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103 KiB
HTML
1381 lines
No EOL
103 KiB
HTML
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<!DOCTYPE html>
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<html lang="en" >
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<head >
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<meta charset="UTF-8">
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<meta http-equiv="X-UA-Compatible" content="IE=edge">
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<!-- Mobile properties -->
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<meta name="HandheldFriendly" content="True">
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<meta name="MobileOptimized" content="320">
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<link rel="stylesheet" href="/gdv/browser/static/django_uswds/uswds/css/uswds.css" />
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<link rel="stylesheet" href="/gdv/browser/static/nwds/css/nwds.css" />
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<link rel="stylesheet" href="/gdv/browser/static/nwds/css/header.css" />
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<link rel="stylesheet" href="/gdv/browser/static/nwds/css/footer.css" />
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<link rel="stylesheet" href="/gdv/browser/static/nwds/css/form.css" />
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<link rel="stylesheet" href="/gdv/browser/static/uswds3/css/uswds-fix.css" />
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<link rel="stylesheet" type="text/css" href="/core/extjs/ext-7.1.0/build/classic/theme-gray/resources/theme-gray-all.css"/>
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<link rel="stylesheet" type="text/css" href="/projects/sviewer/css/style.css" media="screen, projection, print"/>
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<link rel="stylesheet" type="text/css" href="/gdv/browser/static/css/fe4476f2.gdv-all.css"/>
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<link rel="stylesheet" type="text/css" href="/gdv/browser/static/gdv/css/bar.css"/>
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<title>Genome Data Viewer - NCBI</title>
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<!-- Favicons -->
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<link rel="shortcut icon" type="image/ico" href="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon.ico" />
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<link rel="icon" type="image/png" href="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon.png" />
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<!-- 192x192, as recommended for Android
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http://updates.html5rocks.com/2014/11/Support-for-theme-color-in-Chrome-39-for-Android
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-->
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<link rel="icon" type="image/png" sizes="192x192" href="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon-192.png" />
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<!-- 57x57 (precomposed) for iPhone 3GS, pre-2011 iPod Touch and older Android devices -->
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<link rel="apple-touch-icon-precomposed" href="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon-57.png">
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<!-- 72x72 (precomposed) for 1st generation iPad, iPad 2 and iPad mini -->
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<link rel="apple-touch-icon-precomposed" sizes="72x72" href="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon-72.png">
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<!-- 114x114 (precomposed) for iPhone 4, 4S, 5 and post-2011 iPod Touch -->
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<link rel="apple-touch-icon-precomposed" sizes="114x114" href="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon-114.png">
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<!-- 144x144 (precomposed) for iPad 3rd and 4th generation -->
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<link rel="apple-touch-icon-precomposed" sizes="144x144" href="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon-144.png">
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<meta name="robots" content="index, follow"/>
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<!-- Logging params: Pinger defaults -->
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<meta name="ncbi_app" content="GDV" />
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<meta name="ncbi_pdid" content="index" />
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<meta name="ncbi_phid" content="322CA9CA14242AF500006555FC658F1E.1.m_4" />
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<meta name="ncbi_page" content="home"/>
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<meta name="ncbi_op" content="page_view"/>
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<meta name="description" content="Genome Data Viewer"/>
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<script type="text/javascript">/** GDV config settings */
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window.GB = {
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||
config: {
|
||
config: {
|
||
"history": true,
|
||
"localStorage": true,
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||
"chrom_only": true,
|
||
"placed": true,
|
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"primary_only": false,
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||
"rs": false,
|
||
"guard": 1,
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||
"gdvl": 0
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},
