The Assembly and Chromosome that are viewed in the genome browser are indicated on the top center of the page Figure 3.
The current sequence accession and coordinates appear on the line below. The Assembly Indicator appears as a dropdown menu when there are multiple assemblies available in GDV. You can use this menu to switch to view a different assembly for the selected organism. The Chromosome Indicator appears as a drop-down menu that allows you to navigate to different chromosomes or scaffolds within the assembly.
For chromosome-level assemblies, the chromosomes in the assembly will be listed in the menu. For assemblies that lack assembled nuclear chromosomes, e. The "More Chromosomes or scaffolds that have been viewed in a genome browser session including scaffolds not in the top 30 will be listed in the selection menu under a separate sub-heading for ease of future access. These added scaffolds will disappear from the menu when you click "Reset All" on the upper right or start a new genome browser session.
The Search Box Figure 4 is located on the upper left of the page by default and can be used to find a gene or location within the selected assembly. Location information can be provided using a coordinate range, a single point, or a cytogenetic band.
This search box can also be used to search and navigate to a scaffold or contig within the assembly e. If your search finds an exact and unique match, the Sequence Viewer and other widgets on the page will update to show the location of that match.
If you perform a search without a unique match, a new panel will appear with a list of results and their locations. The Ideogram View and Chromosome Region Selector will also be updated to display clickable colored arrowheads indicating the location of search results. In the search results panel, the Genes tab lists genes matching the search term, while the Other Features tab lists related transcripts or other features.
When you click on a row in either tab of the search results, or on the arrowheads in the Ideogram View or Chromosome Region Selector, the Sequence Viewer and other page elements will update to go to that location.
You can click on the x to hide the search results panel. Recent search terms will be remembered by default and shown in a pop-up menu when the cursor is placed within the search box. When the left sidebar is hidden, the search box appears in the upper right of the page.
The right search box has identical behavior to the default search box, and recent searches made in both locations can be retrieved from either location. This widget appears in the left sidebar when there are multiple assemblies available for an organism.
It provides a drop-down menu of available assemblies. Click on the "Switch organism" link to go to the Genome Data Viewer landing page to select from the full list of available organisms and assemblies.
A green highlight surrounds the current chromosome that is viewed in the display. Clicking on a chromosome will update the Sequence Viewer to the selected chromosome.
No chromosome ideograms will be displayed for scaffold- or contig-based assemblies. The locations of gene s or SNP found in the most recent GDV search appear as green or blue arrowheads, respectively, on the chromosomes in this widget. When you hover over a arrowhead, a panel appears with more information. You can click on an arrowhead or within a pop-up panel to navigate to the corresponding location in the Sequence Viewer display.
The Ideogram View widget also provides a count of the non-chromosomal sequences in the assembly. The Chromosome Region Selector Figure 7A is an interactive ideogram that provides context and navigation for the genome browser. The ideogram corresponds to the current chromosome viewed in browser, and the boxed area in blue denotes the region currently shown in the Sequence Viewer. The Chromosome Region Selector widget will automatically update if you navigate or zoom using the Sequence Viewer or other elements on the page.
You can use the Chromosome Region Selector to navigate to a different region in the Sequence Viewer by clicking and dragging within the ideogram to select a different boxed window. You can also select the ends of the blue box with your cursor and adjust the size of the region. Clicking within a chromosome band if applicable will create a box around that band and navigate the Sequence Viewer directly to the sequence corresponding to that cytological region.
When you hover over an arrowhead, a panel appears with more information. A thin line beneath the ideogram shows regions of the chromosome for which there are alternate loci or patch scaffold sequence representations generated by the Genome Research Consortium GRC. Hovering over any of the red-colored portions of the line will open a region-specific information panel Figure 7B containing the region name and coordinates, as well as sequence identifiers for associated alternate loci or patches.
More information about GRC assembly regions can also be found in the Assembly Region Details widget Figure 7C , which is located by default toward the bottom of the left sidebar. Refer to this video for a demonstration of how to use the Chromosome Region Selector.
This widget contains drop-down selection menus and arrows that allow a user to navigate among neighboring genes, transcripts of a gene, and exons of a transcript. The "Region" link opens a menu Figure 8b containing options to configure the padding of the display around the selected gene or trancript. These options are not available when the view is zoomed further out; instead, a warning message appears listing the number of genes annotated on the latest NCBI Genes annotation release in the current display window.
