CINXE.COM
locus tag
<!DOCTYPE html> <html lang="en"> <head> <meta charset="UTF-8" /> <meta property="og:title" content="locus tag" /> <meta property="og:url" content="https://www.ddbj.nig.ac.jp/ddbj/locus_tag-e.html" /> <meta property="og:description" content="locus tagThe locus tags are identifiers systematically assigned to everygene in ..." /> <meta property6="og:image" content="/images/thumbnail/logo_ddbj_fb.png" /> <meta name="viewport" content="width=device-width, initial-scale=1.0" /> <title>locus tag</title> <script async src="https://www.google-analytics.com/analytics.js"></script> <script src="https://code.jquery.com/jquery-3.5.0.js" integrity="sha256-r/AaFHrszJtwpe+tHyNi/XCfMxYpbsRg2Uqn0x3s2zc=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery.hoverintent/1.10.1/jquery.hoverIntent.min.js" integrity="sha512-gx3WTM6qxahpOC/hBNUvkdZARQ2ObXSp/m+jmsEN8ZNJPymj8/Jamf8+/3kJQY1RZA2DR+KQfT+b3JEB0r9YRg==" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/spin.js/4.1.0/spin.min.js" integrity="sha512-CbohqWjAgarTqRHcX1MbwkF2pujwbsCee1PABpnBWC+VqSldvlNEEI5+4OSsR/HbFQOFFpwY2YvZZNjBMxNnXg==" crossorigin="anonymous"></script> <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/jquery.colorbox/1.6.4/jquery.colorbox-min.js"></script> <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/jquery-deparam/0.5.3/jquery-deparam.min.js"></script> <script type="text/javascript" src="https://www.ddbj.nig.ac.jp/assets/js/jquery.trace.js"></script> <script type="text/javascript" src="https://www.ddbj.nig.ac.jp/assets/js/jquery.json_search.js"></script> <link rel="icon" href="https://www.ddbj.nig.ac.jp/assets/images/favicon_ddbj.ico"> <link rel="stylesheet" href="https://www.ddbj.nig.ac.jp/assets/css/colorbox.css" /> <link rel="stylesheet" href="https://www.ddbj.nig.ac.jp/assets/css/main.css" /> <link rel="alternate" type="application/rss+xml" title="My Site RSS" href="/feed.xml" /> <script src="https://www.ddbj.nig.ac.jp/assets/js/main.js"></script> </head> <body data-category="ddbj"> <script src="https://www.ddbj.nig.ac.jp/assets/js/ddbj_common_framework.js" id="DDBJ_common_framework" style="display: block; height: 40px;" data-bottom-menu="true" data-ddbj-home-page="true" data-search="true" ></script> <section class="top-news-view"> <div class="inner"> <ul> <li class="item"> <a href="https://www.ddbj.nig.ac.jp/news/en/2024-10-22-e">On Cyber Threats against DDBJ, a node of the International Nucleotide Sequence Database Collaboration</a> </li> <li class="item"> <a href="https://www.ddbj.nig.ac.jp/news/en/2024-11-22-e">(27st November 9:00-November 28th 12:00)Announcement of D-way/MSS suspension</a> </li> </ul> </div> </section> <div id="primary"> <header id="PageHeader"> <div class="inner"> <div class="page-title"> <p class="title -normal">DDBJ Annotated/Assembled Sequences</p> </div> <nav class="tab-menu-view"> <ul class="tabmenucontainer"> <li class=" -current"> <a href="/ddbj/index-e.html">Home</a> </li> <li class=" -haschild"> <a href="/ddbj/submission-e.html">Submission</a> <ul> <li> <a href="/ddbj/submission-e.html">Before Submission</a> </li> <li> <a href="/ddbj/web-submission-e.html">Web submission</a> </li> <li> <a href="/ddbj/mss-e.html">Mass Submission</a> </li> <li> <a href="/ddbj/update-e.html">Data Update</a> </li> </ul> </li> <li class=" -haschild"> <a href="http://ddbj.nig.ac.jp/arsa/?lang=en">Search</a> <ul> <li> <a href="http://getentry.ddbj.nig.ac.jp/top-e.html">getentry</a> </li> <li> <a