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defs: [],
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defaults: {
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resource: "genome",
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context: "genome",
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||
app: "GDV",
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||
version: "5.3.13"
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},
|
||
navigator: {
|
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version: 521,
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top_section: 1
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},
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||
gdv: {
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||
order: 0,
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||
assemblies: "/projects/genome/gdv-landing/4.3.0-gdvl/assemblies.json"
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},
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url: {
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||
params: "id|acc|context|rid|alignid|alignacc|range|hub|ts|tsid|snp|gdv|guard|type|name|term",
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check: true,
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||
portalcheck: true
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},
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state: {
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||
preserveURL: true,
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||
history: true,
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||
hide: "chr,from,to,mk,search"
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},
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ideo: {
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// specific ideogram heights:
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// human
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9606: {
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height: 160
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},
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// fly (too many bands)
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7227: {
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height: 280
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},
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height: 120,
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nonNuclear: true,
|
||
cyto: "GCF_000001405.13:850,GCF_000001405.26:850"
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||
},
|
||
userdata: {
|
||
loadHubTracks: true
|
||
},
|
||
header: {
|
||
acc: false,
|
||
range: false
|
||
},
|
||
myncbi: {
|
||
fix: true
|
||
},
|
||
search: {
|
||
columns: "name,location,go",
|
||
autoselect: true
|
||
},
|
||
sv_wrap: {
|
||
encodeShown: true
|
||
},
|
||
|
||
exon_nav: {
|
||
paddings: [{
|
||
def: "10%",
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desc: "Use 10% padding"
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||
}, {
|
||
def: "25%",
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||
desc: "Use 25% padding"
|
||
}, {
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||
def: "50%",
|
||
desc: "Use 50% padding"
|
||
}]
|
||
},
|
||
blast: {
|
||
wrap: ".gb-blast-wrap",
|
||
uploadTimeout: 3000
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},
|
||
|
||
gwas: {
|
||
tracks: ['T687068']
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||
},
|
||
|
||
queryAlert: true
|
||
}
|
||
};
|
||
|
||
const baseURL = '/gdv/browser';
|
||
const tracksetHost = '';
|
||
/** NWDS header */
|
||
const useOfficialGovtHeader = true;
|
||
</script>
|
||
<script type="text/javascript">
|
||
|
||
function _GBGetContextInfo(){return {"accs": ["GCF_000001405.39"], "acc": "GCF_000001405.39", "type": "assembly", "addToDefaultTracks": true, "subject": {"data": []}, "assemblies": [{"assm": "GCF_000001405.39"}]};}
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||
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||
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function _GBGetAnnotInfo(){return [{"name": "GRCh38.p14", "acc": "GCF_000001405.40", "gb_acc": "GCA_000001405.29", "ref_acc": "GCF_000001405.40", "similarity": "different", "submitter": "Genome Reference Consortium", "refseq_category": "Reference genome", "taxid": "9606", "species_taxid": "9606", "organism_name": "Homo sapiens (human)", "species": "Homo sapiens", "level": "Chromosome", "release_type": "Patch", "genome_rep": "Full", "release_date": "2022/02/08 00:00", "sortorder": "1C3X01019421205880000014057059", "annotation_release": {"id": 110, "version": "RS_2024_08", "url": "/genome/annotation_euk/Homo_sapiens/GCF_000001405.40-RS_2024_08.html", "release_date": "2024-08-26"}}, {"name": "T2T-CHM13v2.0", "acc": "GCF_009914755.1", "gb_acc": "GCA_009914755.4", "ref_acc": "GCF_009914755.1", "similarity": "different", "submitter": "T2T Consortium", "refseq_category": "Na", "taxid": "9606", "species_taxid": "9606", "organism_name": "Homo sapiens (human)", "species": "Homo sapiens", "level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "release_date": "2022/02/16 00:00", "sortorder": "5C1X01018493827520099147559598", "annotation_release": {"id": 110, "version": "RS_2024_08", "url": "/genome/annotation_euk/Homo_sapiens/GCF_000001405.40-RS_2024_08.html", "release_date": "2024-08-26"}}, {"name": "GRCh37.p13", "acc": "GCF_000001405.25", "gb_acc": "GCA_000001405.14", "ref_acc": "GCF_000001405.25", "similarity": "identical", "submitter": "Genome Reference Consortium", "refseq_category": "Na", "taxid": "9606", "species_taxid": "9606", "organism_name": "Homo sapiens (human)", "species": "Homo