When a single gene is selected, open circles appear toward the right of the Exon Navigator corresponding to the exons of the selected transcript of the selected gene. Hovering over an exon circle reveals text showing the exon number relative to the selected transcript and coordinates on the chromosome accession. Right-clicking on an exon circle reveals an option to view a pop-up window showing the genomic sequence of the exon in FASTA format.
Users can copy text from this window for their own use. The NCBI Sequence Viewer Figure 9 is an application that provides a linear graphical representation of features annotated or aligned to individual sequence accessions. You can use the pan arrows and zoom slider on the left side of the Sequence Viewer toolbar to navigate within this viewer; changes in the displayed range will be automatically propagated elsewhere in the genome browser, including to the Chromosome Region Selector and the Exon Navigator.
Multiple results can be loaded from this menu; only the results displayed in the widget table will have a check mark next to their name. Click the x next to an alignment result in this menu to remove it from GDV. Once loaded to the BLAST widget , the graphical display will update to show the corresponding alignment tracks at top. Track names are provided automatically.
The former provides the raw BLAST hits, while the cleaned alignments track presents a summarized view of co-linear, non-overlapping alignments for each query, connected by thin horizontal lines Figure 10B.
This latter view can be particularly useful if you have aligned a cDNA sequence to the genome assembly, as it tends to connect exon hits together. The Options sub-menu offers 3 choices for the display of alignment tracks. Within the first column of each table row, the query is shown as a thin gray bar in which the portion shaded orange represents the aligned region. Use the table to select specific alignments and update the graphical display.
You can expand the vertical height of the table by dragging the icon located at its base. Hovering over any table row activates a highlight at the corresponding sequence location in the graphical display. Click one or more rows in the table to select specific alignments. Use the icons above the table or right-click within the table to: 1 zoom the sequence display, 2 set markers for those selections, or 3 filter result by identity.
Once an alignment has been selected within the table, click the left-most icon above the table to toggle the Alignment Inspector display for the corresponding assembly sequence.
It provides a graphical display of the relationship of a query's alignments to the assembly and NCBI's current RefSeq gene annotation. It is launched from within the BLAST widget using the left-most icon above the table or by right-clicking and selecting the option.
Thick regions of the cartoons indicate exons, thin regions represent introns, and UTRs are shown in light green. Hovering over any exon or aligned region creates a highlight in the Alignment Inspector column and at the corresponding region of the sequence viewer display in GDV. A single click within any of these highlights in the Alignment Inspector will navigate the GDV display to the locations of specific alignments, genes, transcripts, or exons. Right-click within an exon or aligned region orange for a menu for additional zoom options or to copy the alignment coordinates.
You can also navigate directly to a Gene or RefSeq transcript in the graphical display by clicking on its identifier in the Alignment Inspector. Note that hovering over icons within the Exon Navigator also creates corresponding highlights in the Alignment Inspector.
If the accession is associated with an existing track in the NCBI database, that track will be added to the graphical display. Note: The track must refer to the same assembly as the one currently in the display in order to view data.
There are many more data tracks available for GDV than are displayed by default. You can also configure the track order and how tracks are displayed.
To change the track configuration, select the "Tracks" menu in the Sequence Viewer toolbar and select the "Configure Tracks" option. This is highlighted in orange in Figure You can also access track configuration settings using the configure gear icon located in the track title tooltip or on the far left of the track.
AF Byssochlamys sp. BYSS01 Byssochlamys sp. DSE Caenorhabditis afra Caenorhabditis angaria Caenorhabditis angaria Caenorhabditis becei Caenorhabditis bovis Caenorhabditis brenneri Caenorhabditis briggsae Caenorhabditis elegans Caenorhabditis inopinata Caenorhabditis japonica Caenorhabditis latens Caenorhabditis nigoni Caenorhabditis nigoni Caenorhabditis panamensis Caenorhabditis remanei Caenorhabditis sp.
