499 lines
36 KiB
HTML
499 lines
36 KiB
HTML
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<div class="res_logo"><h1 class="res_name"><a href="/refseq/rsg/">RefSeqGene</a></h1><p class="res_tagline">National Center for Biotechnology Information</p></div>
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<div class="search"><form method="get" action="/gene/"><div class="search_form"><label for="database" class="offscreen_noflow">Search database</label><select id="database"><optgroup label="Recent"><option value="gene" selected="selected">Gene</option><option value="refseq">RefSeq</option><option value="biosample">BioSample</option><option value="books" class="last">Books</option></optgroup><optgroup label="All"><option value="gquery">All Databases</option><option value="assembly">Assembly</option><option value="biocollections">Biocollections</option><option value="bioproject">BioProject</option><option value="biosample">BioSample</option><option value="books">Books</option><option value="clinvar">ClinVar</option><option value="cdd">Conserved Domains</option><option value="gap">dbGaP</option><option value="dbvar">dbVar</option><option value="gene">Gene</option><option value="genome">Genome</option><option value="gds">GEO DataSets</option><option value="geoprofiles">GEO Profiles</option><option value="gtr">GTR</option><option value="ipg">Identical Protein Groups</option><option value="medgen">MedGen</option><option value="mesh">MeSH</option><option value="nlmcatalog">NLM Catalog</option><option value="nuccore">Nucleotide</option><option value="omim">OMIM</option><option value="pmc">PMC</option><option value="protein">Protein</option><option value="proteinclusters">Protein Clusters</option><option value="protfam">Protein Family Models</option><option value="pcassay">PubChem BioAssay</option><option value="pccompound">PubChem Compound</option><option value="pcsubstance">PubChem Substance</option><option value="pubmed">PubMed</option><option value="snp">SNP</option><option value="sra">SRA</option><option value="structure">Structure</option><option value="taxonomy">Taxonomy</option><option value="toolkit">ToolKit</option><option value="toolkitall">ToolKitAll</option><option value="toolkitbookgh">ToolKitBookgh</option></optgroup></select><div class="nowrap"><label for="term" class="offscreen_noflow" accesskey="/">Search term</label><div class="nowrap"><input type="text" name="term" id="term" title="Search Gene" value="" class="jig-ncbiclearbutton jig-ncbiautocomplete" data-jigconfig="isEnabled:false,disableUrl:'NcbiSearchBarAutoComplCtrl'" autocomplete="off" data-sbconfig="ds:'no',pjs:'no',afs:'yes'" /></div><button id="search" type="submit" class="button_search nowrap" cmd="go">Search</button></div></div><input type="hidden" name="p$a" id="p$a" /><input type="hidden" name="p$l" id="p$l" value="PAFStdLayout" /><input type="hidden" name="p$st" id="p$st" value="refseq" /><input name="SessionId" id="SessionId" value="CE8B5AF87C7FFCB1_0191SID" disabled="disabled" type="hidden" /><input name="Snapshot" id="Snapshot" value="/projects/staticsites/rsg/RefseqGene@1.34" disabled="disabled" type="hidden" /></form></div>
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</div>
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<div class="nav_and_browser">
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<div class="localnav"><ul class="jig-ncbilocalnav">
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<li><a title="RefSeqGene Home Page" href="/refseq/rsg/">Home</a></li>
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<li><a title="Browse All RefSeqGenes" href="/refseq/rsg/browse/">Browse</a></li>
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<li><a title="Guide to RefSeqGene" href="/refseq/rsg/guide/">Guide</a></li>
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<li><a href="/refseq/rsg/faq/">FAQ</a></li>
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<li><a title="Locus Specific Databases or LSDB" href="/refseq/rsg/lsdb/">Locus-Specific DBs</a></li>
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<li><a title="Locus Reference Genomic or LRG" href="/refseq/rsg/lrg/">Locus Reference Genomic</a></li>
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<li><a title="About RefSeqGene" href="/refseq/rsg/about/">About RSG</a></li>
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</ul></div>
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</div>
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<!-- was itemctrl -->
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<div class="container">
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<div id="maincontent" class="content col twelve_col last">
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<div class="col1">
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<h1 id="faqs-for-refseqgene-and-lrg">FAQs for RefSeqGene and LRG</h1>
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<div class="toc">
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<ul>
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<li><a href="#request">How do I request a new RefSeqGene?</a></li>
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<li><a href="#exon">How does RefSeqGene number exons?</a></li>
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<li><a href="#list">How can I get a list of RefSeqGenes, LRG, and related transcripts?</a></li>