sapiens", "level": "Chromosome", "release_type": "Patch", "genome_rep": "Full", "release_date": "2013/07/03 00:00", "sortorder": "5C3X01019614910670000014058574", "annotation_release": {"id": 105, "version": "105.20220307", "url": "/genome/annotation_euk/Homo_sapiens/105.20220307", "release_date": "2022-03-10"}, "latest": "GCF_000001405.40"}, {"name": "CHM1_1.1", "acc": "GCF_000306695.2", "gb_acc": "GCA_000306695.2", "ref_acc": "GCF_000306695.2", "similarity": "different", "submitter": "Washington University School of Medicine", "refseq_category": "Na", "taxid": "9606", "species_taxid": "9606", "organism_name": "Homo sapiens (human)", "species": "Homo sapiens", "level": "Chromosome", "release_type": "Major", "genome_rep": "Full", "release_date": "2013/08/01 00:00", "sortorder": "9C3X01019998560630003066959797", "annotation_release": {"id": 108, "version": "108", "url": null, "release_date": "2016-06-06"}}, {"name": "HuRef", "acc": "GCF_000002125.1", "gb_acc": "GCA_000002125.2", "ref_acc": "GCF_000002125.1", "similarity": "identical", "submitter": "J. Craig Venter Institute", "refseq_category": "Na", "taxid": "9606", "species_taxid": "9606", "organism_name": "Homo sapiens (human)", "species": "Homo sapiens", "level": "Chromosome", "release_type": "Major", "genome_rep": "Full", "release_date": "2009/08/12 00:00", "sortorder": "9C3X01019998915680000021259798", "annotation_release": {"id": 106, "version": "106", "url": null, "release_date": "2014-02-03"}}, {"name": "hg002v1.1.mat", "acc": "GCA_018852615.3", "gb_acc": "GCA_018852615.3", "ref_acc": "", "similarity": "", "submitter": "UCSC Genomics Institute", "refseq_category": "Na", "taxid": "9606", "species_taxid": "9606", "organism_name": "Homo sapiens (human)", "species": "Homo sapiens", "level": "Chromosome", "release_type": "Major", "genome_rep": "Full", "release_date": "2024/09/03 00:00", "sortorder": "5C2X01018456586020188526159600", "annotation_release": {}}, {"name": "hg002v1.1.pat", "acc": "GCA_018852605.3", "gb_acc": "GCA_018852605.3", "ref_acc": "", "similarity": "", "submitter": "UCSC Genomics Institute", "refseq_category": "Na", "taxid": "9606", "species_taxid": "9606", "organism_name": "Homo sapiens (human)", "species": "Homo sapiens", "level": "Chromosome", "release_type": "Major", "genome_rep": "Full", "release_date": "2024/09/03 00:00", "sortorder": "5C2X01018532131760188526059600", "annotation_release": {}}, {"name": "Ash1_v2.2", "acc": "GCA_011064465.2", "gb_acc": "GCA_011064465.2", "ref_acc": "", "similarity": "", "submitter": "Johns Hopkins University", "refseq_category": "Na", "taxid": "9606", "species_taxid": "9606", "organism_name": "Homo sapiens (human)", "species": "Homo sapiens", "level": "Chromosome", "release_type": "Major", "genome_rep": "Full", "release_date": "2022/06/02 00:00", "sortorder": "5C3X01018498455440110644659700", "annotation_release": {}}, {"name": "hg01243.v3.0", "acc": "GCA_018873775.2", "gb_acc": "GCA_018873775.2", "ref_acc": "", "similarity": "", "submitter": "Johns Hopkins University", "refseq_category": "Na", "taxid": "9606", "species_taxid": "9606", "organism_name": "Homo sapiens (human)", "species": "Homo sapiens", "level": "Chromosome", "release_type": "Major", "genome_rep": "Full", "release_date": "2021/09/27 00:00", "sortorder": "5C3X01018503024940188737759700", "annotation_release": {}}, {"name": "HG002.pat.cur.20211005", "acc": "GCA_021950905.1", "gb_acc": "GCA_021950905.1", "ref_acc": "", "similarity": "", "submitter": "Human Pangenome Reference Consortium", "refseq_category": "Na", "taxid": "9606", "species_taxid": "9606", "organism_name": "Homo sapiens (human)", "species": "Homo sapiens", "level": "Chromosome", "release_type": "Major", "genome_rep": "Full", "release_date": "2022/02/04 00:00", "sortorder": "5C3X01019150728780219509059800", "annotation_release": {}}, {"name": "HG002.mat.cur.20211005", "acc": "GCA_021951015.1", "gb_acc": "GCA_021951015.1", "ref_acc": "", "similarity": "", "submitter": "Human Pangenome Reference Consortium", "refseq_category": "Na", "taxid": "9606", "species_taxid": "9606", "organism_name": "Homo sapiens (human)", "species": "Homo sapiens", "level": "Chromosome", "release_type": "Major", "genome_rep": "Full", "release_date": "2022/02/04 00:00", "sortorder": "5C3X01019371202590219510159800", "annotation_release": {}}, {"name": "ASM2283312v2", "acc": "GCA_022833125.2", "gb_acc": "GCA_022833125.2", "ref_acc": "", "similarity": "", "submitter": "Celera Genomics", "refseq_category": "Na", "taxid": "9606", "species_taxid": "9606", "organism_name": "Homo sapiens (human)", "species": "Homo sapiens", "level": "Chromosome", "release_type": "Major", "genome_rep": "Full", "release_date": "2022/04/13 00:00", "sortorder": "5C3X01019993912280228331259700", "annotation_release": {}}];}
|
||
|
||
|
||
function _GBGetAssemblyInfo(){
|
||
var defs = {"assemblies": [{"name": "GRCh38.p14", "acc": "GCF_000001405.40", "taxid": 9606, "reference": true, "regions": true, "defaultSeq": "NC_000001.11", "scaffoldCount": 166, "altCount": 514, "orgName": "Homo sapiens", "orgCommonName": "human", "type": "Full-Assembly", "aliases": ["GCF_000001405.40", "GCF_000001405.39", "GCF_000001405.38", "GCF_000001405.37", "GCF_000001405.36", "GCF_000001405.35", "GCF_000001405.34", "GCF_000001405.33", "GCF_000001405.32", "GCF_000001405.31", "GCF_000001405.30", "GCF_000001405.29", "GCF_000001405.28", "GCF_000001405.27", "GCF_000001405.26", "GCA_000001405.29", "GCA_000001405.28", "GCA_000001405.27", "GCA_000001405.26", "GCA_000001405.25", "GCA_000001405.24", "GCA_000001405.23", "GCA_000001405.22", "GCA_000001405.21", "GCA_000001405.20", "GCA_000001405.19", "GCA_000001405.18", "GCA_000001405.17", "GCA_000001405.16", "GCA_000001405.15"], "units": [{"name": "Primary Assembly", "acc": "GCF_000001305.16", "taxid": 9606, "type": "Primary-Unit", "seq": [{"name": "1", "ucsc_name": "chr1", "chrom": 