168 lines
14 KiB
HTML
168 lines
14 KiB
HTML
<!DOCTYPE html>
|
|
<!-- $Id: HGVSDemo.html 47770 2024-07-25 18:40:49Z evgeniev $ -->
|
|
<html lang="en" >
|
|
<head >
|
|
<title>NCBI Sequence Viewer 3.50.0 - HGVS and SNP Search Demo</title>
|
|
<meta charset="UTF-8">
|
|
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
|
|
|
<!-- Mobile properties -->
|
|
<meta name="HandheldFriendly" content="True">
|
|
<meta name="MobileOptimized" content="320">
|
|
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
|
<link rel="preconnect" href="https://fonts.googleapis.com">
|
|
<link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
|
|
<link href="https://fonts.googleapis.com/css2?family=Open+Sans:ital,wght@0,300;0,400;0,500;0,600;0,700;1,300;1,400;1,500;1,600;1,700&family=Roboto:ital,wght@0,100;0,300;0,400;0,500;0,700;1,100;1,300;1,400;1,500;1,700&display=swap" rel="stylesheet">
|
|
<link rel="stylesheet" href="/cgv/static/django_uswds/uswds/css/uswds.css" />
|
|
|
|
<link rel="stylesheet" href="/cgv/static/nwds/css/nwds.css" />
|
|
<link rel="stylesheet" href="/cgv/static/nwds/css/header.css" />
|
|
<link rel="stylesheet" href="/cgv/static/nwds/css/footer.css" />
|
|
<link rel="stylesheet" href="/cgv/static/nwds/css/form.css" />
|
|
|
|
<link rel="stylesheet" href="css/uswds-fix.css" />
|
|
|
|
<style>
|
|
main { font-size: 1.4em; padding-left: 2rem;}
|
|
html { font-size: 10px; font-family: Roboto,sans-serif; }
|
|
h2 {
|
|
color: #336699;
|
|
font-family: Verdana, Georgia;
|
|
font-size: 108%;
|
|
font-weight: bold;
|
|
}
|
|
.content {margin: 1em; font-size:13px;}
|
|
.content h1 { font-size: 2em; }
|
|
li {margin: 1.12em 0;}
|
|
</style>
|
|
|
|
<!-- Favicons -->
|
|
<link rel="shortcut icon" type="image/ico" href="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon.ico" />
|
|
<link rel="icon" type="image/png" href="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon.png" />
|
|
|
|
<link rel="icon" type="image/png" sizes="192x192" href="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon-192.png" />
|
|
|
|
<!-- 57x57 (precomposed) for iPhone 3GS, pre-2011 iPod Touch and older Android devices -->
|
|
<link rel="apple-touch-icon-precomposed" href="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon-57.png">
|
|
<!-- 72x72 (precomposed) for 1st generation iPad, iPad 2 and iPad mini -->
|
|
<link rel="apple-touch-icon-precomposed" sizes="72x72" href="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon-72.png">
|
|
<!-- 114x114 (precomposed) for iPhone 4, 4S, 5 and post-2011 iPod Touch -->
|
|
<link rel="apple-touch-icon-precomposed" sizes="114x114" href="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon-114.png">
|
|
<!-- 144x144 (precomposed) for iPad 3rd and 4th generation -->
|
|
<link rel="apple-touch-icon-precomposed" sizes="144x144" href="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon-144.png">
|
|
|
|
<meta name="robots" content="index, follow"/>
|
|
<meta name="description" content="NCBI Sequence Viewer"/>
|
|
<!-- applog meta tags -->
|
|
<meta name="ncbi_app" content="sviewer-js" />
|
|
<script src="/cgv/static/js/jquery.js"></script>
|
|
<script src="js/sviewer.js"></script>
|
|
|
|
</head>
|
|
<body >
|
|
<div id="header"></div>
|
|
|
|
<nav class="ncbi-topnav">
|
|
<ul class="ncbi-topnav-list">
|
|
<li><a href="." target="_self">NCBI Sequence Viewer Home</a></li>
|
|
<li><a href="/tools/sviewer" target="_blank">Help</a></li>
|
|
<li><a href="/tools/sviewer/release-notes" target="_blank">Release Notes</a></li>
|
|
</ul>
|
|
</nav>
|
|
|
|
<main id="main_content" accesskey="3">
|
|
<div class="content">
|
|
|
|
<h1>Example cases for search by HGVS and SNP</h1><br>
|
|
<p>
|
|
This demo page shows examples of searching within the Graphical Sequence Viewer (SV) using HGVS and SNP identifiers. The search is local, that is, it is applied only to features on the displayed sequence. The search result is indicated by a marker. To see additional details of the marked position, right-click on the marker and select "Marker Details".
