Difference between revisions of "Main Page"
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| − | + | <div class="cite" style="margin-top:5px;background-color:#DC143C;font-size:0.9em;text-align:center;color:white;border-radius:10px"> | |
| − | + | Due to high server resource usage by bots, the database is now restricted to registered users only. Login <b>[http://greenc.sequentiabiotech.com/wiki2/Special:Login here]</b> and sign up <b>[http://greenc.sequentiabiotech.com/wiki2/Special:SemanticSignup here]</b>. | |
| − | + | </div> | |
| − | + | ||
| − | + | {{DISPLAYTITLE:GreeNC}}__NOTOC__ | |
| − | { | + | ==== A Wiki-database of plant lncRNAs (v2.0) ==== |
| − | + | <includeonly><div class="resolution-warning">Warning. For a properly visualization of the information provided for this database, it is recommended a minimum width resolution of 768px.</div></includeonly> | |
| − | + | <div id="main-plants" class="all-width" style="font-size:0.9em"> | |
| − | + | ||
| − | + | {{Main Plant|Actinidia chinensis (Ensembl Plants 51)|Unknown.png}} | |
| − | + | {{Main Plant|Aegilops tauschii (Ensembl Plants 51)|Unknown.png}} | |
| − | | | + | {{Main Plant|Amaranthus hypocondriacus (Phytozome 13)|Unknown.png}} |
| − | | | + | {{Main Plant|Aquilegia coerulea (Phytozome 13)|Aquilegia coerulea.jpg}} |
| − | | | + | {{Main Plant|Arabidopsis halleri (Ensembl Plants 51)|Arabidopsis halleri.jpg}} |
| − | | | + | {{Main Plant|Arabidopsis lyrata (Phytozome 13)|Arabidopsis lyrata.jpg}} |
| − | | | + | {{Main Plant|Arabidopsis thaliana (Phytozome 13)|Arabidopsis thaliana.jpg}} |
| − | | | + | {{Main Plant|Arabis alpina (Ensembl Plants 51)|Unknown.png}} |
| − | | | + | {{Main Plant|Beta vulgaris (Phytozome 13)|Unknown.png}} |
| − | | | + | {{Main Plant|Boechera stricta (Phytozome 13)|Boechera stricta.jpg}} |
| − | | | + | {{Main Plant|Brachypodium stacei (Phytozome 13)|Unknown.png}} |
| − | | | + | {{Main Plant|Brassica napus (Ensembl Plants 51)|Unknown.png}} |
| − | | | + | {{Main Plant|Brassica oleracea capitata (Phytozome 13)|Unknown.png}} |
| − | | | + | {{Main Plant|Brassica rapa (Phytozome 13)|Brassica rapa.jpg}} |
| − | | | + | {{Main Plant|Camelina sativa (Ensembl Plants 51)|Unknown.png}} |
| − | | | + | {{Main Plant|Capsella rubella (Phytozome 13)|Capsella rubella.jpg}} |
| − | | | + | {{Main Plant|Capsicum annuum (Ensembl Plants 51)|Unknown.png}} |
| − | | | + | {{Main Plant|Chara braunii (Ensembl Plants 51)|Unknown.png}} |
| − | | | + | {{Main Plant|Chenopodium quinoa (Phytozome 13)|Unknown.png}} |
| − | | | + | {{Main Plant|Chondrus crispus (Ensembl Plants 51)|Unknown.png}} |
| − | + | {{Main Plant|Chromochloris zofingiensis (Phytozome 13)|Unknown.png}} | |
| − | + | {{Main Plant|Cicer arietinum (Phytozome 13)|Unknown.png}} | |
| − | + | {{Main Plant|Cinnamomum kanehirae (Phytozome 13)|Unknown.png}} | |