1, "topl": 1, "length": 248956422, "acc": "NC_000001.11", "gi": 568815597}, {"name": "2", "ucsc_name": "chr2", "chrom": 1, "topl": 1, "length": 242193529, "acc": "NC_000002.12", "gi": 568815596}, {"name": "3", "ucsc_name": "chr3", "chrom": 1, "topl": 1, "length": 198295559, "acc": "NC_000003.12", "gi": 568815595}, {"name": "4", "ucsc_name": "chr4", "chrom": 1, "topl": 1, "length": 190214555, "acc": "NC_000004.12", "gi": 568815594}, {"name": "5", "ucsc_name": "chr5", "chrom": 1, "topl": 1, "length": 181538259, "acc": "NC_000005.10", "gi": 568815593}, {"name": "6", "ucsc_name": "chr6", "chrom": 1, "topl": 1, "length": 170805979, "acc": "NC_000006.12", "gi": 568815592}, {"name": "7", "ucsc_name": "chr7", "chrom": 1, "topl": 1, "length": 159345973, "acc": "NC_000007.14", "gi": 568815591}, {"name": "8", "ucsc_name": "chr8", "chrom": 1, "topl": 1, "length": 145138636, "acc": "NC_000008.11", "gi": 568815590}, {"name": "9", "ucsc_name": "chr9", "chrom": 1, "topl": 1, "length": 138394717, "acc": "NC_000009.12", "gi": 568815589}, {"name": "10", "ucsc_name": "chr10", "chrom": 1, "topl": 1, "length": 133797422, "acc": "NC_000010.11", "gi": 568815588}, {"name": "11", "ucsc_name": "chr11", "chrom": 1, "topl": 1, "length": 135086622, "acc": "NC_000011.10", "gi": 568815587}, {"name": "12", "ucsc_name": "chr12", "chrom": 1, "topl": 1, "length": 133275309, "acc": "NC_000012.12", "gi": 568815586}, {"name": "13", "ucsc_name": "chr13", "chrom": 1, "topl": 1, "length": 114364328, "acc": "NC_000013.11", "gi": 568815585}, {"name": "14", "ucsc_name": "chr14", "chrom": 1, "topl": 1, "length": 107043718, "acc": "NC_000014.9", "gi": 568815584}, {"name": "15", "ucsc_name": "chr15", "chrom": 1, "topl": 1, "length": 101991189, "acc": "NC_000015.10", "gi": 568815583}, {"name": "16", "ucsc_name": "chr16", "chrom": 1, "topl": 1, "length": 90338345, "acc": "NC_000016.10", "gi": 568815582}, {"name": "17", "ucsc_name": "chr17", "chrom": 1, "topl": 1, "length": 83257441, "acc": "NC_000017.11", "gi": 568815581}, {"name": "18", "ucsc_name": "chr18", "chrom": 1, "topl": 1, "length": 80373285, "acc": "NC_000018.10", "gi": 568815580}, {"name": "19", "ucsc_name": "chr19", "chrom": 1, "topl": 1, "length": 58617616, "acc": "NC_000019.10", "gi": 568815579}, {"name": "20", "ucsc_name": "chr20", "chrom": 1, "topl": 1, "length": 64444167, "acc": "NC_000020.11", "gi": 568815578}, {"name": "21", "ucsc_name": "chr21", "chrom": 1, "topl": 1, "length": 46709983, "acc": "NC_000021.9", "gi": 568815577}, {"name": "22", "ucsc_name": "chr22", "chrom": 1, "topl": 1, "length": 50818468, "acc": "NC_000022.11", "gi": 568815576}, {"name": "X", "ucsc_name": "chrX", "chrom": 1, "topl": 1, "length": 156040895, "acc": "NC_000023.11", "gi": 568815575}, {"name": "Y", "ucsc_name": "chrY", "chrom": 1, "topl": 1, "length": 57227415, "acc": "NC_000024.10", "gi": 568815574}]}, {"name": "ALT_REF_LOCI_1", "acc": "GCF_000001315.3", "taxid": 9606, "type": "Alt-Loci", "seq": 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</script>
|
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<link href="/gdv/browser/static/xideo/css/x-ideo.css" rel="stylesheet" />
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<script src="/gdv/browser/static/xideo/js/d3.js" type="text/javascript"></script>
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<script src="/gdv/browser/static/xideo/js/x-ideo.min.js" type="text/javascript"></script>
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<script type="text/javascript" src="/gdv/browser/static/js/jquery.min.js"></script>
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<style>
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.usa-banner-inner {margin:unset!important;}
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font-weight: 700;
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font-family: Roboto, sans-serif;
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line-height: 48px;
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border-bottom: 3px solid transparent;
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.dropdown-menu {
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color: #1b1b1b;
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</head>
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<body class="gb-browser gdv gb-layout2 generic" >
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<a class="usa-skipnav" href="#main_content">Skip to main page content</a>
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<div class="usa-grid usa-banner-inner">
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<img src="https://www.ncbi.nlm.nih.gov/coreutils/uswds/img/favicons/favicon-57.png" alt="U.S. flag" />
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<p>An official website of the United States government</p>
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<button
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||
class="usa-accordion-button usa-banner-button"
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aria-expanded="false"
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aria-controls="gov-banner-top"
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>
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<span class="usa-banner-button-text">Here's how you know</span>
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<div
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class="usa-banner-content usa-grid usa-accordion-content"
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id="gov-banner-top"
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>
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<div class="usa-banner-guidance-gov usa-width-one-half">
|
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<img
|