|
|
</p>
|
|
<p>See additional examples of markers on the <a href="MarkerDemo.html">Marker Demo</a> page.</p>
|
|
|
|
<p>The search term can be incorporated into the URL of the page so the search results are automatically displayed.<br/>
|
|
See <a href="InlineSearchDemo.html">this page</a> for examples of URLs including a search term.</p>
|
|
|
|
<ol class="sv-indent">
|
|
<li class="sv-indent">
|
|
NC_000007: Homo sapiens chromosome 7, GRCh38 Primary Assembly.<br/>
|
|
Enter any of the following search terms in the Find box: NC_000007:g.65954301; NM_173517:r.805; NM_173517:c.*23; rs869312976.<br/><br/>
|
|
<div class="SeqViewer">
|
|
<div id="SeqViewer1" class="SeqViewerApp" data-autoload>
|
|
<a href="?embedded=true&appname=hgvsdemo&id=NC_000007.14&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD649220238,category:Sequence,annots:Sequence,ShowLabel:false,shown:true,order:1][key:gene_model_track,name:Genes,display_name:Genes,id:STD3194982005,category:Genes,annots:Unnamed,Options:MergeAll,SNPs:false,CDSProductFeats:false,NtRuler:true,AaRuler:true,HighlightMode:2,shown:true,order:12][key:alignment_track,name:Alignments---Refseq%20Alignments,display_name:Refseq%20Alignments,id:STD2449407507,category:Alignments,annots:Refseq%20Alignments,Layout:Adaptive,StatDisplay:15,Color:Show%20Differences,UnalignedTailsMode:glyph,sort_by:,LinkMatePairAligns:false,ShowAlnStat:false,AlignedSeqFeats:false,Label:true,IdenticalBases:false,shown:true,order:16]&assm_context=GCF_000001405.39&c=333300&select=gi|224589819-03f5fcd1-03f61bab-0101-e3c18253-ffea8d58"></a>
|
|
</div>
|
|
</div></li>
|
|
|
|
<li class="sv-indent">
|
|
NG_005895.1: Homo sapiens TSC complex subunit 2 (TSC2), RefSeqGene (LRG_487) on chromosome 16.<br/>
|
|
Enter any of the following search terms in the Find box: NM_001077183:r.1755; NM_001077183:c.1716+105; NP_000539.2:p.549; rs2302172.
|
|
Note that a search for NM_001009944.2:c.*1 fails because the feature represented by the expression is incomplete and the location is not found. A search with the terms NM_002528.7:c.1 or NM_002528.7:r.1 is successful because the feature is found in this sequence. However, features with incomplete coordinates, such as NM_002528.7, will not be reported in the marker details table.
