino acid sequence can be saved in various formats and searched against the sequence database using the <a href="BLAST_(biotechnology)" title="BLAST (biotechnology)">basic local alignment search tool</a> (BLAST) server. The ORF Finder should be helpful in preparing complete and accurate sequence submissions. It is also packaged with the Sequin sequence submission software (sequence analyser).

<div class="mw-heading mw-heading3"><h3 id="Investigator">Investigator</h3></div>

ORF Investigator<a href="#cite_note-17">[17]</a> is a program which not only gives information about the coding and non coding sequences but also can perform pairwise global alignment of different gene/DNA regions sequences. The tool efficiently finds the ORFs for corresponding amino acid sequences and converts them into their single letter amino acid code, and provides their locations in the sequence. The pairwise global alignment between the sequences makes it convenient to detect the different mutations, including <a href="Single_nucleotide_polymorphism" class="mw-redirect" title="Single nucleotide polymorphism">single nucleotide polymorphism</a>. <a href="Needleman%E2%80%93Wunsch_algorithm" title="Needleman–Wunsch algorithm">Needleman–Wunsch algorithms</a> are used for the gene alignment. The ORF Investigator is written in the portable <a href="Perl" title="Perl">Perl</a> <a href="Programming_language" title="Programming language">programming language</a>, and is therefore available to users of all common operating systems.

<div class="mw-heading mw-heading3"><h3 id="Predictor">Predictor</h3></div>

OrfPredictor<a href="#cite_note-18">[18]</a> is a web server designed for identifying protein-coding regions in expressed sequence tag (EST)-derived sequences. For query sequences with a hit in BLASTX, the program predicts the coding regions based on the translation reading frames identified in BLASTX alignments, otherwise, it predicts the most probable coding region based on the intrinsic signals of the query sequences. The output is the predicted peptide sequences in the <a href="FASTA_format" title="FASTA format">FASTA format</a>, and a definition line that includes the query ID, the translation reading frame and the nucleotide positions where the coding region begins and ends. OrfPredictor facilitates the annotation of EST-derived sequences, particularly, for large-scale EST projects.

ORF Predictor uses a combination of the two different ORF definitions mentioned above. It searches stretches starting with a start codon and ending at a stop codon. As an additional criterion, it searches for a stop codon in the 5' <a href="Untranslated_region" title="Untranslated region">untranslated region</a> (UTR or NTR, nontranslated region<a href="#cite_note-Carrington_1990-19">[19]</a>). The OrfPredictor web server was not further supported, the standalone OrfPredictor tool can be downloaded at the following site (<a rel="nofollow" class="external free" href="http://bioinformatics.ysu.edu/publication/tools_download/">http://bioinformatics.ysu.edu/publication/tools_download/</a>).

<div class="mw-heading mw-heading3"><h3 id="ORFik">ORFik</h3></div>

ORFik is a R-package in Bioconductor for finding open reading frames and using Next generation sequencing technologies for justification of ORFs.<a href="#cite_note-20">[20]</a><a href="#cite_note-21">[21]</a>

<div class="mw-heading mw-heading3"><h3 id="orfipy">orfipy</h3></div>

orfipy is a tool written in <a href="Python_(programming_language)" title="Python (programming language)">Python</a> / <a href="Cython" title="Cython">Cython</a> to extract ORFs in an extremely and fast and flexible manner.<a href="#cite_note-22">[22]</a> orfipy can work with plain or gzipped FASTA and FASTQ sequences, and provides several options to fine-tune ORF searches; these include specifying the start and stop codons, reporting partial ORFs, and using custom translation tables. The results can be saved in multiple formats, including the space-efficient BED format. orfipy is particularly faster for data containing multiple smaller FASTA sequences, such as de-novo transcriptome assemblies.<a href="#cite_note-23">[23]</a>

<ul><li><a href="Coding_region" title="Coding region">Coding region</a></li>

<li><a href="Putative_gene" title="Putative gene">Putative gene</a></li>

<li><a href="Sequerome" title="Sequerome">Sequerome</a> – A <a href="Sequence_profiling_tool" title="Sequence profiling tool">sequence profiling tool</a> that links each <a href="BLAST_(biotechnology)" title="BLAST (biotechnology)">BLAST</a> record to the <a href="National_Center_for_Biotechnology_Information" title="National Center for Biotechnology Information">NCBI</a> ORF enabling complete ORF analysis of a BLAST report.</li>

<li><a href="Micropeptide" title="Micropeptide">Micropeptide</a></li></ul>

<div class="mw-heading mw-heading2"><h2 id="References">References</h2></div>

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</ol></div></div>

<div class="mw-heading mw-heading2"><h2 id="External_links">External links</h2></div>

<ul><li><a rel="nofollow" class="external text" href="http://bioweb.uwlax.edu/GenWeb/Molecular/Seq_Anal/Translation/translation.html">Translation and Open Reading Frames</a> <a rel="nofollow" class="external text" href="https://web.archive.org/web/20110406231127/http://bioweb.uwlax.edu/genweb/molecular/seq_anal/translation/translation.html">Archived</a> 2011-04-06 at the <a href="Wayback_Machine" title="Wayback Machine">Wayback Machine</a></li>

<li><a rel="nofollow" class="external text" href="http://horfdb.dfci.harvard.edu/">hORFeome V5.1</a> - A web-based interactive tool for CCSB Human ORFeome Collection</li>

<li><a rel="nofollow" class="external text" href="https://web.archive.org/web/20091128111853/http://ugene.unipro.ru/plugin_orf_marker.html">ORF Marker</a> - A free, fast and multi-platform desktop GUI tool for predicting and analyzing ORFs</li>

<li><a rel="nofollow" class="external text" href="http://web.mit.edu/star/orf/">StarORF</a> - A multi-platform, java-based, GUI tool for predicting and analyzing ORFs and obtaining reverse complement sequence</li>

<li><a rel="nofollow" class="external text" href="http://bioinformatics.ysu.edu/tools/OrfPredictor.html">ORFPredictor</a> <a rel="nofollow" class="external text" href="https://web.archive.org/web/20151222082631/http://bioinformatics.ysu.edu/tools/OrfPredictor.html">Archived</a> 2015-12-22 at the <a href="Wayback_Machine" title="Wayback Machine">Wayback Machine</a> - A webserver designed for ORF prediction and translation of a batch of EST or cDNA sequences</li></ul></div><div><div class="zim-footer">

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