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class="usa-banner-icon usa-media_block-img"
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src="https://www.ncbi.nlm.nih.gov/coreutils/uswds/img/icon-dot-gov.svg"
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alt="Dot gov"
|
||
/>
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<div class="usa-media_block-body">
|
||
<p>
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<strong>The .gov means it’s official.</strong>
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<br />
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Federal government websites often end in .gov or .mil. Before
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sharing sensitive information, make sure you’re on a federal
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<img
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class="usa-banner-icon usa-media_block-img"
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src="https://www.ncbi.nlm.nih.gov/coreutils/uswds/img/icon-https.svg"
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alt="Https"
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/>
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<p>
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<strong>The site is secure.</strong>
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<br />
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The <strong>https://</strong> ensures that you are connecting to the
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and transmitted securely.
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<a href="https://www.ncbi.nlm.nih.gov/" class="logo" aria-label="NCBI Logo" data-ga-action="click_image" data-ga-label="NIH NLM Logo">
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<button class="ncbi-close-button" data-ga-action="close_menu" data-ga-label="account_menu"><span class="fa fa-times"></span><span class="usa-sr-only">Close</span></button>
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|
||
<a id="nws_header_accesskey_3" href="#maincontent" class="usa-sr-only" accesskey="3" tabindex="-1">Main Content</a>
|
||
<a id="nws_header_accesskey_4" href="#" class="usa-sr-only" accesskey="4" tabindex="-1">Main Navigation</a>
|
||
</div>
|
||
<section data-section="Alerts">
|
||
<div class="ncbi-alerts-placeholder"></div>
|
||
</section>
|
||
<!-- ========== END HEADER ========== -->
|
||
|
||
|
||
|
||
|
||
|
||
<main id="main_content" accesskey="3">
|
||
|
||
|
||
|
||
<div class="gdv-displaybar" style="display:none;">
|
||
<div class="gdv-displaybar-ctrl"><span></span></div>
|
||
<div class="gdv-displaybar-content"><div class="node"><div class="content"><p>Have you explored our new <a href="/genome/cgv/">Comparative Genome Viewer (CGV)</a> yet? </p></div></div></div>
|
||
</div>
|
||
|
||
|
||
<div class="page gb-content-page">
|
||
<div class="header gb-page-header">
|
||
|
||
|
||
|
||
<div class="gb-header-left">
|
||
|
||
|
||
|
||
<div class="gb-state gb-off" style="right:unset;">
|
||
<div class="gb-state-panel"
|
||
style="right:unset;top:3em;left:6em;border-radius:4px;text-shadow:none!important;
|
||
box-shadow:unset;font-family:Roboto;font-size:16px;width:635px;padding: 2.5em 3em;">
|
||
<span class="gb-state-panel-close"></span>
|
||
<div class="gb-state-section" style="font-size: 22px;line-height: 25px;">
|
||
<span class="gb-state-header" style="color:black;">URL for current configuration</span>
|
||
</div>
|
||
<div class="gb-state-section" style="font-size:14px;line-height: 22px;padding-top:10px;padding-bottom:25px;">
|
||
<span class="gb-state-comment" style="color: rgba(0,0,0,.6);">This URL is a temporary URL and is valid approximately for 90 days.</span>
|
||
</div>
|
||
<div class="gb-state-section gb-section-url" style="font-size:16px;line-height:24px;color:rgba(0,0,0,.6);">
|
||
<span class="gb-state-url"></span>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
<nav class="ncbi-topnav">
|
||
<ul class="ncbi-topnav-list">
|
||
|
||
<div class="gb-header-links" >
|
||
|
||
|
||
<ul>
|
||
<li>
|
||
<a href="/gdv/browser/" class="gb-link-home" title="Go to landing page">Home</a>
|
||
</li>
|
||
<li>
|
||
<a href="javascript:void(0)" id="gb-share-page" class="gb-share-page" title="Create URL with the current state that can be shared">Share this page</a>
|
||
</li>
|
||
|
||
<li>
|
||
<a href="javascript:void(0)" id="gb-reset-page" class="gb-reset-page" title="Reset saved state">Reset All</a>
|
||
</li>
|
||
<li>
|
||
<div class="dropdown">
|
||
<a href="javascript:void(0)" onclick="GDVtoggleDDMenu(event)">More Tools
|
||
<svg class="usa-icon" aria-hidden="true" focusable="false" role="img">
|
||
<use xlink:href="/gdv/browser/static/django_uswds/uswds/img/sprite.svg#chevron_left"></use>
|
||
</svg>
|
||
</a>
|
||
<div class="dropdown-menu">
|
||
<a href="/cgv/" target="_blank" title="Open NCBI Comparative Genome Viewer (CGV)">Compare genomes</a>
|
||
<a href="/data-hub/genome/?taxon=" target="_blank" title="Open NCBI Datasets for this organism">Download genomes</a>
|
||
<a href="//www.ncbi.nlm.nih.gov/genomes/BioProject/blastpage.cgi?taxid=" target="_blank" title="BLAST this genome">BLAST genome</a>
|
||
</div>
|
||
</div>
|
||
</li>
|
||
<li>
|
||
<div class="dropdown">
|
||
<a href="javascript:void(0)" onclick="GDVtoggleDDMenu(event)">More Info
|
||
<svg class="usa-icon" aria-hidden="true" focusable="false" role="img">
|
||
<use xlink:href="/gdv/browser/static/django_uswds/uswds/img/sprite.svg#chevron_left"></use>
|
||
</svg>
|
||
</a>
|
||
<div class="dropdown-menu">
|
||
<a href="/gdv/browser/help/" target="help">Help</a>
|
||
<a href="/gdv/browser/release-notes/" target="help">Release Notes</a>
|
||
<a href="/gdv/browser/faq/" target="help">FAQ</a>
|
||
<a href="/gdv/browser/browser-agreement/" target="help">Browser Agreement</a>