|
|
<br/><br/>
|
|
<div class="SeqViewer">
|
|
<div id="SeqViewer2" class="SeqViewerApp" data-autoload>
|
|
<a href="?embedded=true&appname=hgvsdemo&id=ng_005895.1&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD649220238,category:Sequence,annots:Sequence,ShowLabel:false,shown:true,order:1][key:gene_model_track,name:Genes,display_name:Genes,id:STD3194982005,category:Genes,annots:Unnamed,Options:ShowAll,SNPs:true,CDSProductFeats:false,NtRuler:true,AaRuler:true,HighlightMode:2,shown:true,order:5][key:alignment_track,name:Alignments,display_name:Alignments%20-%20Reference%20transcript%20alignments,id:STD1042840653,category:Alignments,annots:Reference%20transcript%20alignments,Layout:Adaptive,StatDisplay:15,Color:Show%20Differences,UnalignedTailsMode:glyph,sort_by:,LinkMatePairAligns:false,ShowAlnStat:false,AlignedSeqFeats:false,Label:true,IdenticalBases:false,shown:true,order:6][key:SNP_track,name:T1716514,display_name:Cited%20Variations\,%20dbSNP%20b152%20v2,id:T1716514,dbname:VDB,category:Variation,subcategory:dbSNP,annots:NA000146873.10\232,Layout:Adaptive,shown:true,order:9][key:SNP_track,name:T1716515,display_name:Clinical\,%20dbSNP%20b152%20v2,id:T1716515,dbname:VDB,category:Variation,subcategory:dbSNP,annots:NA000146873.10\2320,Layout:Adaptive,shown:true,order:11]"></a>
|
|
</div>
|
|
</div></li>
|
|
|
|
<li class="sv-indent">
|
|
BX571818.3: human DNA sequence from clone RP11-38J22 on chromosome 1, complete sequence.<br/>
|
|
Enter any of the following search terms in the Find box: BX571818.3:g.62748; CAH73262.1:p.80. CAH73262.1 is found as a search term because this was a protein accession defined by BX571818.
|
|
The Search term RP11-38J22.4-001:r.70 does not work because you cannot search for RNA sequence coordinates on this accession
|
|
<br/><br/>
|
|
<div class="SeqViewer">
|
|
<div id="SeqViewer3" class="SeqViewerApp" data-autoload>
|
|
<a href="?embedded=true&appname=hgvsdemo&id=BX571818.3&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD649220238,category:Sequence,annots:Sequence,ShowLabel:false,shown:true,order:1]&c=null&select=gi|40252459-0000f6a7-000110d4-0103-683b0156-ffea8d58"></a>
|
|
</div>
|
|
</div></li>
|
|
|
|
<li class="sv-indent">
|
|
Z68280.1: Human DNA sequence from clone LA04NC01-25A3 on chromosome 4, complete sequence.<br/>
|
|
Enter the following search term in the Find box: CAI95603.1:p.387
|
|
<br/><br/>
|
|
<div class="SeqViewer">
|
|
<div id="SeqViewer4" class="SeqViewerApp" data-autoload>
|
|
<a href="?embedded=true&appname=hgvsdemo&id=1130692&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD649220238,category:Sequence,annots:Sequence,ShowLabel:false,shown:true,order:1][key:gene_model_track,name:Genes,display_name:Genes,id:STD3194982005,category:Genes,annots:Unnamed,Options:ShowAll,SNPs:true,CDSProductFeats:false,NtRuler:true,AaRuler:true,HighlightMode:2,shown:true,order:7]&c=ffff99&select=gi|1130692-00005658-0000a87d-0103-5ec52c72-ffea8d58"></a>
|
|
</div>
|
|
</div></li>
|
|
|
|
<li class="sv-indent">
|
|
NM_002020.4: Homo sapiens fms related tyrosine kinase 4 (FLT4), transcript variant 2, mRNA.<br/>
|
|
Enter any of the following search terms in the Find box: NM_002020.4:r.1513; NM_002020.4:c.1434; NP_002011.2:p.478
|
|
<br/><br/>
|
|
<div class="SeqViewer">
|
|
<div id="SeqViewer5" class="SeqViewerApp" data-autoload>
|
|