JCM Candida sp. NI Cetradonia linearis Chaenocephalus aceratus Blackfin icefish Chaetomium cochliodes Chaetomium globosum Chaetomium thermophilum Chaetomium thermophilum var. CBS Chaetothyriales sp. AAM3 Charadrius alexandrinus Kentish plover Charadrius vociferus Killdeer Chatrabus melanurus Pony toadfish Cheirogaleus medius Lesser dwarf lemur Chelonia mydas Green sea turtle Chelonoidis abingdonii Abingdon island giant tortoise Chelydra serpentina Common snapping turtle Chenopodium pallidicaule Chenopodium quinoa Quinoa Chenopodium suecicum Cherax destructor Cherax quadricarinatus Chilo suppressalis Striped riceborer Chiloscyllium plagiosum Whitespotted bambooshark Chiloscyllium punctatum Brownbanded bambooshark Chinchilla lanigera Long-tailed chinchilla Chionodraco hamatus Antarctic icefish Chionodraco myersi Myers' icefish Chironomus riparius Chironomus tentans Chiroxiphia lanceolata Lance-tailed manakin Chiua virens Chlamydomonas applanata Chlamydomonas asymmetrica Chlamydomonas eustigma Chlamydomonas reinhardtii Chlamydomonas sp.
AIC Chlamydomonas sp. WS3 Chlamydomonas sp. A99 Chlorella sp. ArMB Chlorella sp. CH Chlorella sp. Dachan Chlorella sp. CF Chloroidium sp. JM Chlorokybus atmophyticus Chloromonas sp. AAM2 Chlorophyta sp.
Silveira Coccinella septempunctata Seven-spotted ladybird Coccinonectria pachysandricola Coccomyxa sp. LA Coccomyxa sp. M60 Coelastrella sp. UTEX B Coemansia reversa Coffea arabica Coffee Coffea canephora Coffea eugenioides Coilia nasus Japanese grenadier anchovy Coix aquatica Coix lacryma-jobi Job's tears Cokeromyces recurvatus Coleophoma crateriformis Coleophoma cylindrospora Colias croceus Clouded yellow Colinus virginianus Northern bobwhite Colius striatus Speckled mousebird Colletotrichum acutatum Colletotrichum asianum Colletotrichum chlorophyti Colletotrichum coccodes Colletotrichum destructivum Colletotrichum falcatum Colletotrichum fioriniae Colletotrichum fructicola Colletotrichum gloeosporioides Colletotrichum godetiae Colletotrichum graminicola Colletotrichum graminicola M1.
COLG25 Colletotrichum sp. COLG31 Colletotrichum sp. JS Colletotrichum spinosum Colletotrichum sublineola Colletotrichum tanaceti Colletotrichum tofieldiae Colletotrichum trifolii Colletotrichum truncatum Collichthys lucidus Big head croaker Collybia sp. MG36 Colobus angolensis Angolan colobus Colocasia esculenta Taro Colubraria reticulata Columba livia Rock pigeon Condylostoma magnum Condylostylus patibulatus Condylura cristata Star-nosed mole Conidiobolus coronatus Conidiobolus incongruus Coniella lustricola Coniferiporia sulphurascens Coniochaeta hoffmannii Coniochaeta ligniaria Coniochaeta prunicola Coniochaeta pulveracea Coniochaeta sp.
AEA Coniochaeta sp. IL Coniochaeta sp. NC Coniochaeta sp. YLH Coniophora puteana Coniosporium apollinis Coniothyrium glycines Connochaetes taurinus Brindled gnu Conringia planisiliqua Contarinia nasturtii Swede midge Conus consors Conus tribblei Copidosoma floridanum Coprinellus micaceus Coprinopsis cinerea Coprinopsis marcescibilis Coprinopsis strossmayeri Coprinus comatus Corallochytrium limacisporum Corapipo altera White-ruffed manakin Corbicula fluminea Corchorus capsularis Corchorus olitorius Cordyceps cicadae Cordyceps farinosa Cordyceps fumosorosea Cordyceps javanica Cordyceps militaris Cordyceps militaris CM01 Cordyceps pruinosa Cordyceps sp.