|
||
<a href="//nlmenterprise.co1.qualtrics.com/jfe/form/SV_5iL6W3r2A7vY52R?ncbi_app=GDV" target="help">Feedback</a>
|
||
</div>
|
||
</div>
|
||
</li>
|
||
|
||
</ul>
|
||
<script>
|
||
GDVtoggleDDMenu = function(e) {
|
||
var div = !e ? null : e.currentTarget.parentNode,
|
||
current = $('.dropdown.shown-menu')[0];
|
||
if (!div || div.className.search('dropdown') < 0) {
|
||
$('.dropdown.shown-menu').each((i,d)=>d.classList.remove('shown-menu'));
|
||
window.removeEventListener('click', GDVtoggleDDMenu);
|
||
} else {
|
||
if (current != div) GDVtoggleDDMenu();
|
||
if (div.classList.toggle('shown-menu')) {
|
||
window.addEventListener('click', GDVtoggleDDMenu);
|
||
e.stopPropagation();
|
||
} else GDVtoggleDDMenu();
|
||
}
|
||
};
|
||
</script>
|
||
</div>
|
||
|
||
|
||
|
||
|
||
|
||
</ul>
|
||
</nav>
|
||
|
||
<div style="padding-left:30px;">
|
||
<div class="header">
|
||
<div class="res_name" style="color: #1b1b1b;font-family: Roboto;padding: 15px 0;font-size: 36px;line-height:42px;font-weight: 300;">
|
||
<a href="/gdv/browser/" title="Go to GDV landing page">Genome Data Viewer</a>
|
||
</div>
|
||
</div>
|
||
<div class="gb-page-content-top">
|
||
<div class="gdv-hidden">
|
||
|
||
<div widget-name="top-bar" class="gb-top-control-bar">
|
||
|
||
|
||
<div class="gb-search-bar gb-search-top gb-hidden">
|
||
<span>
|
||
<div class="gb-header">
|
||
<span>Search assembly</span>
|
||
</div>
|
||
<div class="gb-search-ctrl">
|
||
<label for="loc-search-top" aria-label="Search"></label>
|
||
<input id="loc-search-top" type="text" placeholder=""/ value="None">
|
||
<span class="gb-search-go" aria-label="Search"></span>
|
||
</div>
|
||
<div class="comment">
|
||
<span class="gb-search-help" title="Expand for search examples">Examples</span>
|
||
<ul search-id="loc-search-top"></ul>
|
||
</div>
|
||
</span>
|
||
<div class="gb-search gb-search-content gb-hidden" for="loc-search-top">
|
||
<div class="gb-ctrl">
|
||
<span class="gb-close"></span>
|
||
</div>
|
||
<div class="content-results">
|
||
<ul class="content-tabs"></ul>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
<div>
|
||
<span class="gb-org"></span>
|
||
<assembly-wrap>
|
||
<span class="gb-assm">
|
||
<span>Assembly:</span>
|
||
<span class="gb-select">
|
||
<select></select>
|
||
</span>
|
||
</span>
|
||
<span>▪</span>
|
||
<span class="gb-range">
|
||
<span class="gb-select">
|
||
<select></select>
|
||
</span>
|
||
</span>
|
||
</assembly-wrap>
|
||
</div>
|
||
|
||
</div>
|
||
|
||
</div>
|
||
</div>
|
||
<div class="gb-page-content">
|
||
<div class="content-left">
|
||
<div class="gb-region-navigator gb-hidden gb-top">
|
||
|
||
<div section-name="header" class="gb-section gb-disabled">
|
||
<div class="gb-org"></div>
|
||
<div class="gb-assm"></div>
|
||
</div>
|
||
|
||
|
||
|
||
<div section-name="loc-search-top" class="gb-section gb-search-top gb-disabled">
|
||
<div>
|
||
<div class="gb-header">
|
||
<span>Search assembly</span>
|
||
</div>
|
||
<div class="gb-search-ctrl">
|
||
<label for="loc-search" aria-label="Search"></label>
|
||
<input id="loc-search" type="text" placeholder="" value="None"/>
|
||
<span class="gb-search-go" aria-label="Search"></span>
|
||
</div>
|
||
<div class="comment">
|
||
<span class="gb-search-help" title="Expand for search examples">Examples</span>
|
||
<ul search-id="loc-search"></ul>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
<div section-name="loc-search" for="loc-search" class="gb-section gb-search gb-search-content gb-disabled gb-hidden">
|
||
<div class="gb-section-body">
|
||
<div class="gb-ctrl">
|
||
<span class="gb-close"></span>
|
||
</div>
|
||
<div class="content-results">
|
||
<ul class="content-tabs"></ul>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
<div section-name="assembly-selector" class="gb-section gb-disabled">
|
||
|
||
<h4 title="Pick assembly">
|
||
<span></span>
|
||
<span>Assemblies</span>
|
||
</h4>
|
||
<div class="gb-section-body gb-assm-selector">
|
||
|
||
<div class="gb-switch">
|
||
<a href="/gdv" title="Go to landing page to switch organism">Switch organism</a>
|
||
</div>
|
||
<div class="gb-form">
|
||
<span>Assembly</span>
|
||
<select></select>
|
||
</div>
|
||
<div class="gb-assm-selector-comment">
|
||
<span class="comment">Select an assembly to change view</span>
|
||
</div>
|
||
<div class="gb-roi-wrap gb-hidden">
|
||
<h4>
|
||
<span>Locations</span>
|
||
</h4>
|
||
<div class="gb-roi-none gb-comment">No regions for assembly</div>
|
||
<div class="gb-roi-grid"></div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
<div section-name="ideo" config="nonNuclear:true" section-class="gb-ideo-selector-wrap" class="gb-section gb-ideo-selector-wrap gb-disabled gb-open" >
|
||
|
||
<h4 title="">
|
||
<span></span>
|
||
<span>Ideogram View</span>
|
||
</h4>
|
||
<div class="gb-section-body">
|
||
<div class="gb-ideo-selector"></div>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
|
||
|
||
<div class="gb-section gb-disabled" section-name="user-data">
|
||
|
||
<h4 title="Configure tracks, upload data, add remote tracks or track hubs">
|
||
<span></span>
|
||
<span>Tracks and User Data</span>
|
||
</h4>
|
||
<div class="gb-section-body">
|
||
<div class="gb-user-data">
|
||
<div class="gb-track-sect">
|
||
<span>
|
||
<a class="gb-select gb-menu-empty" href="#menu">- no added tracks or track hubs -</a>
|
||
<a class="gb-menu" href="#menu" role="button">
|
||
<span>Options</span>
|
||
</a>
|
||
</span>
|
||
</div>
|
||
<div class="gb-file-upload gb-upload">
|
||
<div class="gb-track-data">
|
||
<div class="gb-name"></div>
|
||
<div class="gb-track-grid">
|
||
<div class="grid-header">
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th class="gbs-name">Name</th>
|
||
<th class="gbs-location">Location</th>