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</ul>
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</div>
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<h2 id="request">How do I request a new RefSeqGene?</h2>
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<p>You may request a new RefSeqGene by contacting the <a href="/projects/RefSeq/update.cgi">RefSeq Help Desk</a>. At a minimum, we need to know:</p>
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<ul>
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<li>The symbol for the gene (or its HGNC id or GeneID)</li>
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<li>The accession and version of each cDNA you would like to use as a reference standard.</li>
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<li>Your contact information so we can contact you if we have any question.</li>
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</ul>
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<p>Optionally, we would also like to know:</p>
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<ul>
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<li>How much flanking sequence to use in generating the RefSeqGene. Our default is to start 5 kb upstream and extend 2 kb downstream.</li>
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<li>Whether you have identified any rare alleles in the current reference assembly and that should be altered in the RefSeqGene.</li>
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<li>Any cDNAs that have commonly been used for the gene, and that should be aligned to the RefSeqGene.</li>
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</ul>
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<h2 id="exon">How does RefSeqGene number exons?</h2>
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<p>The RefSeqGene/LRG collaboration has received multiple requests for a stable numbering system for <span class="textfilter"> exon </span> s represented on its sequences. Until May, 2013, NCBI's RefSeq group numbered exons and provided those numbers on the exon features of cDNAs as well as on RefSeqGenes. These values were based on all the exons known for a gene, from 5' to 3'. These numbers were not stable, because as new exons were discovered for a gene, the numbers were re-calculated. This practice resulted in some confusion.</p>
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<p>RefSeqGene/LRG decided to provide a more stable system, based not on all exons identified for a gene, but on a representive set of exons based initially on the reference standard cDNAs for a RefSeqGene. Because the reference standard cDNAs of RefSeqGenes do not change often, and because they do not change after an LRG is published for the same sequence, these exon numbers will be much more stable. They will still be assigned 5'->3', with overlapping exons from mulitple transcript variants differentiated by a letter suffix, <em>e.g</em> . 2a, 2b. These labels will be reported on the RefSeqGene, <em>e.g.</em>
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(<a href="/nuccore/257196128?report=graph">http://www.ncbi.nlm.nih.gov/nuccore/257196128?report=graph</a>) but not the associated transcripts.</p>
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<p>When the LRG is created, and thus when the exon locations have been finalized, the <span class="textfilter"> exon </span> numbers will not change. If there are other commonly used numbering systems for exons, they will be added to the annotation as long as there is attribution (an organization or citation) for the alterative system. In other words, the RefSeqGene/LRG mechanism will provide stable <span class="textfilter"> exon </span> numbers, defined on stable coordinates, for human genes. The goal is to develop the standard for referring to exons by number.</p>
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<h2 id="list">How can I get a list of RefSeqGenes, LRG, and related transcripts?</h2>
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<p>RefSeqGene maintains a report, available by FTP (<a href="https://ftp.ncbi.nih.gov/refseq/H_sapiens/RefSeqGene/LRG_RefSeqGene">ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/RefSeqGene/LRG_RefSeqGene</a>), that enumerates the RefSeqGene accession.version, the corresponding LRG when available, and accessions of transcripts and proteins annotated on the RefSeqGene. Transcripts and proteins that are defined as reference standards, <em>vs</em> . those available by alignment only, are indicated in the last column. RefSeqGene provides alignments of transcripts previously used as reporting standards, even if not RefSeqs, to facilitate mapping from one coordinate system to another. <a href="/projects/RefSeq/update.cgi">Contact us</a> to request additional alignments, and please provide the accession and version of the public sequence, along with the accession of the RefSeqGene.</p>
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<script type='text/javascript' src='/portal/js/portal.js'></script><script type="text/javascript" src="//static.pubmed.gov/portal/portal3rc.fcgi/4205256/js/3879255/4121861/1049001/3911033/4087685.js" snapshot="refseq"></script></body>
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</html>
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