BD Cricetomys gambianus Gambian giant pouched rat Cricetulus griseus Chinese hamster Cristatella mucedo Crithidia acanthocephali Crithidia bombi Crithidia expoeki Crithidia fasciculata Crithidia mellificae Crocidura indochinensis Crocodylus porosus Australian saltwater crocodile Crocuta crocuta Spotted hyena Cronartium comandrae Cronartium quercuum Cronartium ribicola Crotalus horridus Timber rattlesnake Crotalus mitchellii Speckled rattlesnake Crotalus pyrrhus Crotalus viridis Western rattlesnake Crucibulum laeve Crucihimalaya himalaica Cryomyces antarcticus Cryomyces minteri Cryphonectria macrospora Cryphonectria nitschkei Cryphonectria parasitica Chestnut blight fungus Cryphonectria radicalis Cryptococcus amylolentus Cryptococcus cf.
M2 Dunaliella sp. RO Dunaliella sp. WIN1 Dunaliella sp. YS1 Durio zibethinus Dysdera silvatica Echeneis naucrates Live sharksucker Echinochloa crus-galli Echinococcus canadensis Echinococcus granulosus Echinococcus multilocularis Echinococcus oligarthrus Echinops telfairi Small Madagascar hedgehog Echinostoma caproni Echium plantagineum Ectocarpus siliculosus Ectocarpus sp.
AC Escovopsis sp. Ae Escovopsis sp. Eurotiomycetes sp. MA Eurotiomycetes sp. Exophiala spinifera Exophiala xenobiotica Exserohilum turcicum Exutisphaerella laricina Exutisphaerella laricina Fagopyrum esculentum Common buckwheat Fagopyrum tataricum Tartarian buckwheat Fagus sylvatica European beech Falciphora oryzae Falciphora oryzae Falco cherrug Saker falcon Falco peregrinus Peregrine falcon Fasciola gigantica Fasciola hepatica Liver fluke Fasciolopsis buski Felis catus Domestic cat Felis nigripes Black-footed cat Ferrisia virgata Striped mealybug Fibroporia radiculosa Fibularhizoctonia sp.
CBS Ficedula albicollis Collared flycatcher Ficus carica Common fig Ficus erecta Filobasidium wieringae Fistulifera solaris Fistulina hepatica Flammulina velutipes Floccularia luteovirens Folsomia candida Fomitiporia mediterranea Fomitopsis palustris Fomitopsis pinicola Fomitopsis rosea Fonsecaea erecta Fonsecaea monophora Fonsecaea multimorphosa Fonsecaea nubica Fonsecaea pedrosoi Fonticula alba Fonticula-like sp.
ARF18 Fungal sp. EF Fungal sp. Mo Fungal sp. AF-4 Fusarium sp. AF-6 Fusarium sp. AF-8 Fusarium sp. FOSC 3-a Fusarium sp. JS Fusarium sp. Na10 Fusarium sporotrichioides Fusarium subtropicale Fusarium temperatum Fusarium tricinctum Fusarium tucumaniae Fusarium udum Fusarium venenatum Fusarium verticillioides Fusarium virguliforme Fusarium xylarioides Fusarium xyrophilum Fusarium xyrophilum Fusarium xyrophilum Gadiculus argenteus Silvery cod Gadus chalcogrammus Walleye pollock Gadus morhua Atlantic cod Gaeumannomyces graminis Gaeumannomyces sp.
JS Gaeumannomyces tritici Gaeumannomyces tritici Ra-1 Galdieria phlegrea Galdieria sulphuraria Galendromus occidentalis Western predatory mite Galeopterus variegatus Sunda flying lemur Galerina marginata Galleria mellonella Greater wax moth Gallirallus okinawae Gallus gallus Chicken Gamarada debralockiae Gambusia affinis Western mosquitofish Gambusia holbrooki Eastern mosquitofish Ganaspis brasiliensis Ganoderma australe Ganoderma boninense Ganoderma lucidum Ganoderma lucidum Xiangnong No.
Globodera ellingtonae Globodera pallida Globodera rostochiensis Gloeophyllum trabeum Gloeostereum incarnatum Glomus cerebriforme Glonium stellatum Glossina austeni Glossina brevipalpis Glossina fuscipes Glossina morsitans Glossina pallidipes Glossina palpalis Glossosoma conforme Glycine max Soybean Glycine soja Glycine tomentella Golovinomyces cichoracearum Golovinomyces magnicellulatus Golubevia pallescens Gomphus bonarii Gomphus sp.