|
||
<th class="ctrl">
|
||
<span></span>
|
||
</th>
|
||
</tr>
|
||
<tr>
|
||
<th class="gb-acc" colspan="3"></th>
|
||
</tr>
|
||
</thead>
|
||
</table>
|
||
</div>
|
||
<div class="grid-data-wrap">
|
||
<div class="grid-data">
|
||
<table>
|
||
<tbody>
|
||
<tr>
|
||
<td></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div class="grid-ctrl">
|
||
<select>
|
||
<option>chr</option>
|
||
</select>
|
||
<span>
|
||
<input type="image" src="/gdv/browser/static/img/first-b.png" title="first" alt="first page"/>
|
||
<input type="image" src="/gdv/browser/static/img/prev-b.png" title="previous" alt="previous page"/>
|
||
<input type="text" id="gb-track-data-page"/>
|
||
<input type="image" src="/gdv/browser/static/img/next-b.png" title="next" alt="next page"/>
|
||
<input type="image" src="/gdv/browser/static/img/last-b.png" title="last" alt="last page"/>
|
||
</span>
|
||
</div>
|
||
<div class="grid-ctrl-info">
|
||
<label for="gb-track-data-page">Page 1 of 1</label>
|
||
</div>
|
||
</div>
|
||
<div class="gb-track-info"></div>
|
||
</div>
|
||
<div class="gb-file-progress"></div>
|
||
|
||
<div class="gb-uud-help">
|
||
<style>.gb-data-formats {
|
||
display: table;
|
||
}
|
||
.gb-data-formats li {
|
||
display: table-row;
|
||
}
|
||
.gb-data-formats span,
|
||
.gb-data-formats strong,
|
||
.gb-data-formats a {
|
||
display: table-cell;
|
||
}
|
||
.gb-data-formats strong {
|
||
color: #557;
|
||
white-space: nowrap;
|
||
font-weight: normal;
|
||
}
|
||
.gb-data-formats span {
|
||
padding: .1em .5em;
|
||
}</style>
|
||
<p>
|
||
<span>
|
||
Supported File/Data types
|
||
</span>
|
||
</p>
|
||
<ul>
|
||
<li>Uploaded tracks</li>
|
||
<ul class="gb-data-formats">
|
||
<li><strong>BED</strong>
|
||
</li>
|
||
<li><strong>GFF3</strong>
|
||
</li>
|
||
<li><strong>GTF</strong>
|
||
</li>
|
||
<li><strong>GVF</strong>
|
||
</li>
|
||
<li><strong>VCF</strong>
|
||
</li>
|
||
<li><strong>HGVS</strong>
|
||
</li>
|
||
<li><strong>WIG</strong>
|
||
</li>
|
||
<li><strong>ASN.1</strong><span> (text and binary)</span>
|
||
</li>
|
||
</ul>
|
||
<li>Remote tracks</li>
|
||
<ul class="gb-data-formats">
|
||
<li><strong>Remote BAM</strong><span>.bai or CSI index file present at same location</span>
|
||
</li>
|
||
<li><strong>Remote VCF</strong><span>un-indexed up to 2000 lines or with an index file present at the same location</span>
|
||
</li>
|
||
<li><strong>BigBed</strong>
|
||
</li>
|
||
<li><strong>BigWig</strong>
|
||
</li>
|
||
</ul>
|
||
</ul>
|
||
</div>
|
||
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
<div class="gb-section gb-disabled" section-name="blast-wrap">
|
||
<h4 title="">
|
||
<span></span>
|
||
<span>BLAST</span>
|
||
<span class="gb-help gb-blast-help" help_id="blast-widget" title="Context help"></span>
|
||
</h4>
|
||
<div class="gb-section-body">
|
||
<div class="gb-blast-wrap">
|
||
<div class="gb-blast-progress">
|
||
<span></span>
|
||
</div>
|
||
<div class="gb-blast-popup-wrap">
|
||
<span class="gb-blast-popup">
|
||
<a class="gb-blast-select" href="#menu" role="button">--- No BLAST RIDs ---</a>
|
||
<a class="gb-blast-add" href="#menu" role="button">Tools</a>
|
||
</span>
|
||
<div class="gb-blast-input">
|
||
<input type="text" placeholder="BLAST RID or URL" title="Enter RID or paste BLAST RID URL here and press Enter. Press Esc to cancel"/>
|
||
<span class="gb-enter"></span>
|
||
</div>
|
||
</div>
|
||
|
||
<div class="gb-blast-rid">
|
||
<h5 class="gb-toggle gb-closed">
|
||
<span>Details</span>
|
||
</h5>
|
||
<div class="gb-blast-desc gb-closed"></div>
|
||
|
||
<div class="gb-blast-items">
|
||
<ul>
|
||
<li class="gb-item-inspect" title="Show alignments inspector"></li>
|
||
<li class="gb-item-zoom" title="Zoom on enclosing range for selected alignments"></li>
|
||
<li class="gb-item-marker" title="Add marker(s) for selected alignment(s)"></li>
|
||
<li class="gb-item-filter" title="Filter alignments"></li>
|
||
</ul>
|
||
</div>
|
||
<h5>
|
||
<span>Alignments</span>
|
||
</h5>
|
||
<div class="gb-blast-al">
|
||
<a href="#menu"></a>
|
||
<div class="gb-blast-header"></div>
|
||
<div class="gb-blast-hits-wrap">
|
||
<div class="gb-blast-hits"></div>
|
||
</div>
|
||
</div>
|
||
|
||
<div class="gb-blast-comment gb-divider">
|
||
<span></span>
|
||
<div></div>
|
||
</div>
|
||
</div>
|
||
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
|
||
<div class="gb-section gb-disabled" section-name="track-search">
|
||
|
||
<h4 title="Search track by accession">
|
||
<span></span>
|
||
<span>Tracks by Accession</span>
|
||
</h4>
|
||
<div class="gb-section-body">
|
||
<div class="gbt-search">
|
||
<div class="gb-header">
|
||
<span>Search tracks</span>
|
||
</div>
|
||
<div class="gb-search-ctrl">
|
||
<label for="gbt-search" alt="search history" aria-label="Search History"></label>
|
||
<input id="gbt-search" type="text" placeholder="GEO, SRR, dbGaP or dbVar accession"/>
|
||
<span class="gb-search-go"></span>
|
||
</div>
|
||
|
||
<div class="gbt-search-help">
|
||
<p>
|
||
<span>Supported accession types</span>
|
||
</p>
|
||
<ul>
|
||
<li><span>GEO accessions:</span>
|
||
</li>
|
||
<li>
|
||
<a>GSE25249</a><span>(for GRCh37)</span>
|
||
</li>
|
||
<li>
|
||
<a>GSM1541970</a><span>(for GRCm38)</span>
|
||
</li>
|
||
<li><span>SRR accessions:</span>
|
||
</li>
|
||
<li><a>SRR834589</a><span>(for GRCh37)</span>
|
||
</li>
|
||
<li><span>dbGaP accessions:</span>
|
||
</li>
|
||
<li><a>pha000001</a><span>(for GRCh38)</span>
|
||
</li>
|
||
<li><span>dbVar accessions:</span>
|
||
</li>
|
||
<li>
|
||
<a>nstd82</a><span>(for GRCh38)</span>
|
||
</li>
|
||
</ul>
|
||
</div>
|
||
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
<div class="gb-section gb-disabled gb-hidden" section-name="region-details">
|
||
|
||
<h4 title="">
|
||
<span></span>
|
||
<span>Assembly Region Details</span>