<a href="?embedded=true&appname=hgvsdemo&id=NM_002020&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD649220238,category:Sequence,annots:Sequence,ShowLabel:false,shown:true,order:1][key:gene_model_track,name:Genes,display_name:Genes,id:STD3194982005,category:Genes,annots:Unnamed,Options:ShowAll,SNPs:false,CDSProductFeats:true,NtRuler:true,AaRuler:true,HighlightMode:2,shown:true,order:3][key:feature_track,name:STS%20Markers,display_name:STS%20Markers,id:STD839026914,subkey:STS,category:Features,subcategory:STS%20Markers,annots:STS,Layout:Adaptive,LinkedFeat:Packed,shown:true,order:4][key:feature_track,name:Other%20features---polyA_site,display_name:polyA_site%20Features,id:STD3911386278,subkey:polyA_site,category:Features,subcategory:polyA_site%20Features,annots:Unnamed,Layout:Adaptive,LinkedFeat:Packed,shown:true,order:5][key:feature_track,name:Other%20features---regulatory,display_name:regulatory%20Features,id:STD2883984253,subkey:regulatory,category:Features,subcategory:regulatory%20Features,annots:Unnamed,Layout:Adaptive,LinkedFeat:Packed,shown:true,order:6]&c=00ff00"></a>
|
|
</div>
|
|
</div></li>
|
|
|
|
<li class="sv-indent">
|
|
M11313.1: Human alpha-2-macroglobulin mRNA, complete cds.<br/>
|
|
Enter any of the following search terms in the Find box: M11313.1:c.1985; AAA51551.1:p.662
|
|
<br/><br/>
|
|
<div class="SeqViewer">
|
|
<div id="SeqViewer6" class="SeqViewerApp" data-autoload>
|
|
<a href="?embedded=true&appname=hgvsdemo&id=M11313&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD649220238,category:Sequence,annots:Sequence,ShowLabel:false,shown:true,order:1][key:gene_model_track,name:Genes,display_name:Genes,id:STD3194982005,category:Genes,annots:Unnamed,Options:ShowAll,SNPs:false,CDSProductFeats:true,NtRuler:true,AaRuler:true,HighlightMode:2,shown:true,order:7]&v=1:4577"></a>
|
|
</div>
|
|
</div></li>
|
|
|
|
<li class="sv-indent">
|
|
NP_000928.1: DNA-directed RNA polymerase II subunit RPB1 [Homo sapiens].<br/>
|
|
Enter the following search term in the Find box: NP_000928.1:p.773
|
|
<br/><br/>
|
|
<div class="SeqViewer">
|
|
<div id="SeqViewer7" class="SeqViewerApp" data-autoload>
|
|
<a href="?embedded=true&appname=hgvsdemo&id=4505939&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD649220238,category:Sequence,annots:Sequence,ShowLabel:false,shown:true,order:1][key:feature_track,name:Other%20features---Protein,display_name:Protein%20Features,id:STD2439759237,subkey:Prot,category:Features,subcategory:Protein%20Features,annots:Unnamed,Layout:Adaptive,LinkedFeat:Packed,shown:true,order:2][key:feature_track,name:Other%20features---region---CDD,display_name:region%20Features%20-%20CDD,id:STD361885503,subkey:region,category:Features,subcategory:region%20Features,annots:CDD,Layout:Adaptive,LinkedFeat:Packed,shown:true,order:3][key:feature_track,name:Other%20features---region---Unnamed,display_name:region%20Features,id:STD408713146,subkey:region,category:Features,subcategory:region%20Features,annots:Unnamed,Layout:Adaptive,LinkedFeat:Packed,shown:true,order:4][key:feature_track,name:Other%20features---site---CDD,display_name:site%20Features%20-%20CDD,id:STD2917610742,subkey:site,category:Features,subcategory:site%20Features,annots:CDD,Layout:Adaptive,LinkedFeat:Packed,shown:true,order:5]"></a>
|
|
</div>
|
|
</div></li>
|
|
|
|
</ol>
|
|
</div>
|
|
</main>
|
|
<div id="footer"></div>
|
|
<script>
|
|
$(document).ready(function(){
|
|
$('#header').load("header.html");
|
|
$('#footer').load("footer.html");
|
|
});
|
|
</script>
|
|
</body>
|
|
</html>
|