MG54 Gonapodya prolifera Gongronella sp. AAB Halamphora sp. NKZ Haliotis laevigata Greenlip abalone Haliotis rubra Blacklip abalone Haliotis rufescens Red abalone Halocafeteria seosinensis Halteria grandinella Halyomorpha halys Brown marmorated stink bug Hamiltosporidium magnivora Hamiltosporidium tvaerminnensis Hammondia hammondi Handroanthus impetiginosus Hanseniaspora clermontiae Hanseniaspora gamundiae Hanseniaspora guilliermondii Hanseniaspora hatyaiensis nom. Hanseniaspora jakobsenii Hanseniaspora lachancei Hanseniaspora meyeri Hanseniaspora nectarophila Hanseniaspora occidentalis Hanseniaspora opuntiae Hanseniaspora osmophila Hanseniaspora pseudoguilliermondii Hanseniaspora singularis nom.
Hanseniaspora sp. CRUB Hanseniaspora thailandica Hanseniaspora uvarum Hanseniaspora valbyensis Hanseniaspora vineae Haplochromis burtoni Burton's mouthbrooder Harmonia axyridis Harpegnathos saltator Jerdon's jumping ant Hawksworthiomyces lignivorus Hebeloma cylindrosporum Helianthus annuus Common sunflower Helicocarpus griseus Heliconius aoede Heliconius cydno Heliconius elevatus Heliconius ethilla Heliconius hecale Heliconius hecuba Heliconius heurippa Heliconius hierax Heliconius ismenius Heliconius melpomene Postman butterfly Heliconius numata Heliconius pachinus Heliconius pardalinus Heliconius timareta Heliconius wallacei Heliconius xanthocles Helicosporidium sp.
F Hemicentrotus pulcherrimus Hemignathus wilsoni Akiapolaau Hemileia vastatrix Hemitragus hylocrius Nilgiri tahr Henneguya salminicola Hepatospora eriocheir Hericium alpestre Hericium coralloides Hericium erinaceus Hermetia illucens Herpetomonas muscarum Herpomyces periplanetae Herpotrichiellaceae sp.
UM Herrania umbratica Hesseltinella vesiculosa Heterobasidion annosum Heterobasidion irregulare Heterobasidion parviporum Heterocephalus glaber Naked mole-rat Heterococcus sp. D Hypholoma sublateritium Hyphopichia burtonii Hyphopichia gotoi Hyphopichia heimii Hyphopichia homilentoma Hyphopichia pseudoburtonii Hyphopichia rhagii Hypochthonius rufulus Hypocrella siamensis Hypolimnas misippus Hypomyces perniciosus Hypophthalmichthys molitrix Silver carp Hypophthalmichthys nobilis Bighead carp Hypoplectrus puella Barred hamlet Hyposmocoma kahamanoa Hypothenemus hampei Coffee berry borer Hypoxylon pulicicidum Hypoxylon sp.
CI-4A Hypoxylon sp. CO Hypoxylon sp. EB Hypoxylon sp. XGBa Ictalurus punctatus Channel catfish Ictidomys tridecemlineatus Thirteen-lined ground squirrel Ilyonectria destructans Ilyonectria mors-panacis Indri indri Inia geoffrensis Boutu Intoshia linei Ipomoea batatas Sweet potato Ipomoea nil Japanese morning glory Ipomoea purpurea Common morning-glory Ipomoea trifida Ipomoea triloba Trilobed morning glory Irpex lacteus Isatis lusitanica Isatis tinctoria Isoperla grammatica Ixodes ricinus Castor bean tick Ixodes scapularis Black-legged tick Jaapia argillacea Jaculus jaculus Lesser Egyptian jerboa Jaltomata sinuosa Jaminaea rosea Jatropha curcas Jimgerdemannia flammicorona Jimgerdemannia lactiflua Juglanconis juglandina Juglanconis oblonga Juglanconis sp.