|
||
</h4>
|
||
<div class="gb-section-body gb-region-details">
|
||
<h5>Features of Interest</h5>
|
||
<div class="gb-region-alts gb-none gb-hidden">
|
||
<h6>
|
||
Other sequence representations
|
||
<span class="gb-none">- none for the region</span>
|
||
<span class="gb-info">- loading …</span>
|
||
</h6>
|
||
<div class="gb-data">
|
||
<div class="grid-header">
|
||
<table>
|
||
<tr>
|
||
<th class="gb-name">Sequence ID</th>
|
||
<th>Type</th>
|
||
</tr>
|
||
<tr>
|
||
<td class="gb-row-header" colspan="2"></td>
|
||
</tr>
|
||
</table>
|
||
</div>
|
||
<div class="grid-data">
|
||
<table>
|
||
<tr>
|
||
<td></td>
|
||
</tr>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div class="gb-back">Back to region <a href="#back"></a></div>
|
||
</div>
|
||
<div class="gb-region-issues gb-hidden"></div>
|
||
<div class="gb-region-similar gb-hidden"></div>
|
||
<div class="gb-region-details-alt gb-hidden">Not applicable for this organism/assembly</div>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
<div class="gb-section gb-disabled" section-name="gene-history">
|
||
|
||
<h4 title="">
|
||
<span></span>
|
||
<span>History</span>
|
||
</h4>
|
||
<div class="gb-section-body">
|
||
<div class="gb-gene-history">
|
||
<select>
|
||
<option>--- current selection ---</option>
|
||
</select>
|
||
</div>
|
||
<div class="gb-gene-history-comment">
|
||
<span class="comment">Select gene from history</span>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
</div>
|
||
</div>
|
||
<div class="content-right">
|
||
<div class="gdv-hidden">
|
||
|
||
<div widget-name="range-header">
|
||
<div class="gb-range-header"></div>
|
||
</div>
|
||
|
||
|
||
<div widget-name="region-selector">
|
||
<div class="gb-ideo-region-wrap">
|
||
<div class="gb-slider-wrap" title="Right click for help menu">
|
||
<div class="gb-slider"><div></div></div>
|
||
<div class="gb-hair"><div></div></div>
|
||
</div>
|
||
<div class="gb-ideo-region">
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
<div widget-name="exon-navigator">
|
||
<div class="gb-exon-navigator">
|
||
<div class="gb-exon-wrap gb-no-genes gb-no-track gb-hidden">
|
||
<div class="gb-exon-mask-wrap">
|
||
<div class="gb-exon-mask"></div>
|
||
</div>
|
||
<div class="gb-exon-track">
|
||
<span title="Select gene track" class="gb-exon-cell">
|
||
<a href="#" class="gb-exon-track-menu">❖</a>
|
||
</span>
|
||
</div>
|
||
<div class="gb-exon-body">
|
||
<span class="gb-exon-gene-wrap">
|
||
<div class="gb-exon-genes">
|
||
<span class="gb-exon-gene-body">
|
||
<div class="gb-exon-set">
|
||
<span class="gb-exon-cell">
|
||
<a href="#" class="gb-exon-menu gb-menu-mark">Region</a>
|
||
</span>
|
||
<span class="gb-exon-cell gb-exon-gene-set">
|
||
<span class="gb-header">Gene</span>
|
||
<span class="gb-gene-cell">
|
||
<span class="gb-exon-gene-go gb-prev" title="Previous gene"></span>
|
||
<select></select>
|
||
<span class="gb-exon-gene-go gb-next" title="Next gene"></span>
|
||
</span>
|
||
</span>
|
||
</div>
|
||
</span>
|
||
<span class="gb-exon-split"></span>
|
||
</div>
|
||
</span>
|
||
<span class="gb-exon-transcript-wrap">
|
||
<span class="gb-exon-cell gb-exon-transcript-set">
|
||
<span class="gb-header"></span>
|
||
<span class="gb-transcript-cell">
|
||
<select></select>
|
||
</span>
|
||
</span>
|
||
<span class="gb-exon-page-wrap">
|
||
<div class="gb-exon-details-wrap gb-no-print">
|
||
<span class="gb-exon-page-details"></span>
|
||
</div>
|
||
<div class="gb-exon-page-exons gb-no-print">
|
||
<span class="gb-exon-page-go gb-prev" title="Select previous exon"></span>
|
||
<span class="gb-exon-page-go gb-next" title="Select next exon"></span>
|
||
<span class="gb-exon-page">
|
||
<div class="gb-exon-page-body"></div>
|
||
<div class="gb-exon-slider">
|
||
<div></div>
|
||
</div>
|
||
</span>
|
||
</div>
|
||
</span>
|
||
<span class="gb-exon-page-msg">No exons</span>
|
||
</span>
|
||
</div>
|
||
<div class="gb-exon-gene-spare">
|
||
<div>
|
||
<span class="gb-exon-flank gb-left">
|
||
<a href="#" title="Previous gene out of view" class="gb-no-gene"></a>
|
||
</span>
|
||
<span class="gb-exon-msg">Exon Navigator</span>
|
||
<span class="gb-exon-flank gb-right">
|
||
<a href="#" title="Next gene out of view" class="gb-no-gene"></a>
|
||
</span>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
<div widget-name="blast-view">
|
||
<div class="gb-blast-view gb-empty gb-hidden">
|
||
<div>
|
||
<div class="gb-blast-top">
|
||
<div>
|
||
<span class="gb-blast-help" help_id="blast-inspector" title="Blast Inspector help"></span>
|
||
<span title="Close inspector"></span>
|
||
</div>
|
||
<h4>
|
||
<span></span>
|
||
<span>BLAST Alignment Inspector</span>
|
||
<span></span>
|
||
<span></span>
|
||
</h4>
|
||
|
||
</div>
|
||
<div class="gb-blast-view-data">
|
||
<div class="gb-blast-header">
|
||
<div></div>
|
||
<div>
|
||
<div class="gb-blast-group-wrap">
|
||
<div class="gb-blast-group-header"></div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="gb-blast-hits"></div>
|
||
</div>
|
||
<div class="gb-comment"></div>
|
||
</div>
|
||
<div class="gb-divider"></div>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
<div class="gb-hub-status" widget-name="hub-status">
|
||
<div></div>
|
||
</div>
|
||
|
||
|
||
<div config="appname:'DataViewer', toolbar:'-s'" widget-name="seqview-wrap">
|
||
<div class="seqview-wrap" options="toolbar:'-s'">
|
||
<div></div>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="gb-page-content-bottom">
|
||
</div>
|
||
</div>
|
||
|
||
|
||
<div class="gdv-status"></div>
|
||
|
||
<div class="gb-data-canvas">
|
||
<span></span>
|
||
<canvas>
|
||
</canvas>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
</main>
|
||
|
||
|
||
<!-- ========== BEGIN FOOTER ========== -->
|
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