href="http://ddbj.nig.ac.jp/arsa/?lang=en">ARSA</a> </li> </ul> </li> <li class=" -haschild"> <a href="/ddbj/flat-file-e.html">Flat file</a> <ul> <li> <a href="/ddbj/feature-table-e.html">Feature Table</a> </li> <li> <a href="/ddbj/features-e.html">Feature key</a> </li> <li> <a href="/ddbj/qualifiers-e.html">Qualifier key</a> </li> <li> <a href="/ddbj/sequence-e.html">Nucleotide Sequences</a> </li> <li> <a href="/ddbj/organism-e.html">Organism qualifier</a> </li> <li> <a href="/ddbj/identifiers-e.html">Identifiers</a> </li> <li> <a href="/ddbj/location-e.html">Description of Location</a> </li> <li> <a href="/ddbj/cds-e.html">Protein Coding Sequence</a> </li> <li> <a href="/ddbj/geneticcode-e.html">The Genetic Codes</a> </li> <li> <a href="/ddbj/code-e.html">Codes Used in Sequence Description</a> </li> <li> <a href="/ddbj/example-e.html">Description Examples of Sequence Data</a> </li> </ul> </li> <li class=" -haschild"> <a href="/ddbj/data-categories-e.html">Data categories</a> <ul> <li> <a href="/ddbj/genome-e.html">Data Submission from Genome Project</a> </li> <li> <a href="/ddbj/pseudohaplotype-e.html">Pseudohaplotype</a> </li> <li> <a href="/ddbj/wgs-e.html">WGS</a> </li> <li> <a href="/ddbj/finished_level_genome-e.html">Finished level genomic sequences</a> </li> <li> <a href="/ddbj/metagenome-assembly-e.html">Metagenome Assembly</a> </li> <li> <a href="/ddbj/single-amplified-genome-e.html">Single amplified genome</a> </li> <li> <a href="/ddbj/htg-e.html">HTG</a> </li> <li> <a href="/ddbj/environmental-e.html">Environmental sample</a> </li> <li> <a href="/ddbj/env-e.html">ENV</a> </li> <li> <a href="/ddbj/tls-e.html">TLS</a> </li> <li> <a href="/ddbj/transcriptome-e.html">Data Submission from Transcriptome Project</a> </li> <li> <a href="/ddbj/tsa-e.html">TSA</a> </li> <li> <a href="/ddbj/est-e.html">EST</a> </li> <li> <a href="/ddbj/htc-e.html">HTC</a> </li> <li> <a href="/ddbj/tpa-e.html">Third Party Data (TPA)</a> </li> </ul> </li> <li class=""> <a href="/faq/en/index-e.html?tag=ddbj">FAQ</a> </li> <li class=" -haschild"> <a href="/ddbj/index-e.html">Other</a> <ul> <li> <a href="/ddbj/patent-data-e.html">Patent</a> </li> <li> <a href="/ddbj/mga-e.html">MGA</a> </li> </ul> </li> </ul> </nav> </div> </header> <section id="NavigationAndMainView"> <div class="inner"> <div class="subview"> <nav id="TableOfContents" class="internal-link"> </nav> </div> <section id="MainContentView" class="mainview"> <header class="header"> <nav class="breadcrumb-view"> <ul> <li> <a href="https://www.ddbj.nig.ac.jp/index-e.html">Home</a> </li> <li> <a href="https://www.ddbj.nig.ac.jp/ddbj/index-e.html">ddbj</a> </li> <li><a>locus tag</a></li> </ul> </nav> <h1 class="title">locus tag</h1> </header> <main class="md-content"> <h2 id="locus_tag">locus tag</h2> <p>The locus tags are identifiers systematically assigned to every gene in a genome. INSD (DDBJ/ENA/GenBank) introduced the locus tag to prevent confusion caused by similar names assigned to different genes of different genomes. All component sequences of a genome assembly such as chromosomes and plasmids should use the same locus tag prefix in the /locus_tag qualifiers to systematically distinguish genes.