PJa Lachancea thermotolerans Lachancea waltii Lachnellula arida Lachnellula cervina Lachnellula hyalina Lachnellula occidentalis Lachnellula subtilissima Lachnellula suecica Lachnellula willkommii Lachnum nothofagi Lactarius deliciosus Lactarius echinatus Lactarius hatsudake Lactarius indigo Lactarius piperatus Lactarius sp. MG Lactarius sp. MG50 Lactarius trivialis Lactarius volemus Lactifluus hygrophoroides Lactifluus pinguis Lactifluus rugatus Lactuca sativa Ladona fulva Scarce chaser Laemonema laureysi Laetiporus sulphureus Lagenaria siceraria White-flowered gourd Lagenidium giganteum Lagenorhynchus obliquidens Pacific white-sided dolphin Lagopus muta Rock ptarmigan Lamellibrachia luymesi Lampris guttatus North Atlantic opah Lamprogrammus exutus Lanistes nyassanus Lanzia echinophila Laodelphax striatellus Small brown planthopper Laparus doris Larimichthys crocea Large yellow croaker Larix sibirica Lasallia hispanica Lasallia pustulata Lasiodiplodia gonubiensis Lasiodiplodia pseudotheobromae Lasiodiplodia sp.
COLG20 Lasiodiplodia sp. LEC01 Lecanicillium sp. P Magnaporthe sp. MG03 Magnaporthe sp. MG05 Magnaporthe sp. MG07 Magnaporthe sp. MG08 Magnaporthe sp. MG12 Magnaporthiopsis incrustans Magnaporthiopsis poae Magnaporthiopsis poae ATCC Magnaporthiopsis rhizophila Magnolia ashei Magnusiomyces capitatus Magnusiomyces clavatus Magnusiomyces clavatus Magnusiomyces ingens Magnusiomyces tetraspermus Malaclemys terrapin Diamondback terrapin Malacocephalus occidentalis Western softhead grenadier Malassezia caprae Malassezia cuniculi Malassezia dermatis Malassezia equina Malassezia furfur Malassezia globosa Malassezia japonica Malassezia nana Malassezia obtusa Malassezia pachydermatis Malassezia restricta Malassezia slooffiae Malassezia sp.
Malassezia sympodialis Malassezia vespertilionis Malassezia yamatoensis Malbranchea cinnamomea Malurus cyaneus Superb fairywren Malus baccata Malus domestica Apple Mamestra configurata Bertha armyworm Mamiellophyceae sp. Metschnikowia colocasiae Metschnikowia continentalis Metschnikowia cubensis Metschnikowia dekortorum Metschnikowia drakensbergensis Metschnikowia drosophilae Metschnikowia fructicola Metschnikowia hamakuensis Metschnikowia hawaiiana Metschnikowia hawaiiensis Metschnikowia hibisci Metschnikowia kamakouana Metschnikowia kipukae Metschnikowia lochheadii Metschnikowia matae Metschnikowia mauinuiana Metschnikowia orientalis Metschnikowia proteae Metschnikowia pulcherrima Metschnikowia reukaufii Metschnikowia santaceciliae Metschnikowia shivogae Metschnikowia similis Metschnikowia sp.
AWRI Metschnikowia sp. JCM Metschnikowia sp. M2Y3 Metschnikowia sp. UWOPS JA9 Micoletzkya japonica Micractinium conductrix Micractinium conductrix Microbotryum intermedium Microbotryum lychnidis-dioicae Microbotryum lychnidis-dioicae p1A1 Lamole Microbotryum saponariae Microbotryum silenes-acaulis Microbotryum silenes-dioicae Microbotryum violaceum Microcaecilia unicolor Microcebus griseorufus Microcebus mittermeieri Mittermeier's mouse lemur Microcebus murinus Gray mouse lemur Microcebus ravelobensis Microcebus sp.
ASPa Micromonas sp. SAG5 Micromonas sp. GenBank growth statistics for both the traditional GenBank divisions and the WGS division are available from each release. An annotated sample GenBank record for a Saccharomyces cerevisiae gene demonstrates many of the features of the GenBank flat file format. The GenBank database is designed to provide and encourage access within the scientific community to the most up-to-date and comprehensive DNA sequence information. However, some submitters may claim patent, copyright, or other intellectual property rights in all or a portion of the data they have submitted.
NCBI is not in a position to assess the validity of such claims, and therefore cannot provide comment or unrestricted permission concerning the use, copying, or distribution of the information contained in GenBank. Some authors are concerned that the appearance of their data in GenBank prior to publication will compromise their work.
GenBank will, upon request, withhold release of new submissions for a specified period of time. However, if the accession number or sequence data appears in print or online prior to the specified date, your sequence will be released. In order to prevent the delay in the appearance of published sequence data, we urge authors to inform us of the appearance of the published data.
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