CINXE.COM
ENV
<!DOCTYPE html> <html lang="en"> <head> <meta charset="UTF-8" /> <meta property="og:title" content="ENV" /> <meta property="og:url" content="https://www.ddbj.nig.ac.jp/ddbj/env-e.html" /> <meta property="og:description" content="The ENV division of DDBJ contains sequence data and other information on environ..." /> <meta property6="og:image" content="/images/thumbnail/logo_ddbj_fb.png" /> <meta name="viewport" content="width=device-width, initial-scale=1.0" /> <title>ENV</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">(27th November 9:00-November 28th 12:00)Announcement of D-way/MSS suspension</a> </li> <li class="item"> <a href="https://www.ddbj.nig.ac.jp/news/en/">(12th December 8:00-20th December 12:00(JST)) Suspension of DDBJ services due to NIG supercomputer maintenance</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=""> <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 -current"> <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>ENV</a></li> </ul> </nav> <h1 class="title">ENV</h1> </header> <main class="md-content"> <p>The ENV division of DDBJ contains sequence data and other information on environmental samples. Though frequently confused, <span class="red"><strong>the term, ‘environmental samples’, does NOT mean “wild type”</strong></span>.<br /> Environmental samples are identified sequences derived by direct molecular isolation from a bulk environmental DNA sample (by PCR with or without subsequent cloning of the product, DGGE, or other anonymous methods) with no reliable identification of the source organism.</p> <p>The ENV division contains (but is not limited to) the following types of data:</p> <ul> <li>sequences derived by direct molecular isolation from soil, sea water, etc.</li> <li>clinical samples, gut contents, and other sequences from anonymous organisms that may be associated with a particular host</li> <li>mixed culture derived from an environmental sample</li> </ul> <p>Environmental samples do not include endosymbionts that can be reliably recovered from a particular host, organisms from a readily identifiable but uncultured field sample (e.g., many cyanobacteria), or phytoplasmas that can be reliably recovered from diseased plants (even though these cannot be grown in axenic culture).</p> <dl> <dt>Notes on environmental sample submission</dt> <dd> <ul> <li>In many cases of environmental samples, we assign the lineage that as far as submitters could specify is used for the description of organism name with the header “uncultured”. See also <a href="/ddbj/organism-e.html#env">Organism Qualifier 3. Environmental sample</a> for further detail.</li> <li>The <a href="/ddbj/qualifiers-e.html#environmental_sample">environmental_sample</a> qualifier is required in <a href="/ddbj/features-e.html#source">source</a> feature.</li> <li>The <a href="/ddbj/qualifiers-e.html#isolation_source">isolation_source</a> qualifier is required in <a href="/ddbj/features-e.html#source">source</a> feature to describe origin of the sample.</li> <li>Either <a href="/ddbj/qualifiers-e.html#clone">clone</a> or <a href="/ddbj/qualifiers-e.html#isolate">isolate</a> qualifier is required as an identifier.</li> <li>Do not use <a href="/ddbj/qualifiers-e.html#strain">strain</a> qualifier.</li> </ul> </dd> </dl> <h2 id="flat-file">Sample flat file</h2> <p>Aspects of environmental samples</p> <ul> <li><a href="/ddbj/flat-file-e#LocusB">LOCUS</a> line provides the division name, “ENV”.</li> <li><a href="/ddbj/flat-file-e#KeywordsB">KEYWORDS</a> line provides the keyword name, “ENV”.</li> <li>In may cases, <a href="/ddbj/flat-file-e#OrganismB">ORGANISM</a> line includes “environmental samples”. Please note there are some exceptions.</li> </ul> <!