</p> <h2 id="locus_tag_prefix">locus tag prefix registration</h2> <p>A genome assembly submission requires a <a href="/bioproject/submission-e.html">BioProject</a> and a <a href="/biosample/submission-e.html">BioSample</a>. Register a locus tag prefix during the BioSample submission. Enter a prefix you want to use in the <a href="/biosample/attribute-e.html#locus_tag_prefix">locus_tag_prefix attribute</a> provided by the BioSample <a href="/biosample/overview-e.html#genome-assembly-sample">packages used for genome assembly samples</a>. The locus_tag prefix should consist of 3-12 alpha-numeric characters and should start with a letter, but numerals can be used after the 2nd character (e.g. A1C). There should be no symbols such as ‘-‘, ‘_’ and ‘*’. <br /> A locus tag prefix cannot be changed after registration, so avoid to register a prefix following an organism name or a strain name which may be changed in the future.</p> <h2 id="locus_tag_qualifier">/locus_tag qualifier</h2> <p>Submit genome assembled sequences to DDBJ through <a href="/ddbj/mss-e.html">Mass Submission System</a>. <br /> In /locus_tag qualifiers, enter the prefix which has been registered in the corresponding BioSample. Assign /locus_tag qualifiers to both protein-coding genes and non-coding RNA genes. Separate the prefix and the tag value by an underscore (e.g. A1C_00001). It is recommended to use the same numbering convention for all /locus_tag qualifiers in order of appearance regardless of types of annotating genes such as protein-coding, structural RNA and originating chromosome. However, if you want to include information regarding chromosome number and RNA type, you may add these information after the underscode following the prefix.</p> <div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>ABC_I00001 for gene 1, chromosome I ABC_II00001 for gene 1, chromosome II ABC_r1112 for ribosomal RNA genes ABC_t1113 for tRNA genes </code></pre></div></div> <p>Add the /locus_tag qualifiers to the following features (do not add to <a href="/ddbj/features-e.html#repeat_region">repeat_region</a>).</p> <ul> <li><a href="/ddbj/features-e.html#mRNA">mRNA</a></li> <li><a href="/ddbj/features-e.html#cds">CDS</a></li> <li><a href="/ddbj/features-e.html#5UTR">5’UTR</a></li> <li><a href="/ddbj/features-e.html#3UTR">3’UTR</a></li> <li><a href="/ddbj/features-e.html#intron">intron</a></li> <li><a href="/ddbj/features-e.html#exon">exon</a></li> <li><a href="/ddbj/features-e.html#tRNA">tRNA</a></li> <li><a href="/ddbj/features-e.html#rRNA">rRNA</a></li> <li><a href="/ddbj/features-e.html#ncRNA">ncRNA</a></li> <li><a href="/ddbj/features-e.html#tmRNA">tmRNA</a></li> <li><a href="/ddbj/features-e.html#precursor_RNA">precursor_RNA</a></li> <li><a href="/ddbj/feature-table.html#prim_transcript">prim_transcript</a></li> <li><a href="/ddbj/features-e.html#misc_RNA">misc_RNA</a></li> </ul> <p>Use the same value in the /locus_tag qualifiers of exon/CDS/mRNA features which constitute single gene. One locus_tag should be associated with one <a href="/ddbj/qualifiers-e.html#gene">/gene</a>.</p> <h2 id="add">How to add /locus_tag</h2> <p>A new /locus_tag can be added in either of the following ways when updating genome sequences and annotations.</p> <p>No. 1: Deletion and addition</p> <div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>Before After ABC_0022 ABC_4568 (new gene) ABC_0023 ABC_0023 </code></pre></div></div> <p>No. 2: Add into the gap</p> <div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>Before After ABC_0020 ABC_0020 ABC_0021 (new gene) ABC_0030 ABC_0030 </code></pre></div></div> <p>Decimal integers like versioning (e.g. ABC_0020.1) can not be used.</p> </main> </section> </div> </section> </div> <footer></footer> <div id="back-top"></div> </body> </html>