-- end list --> <pre><code><a id="LocusA" href="/ddbj/flat-file-e#LocusB">LOCUS</a> <a id="LocusNameA" href="/ddbj/flat-file-e#LocusNameB">AB000000</a> <a id="SequenceLengthA" href="/ddbj/flat-file-e#SequenceLengthB">450 bp</a> <a id="MoleculeTypeA" href="/ddbj/flat-file-e#MoleculeTypeB">mRNA</a> <a id="MoleculeFormA" href="/ddbj/flat-file-e#MoleculeFormB">linear</a> <a id="DivisionA" href="/ddbj/flat-file-e#DivisionB">ENV</a> <a id="ModificationDateA" href="/ddbj/flat-file-e#ModificationDateB">16-DEC-2012</a> <a id="DefinitionA" href="/ddbj/flat-file-e#DefinitionB">DEFINITION</a> Uncultured Acetobacter sp. gene for 16S ribosomal RNA, partial sequence, clone: M12-34. <a id="AccessionA" href="/ddbj/flat-file-e#AccessionB">ACCESSION</a> AB000000 <a id="VersionA" href="/ddbj/flat-file-e#VersionB">VERSION</a> AB000000.1 <a id="KeywordsA" href="/ddbj/flat-file-e#KeywordsB">KEYWORDS</a> ENV. <a id="SourceA" href="/ddbj/flat-file-e#SourceB">SOURCE</a> uncultured Acetobacter sp. <a id="OrganismA" href="/ddbj/flat-file-e#OrganismB">ORGANISM</a> uncultured Acetobacter sp. Bacteria; Proteobacteria; Alphaproteobacteria; Rhodospirillales; Acetobacteraceae; Acetobacter; environmental samples. <a id="Reference1A" href="/ddbj/flat-file-e#Reference1B">REFERENCE 1</a> (bases 1 to 450) <a id="AuthorsA" href="/ddbj/flat-file-e#AuthorsB">AUTHORS</a> Mishima,H. and Shizuoka,T. <a id="TitleA" href="/ddbj/flat-file-e#TitleB">TITLE</a> Direct Submission <a id="JournalA" href="/ddbj/flat-file-e#JournalB">JOURNAL</a> Submitted (15-DEC-2012) to the DDBJ/EMBL/GenBank databases. Contact:Hanako Mishima National Institute of Genetics, DNA Data Bank of Japan; Yata 1111, Mishima, Shizuoka 411-8540, Japan <a id="Reference2A" href="/ddbj/flat-file-e#Reference2B">REFERENCE 2</a> AUTHORS Mishima,H., Shizuoka,T. and Fuji,I. TITLE Phylogenetic Profile of Sediment in Japan JOURNAL Env Biol 12, 34-36 (2013) <a id="CommentA" href="/ddbj/flat-file-e#CommentB">COMMENT</a> <a id="FeaturesA" href="/ddbj/flat-file-e#FeaturesB">FEATURES</a> Location/Qualifiers <a id="FeaturesSourceA" href="/ddbj/flat-file-e#FeaturesSourceB">source</a> <a href="/ddbj/location-e.html">1..450</a> /<a href="/ddbj/qualifiers-e.html#clone">clone</a>="M12-34" /<a href="/ddbj/qualifiers-e.html#collection_date">collection_date</a>="2007" /db_xref="taxon:114714" /<a href="/ddbj/qualifiers-e.html#environmental_sample">environmental_sample</a> /<a href="/ddbj/qualifiers-e.html#geo_loc_name">geo_loc_name</a>="Japan: Osaka" /<a href="/ddbj/qualifiers-e.html#isolation_source">isolation_source</a>="PCR-derived sequence from sediment" /<a href="/ddbj/qualifiers-e.html#mol_type">mol_type</a>="genomic DNA" /<a href="/ddbj/qualifiers-e.html#organism">organism</a>="uncultured Acetobacter sp." <a href="/ddbj/features.html#rRNA">rRNA</a> <a href="/ddbj/location-e.html"><1..>450</a> /<a href="/ddbj/qualifiers-e.html#product">product</a>="16S ribosomal RNA" <a id="BaseCountA" href="#BaseCountB">BASE COUNT</a> 199 a 223 c 198 g 230 t <a id="OriginA" href="#OriginB">ORIGIN</a> 1 agtcgcacga aggtttcggc cttagtggcg gacgggtgag taacgcgtag gaatctatcc : -- The rest of nucleotide sequence is omitted -- : <a id="EndA" href="/ddbj/flat-file-e#EndB">//</a></code></pre> </main> <aside class="related-pages"> <h2 class="caption">Related pages</h2> <div class="navigation"> <nav> <ul> <li> <a href="/ddbj/genome-e.html">Data Submission from Genome Project</a> </li> <li> <a href="/ddbj/environmental-e.html">Submission of environmental sequences</a> </li> <li> <a href="/ddbj/transcriptome-e.html">Data Submission from Transcriptome Project</a> </li> <li> <a href="/ddbj/tpa-e.html">Third Party Data (TPA)</a> </li> </ul> </nav> </div> </aside> </section> </div> </section> </div> <footer></footer> <div id="back-top"></div> </body> </html>