| − | + | {{Main Plant|Citrullus lanatus (Ensembl Plants 51)|Unknown.png}} | |
| − | + | {{Main Plant|Coffea canephora (Ensembl Plants 51)|Unknown.png}} | |
| − | |- | + | {{Main Plant|Corchorus capsularis (Ensembl Plants 51)|Unknown.png}} |
| − | + | {{Main Plant|Cucumis melo (Ensembl Plants 51)|Unknown.png}} | |
| − | + | {{Main Plant|Cucumis sativus (Ensembl Plants 51)|Cucumis sativus.jpg}} | |
| − | + | {{Main Plant|Cyanidioschyzon merolae (Ensembl Plants 51)|Unknown.png}} | |
| − | + | {{Main Plant|Cynara cardunculus (Ensembl Plants 51)|Unknown.png}} | |
| − | + | {{Main Plant|Dioscorea alata (Phytozome 13)|Unknown.png}} | |
| − | + | {{Main Plant|Eragrostis curvula (Ensembl Plants 51)|Unknown.png}} | |
| − | | | + | {{Main Plant|Eragrostis tef (Ensembl Plants 51)|Unknown.png}} |
| − | | | + | {{Main Plant|Glycine max (Phytozome 13)|Glycine max.jpg}} |
| − | | | + | {{Main Plant|Gossypium barbadense (Phytozome 13)|Unknown.png}} |
| − | | | + | {{Main Plant|Gossypium darwinii (Phytozome 13)|Unknown.png}} |
| − | | | + | {{Main Plant|Gossypium hirsutum (Phytozome 13)|Unknown.png}} |
| − | | | + | {{Main Plant|Gossypium mustelinum (Phytozome 13)|Unknown.png}} |
| − | | | + | {{Main Plant|Gossypium raimondii (Ensembl Plants 51)|Gossypium raimondii.jpg}} |
| − | | | + | {{Main Plant|Gossypium tomentosum (Phytozome 13)|Unknown.png}} |
| − | | | + | {{Main Plant|Helianthus annuus (Phytozome 13)|Unknown.png}} |
| − | | | + | {{Main Plant|Hordeum vulgare (Phytozome 13)|Unknown.png}} |
| − | | | + | {{Main Plant|Juglans regia (Ensembl Plants 51)|Unknown.png}} |
| − | | | + | {{Main Plant|Kalanchoe fedtschenkoi (Phytozome 13)|Unknown.png}} |
| − | < | + | {{Main Plant|Lactuca sativa (Phytozome 13)|Unknown.png}} |
| − | + | {{Main Plant|Leersia perrieri (Ensembl Plants 51)|Unknown.png}} | |
| − | + | {{Main Plant|Lupinus albus (Phytozome 13)|Unknown.png}} | |
| − | + | {{Main Plant|Lupinus angustifolius (Ensembl Plants 51)|Unknown.png}} | |
| − | + | {{Main Plant|Manihot esculenta (Phytozome 13)|Manihot esculenta.jpg}} | |
| − | + | {{Main Plant|Marchantia polymorpha (Phytozome 13)|Unknown.png}} | |
| − | < | + | {{Main Plant|Medicago truncatula (Ensembl Plants 51)|Medicago truncatula.jpg}} |
| − | + | {{Main Plant|Musa acuminata (Ensembl Plants 51)|Musa acuminata.jpg}} | |
| − | + | {{Main Plant|Nicotiana attenuata (Ensembl Plants 51)|Unknown.png}} | |
| + | {{Main Plant|Nymphaea colorata (Phytozome 13)|Unknown.png}} | ||
| + | {{Main Plant|Olea europaea (Phytozome 13)|Unknown.png}} | ||
| + | {{Main Plant|Oropetium thomaeum (Phytozome 13)|Unknown.png}} | ||
| + | {{Main Plant|Oryza barthii (Ensembl Plants 51)|Unknown.png}} | ||
| + | {{Main Plant|Oryza brachyantha (Ensembl Plants 51)|Unknown.png}} | ||
| + | {{Main Plant|Oryza glaberrima (Ensembl Plants 51)|Unknown.png}} | ||
| + | {{Main Plant|Oryza glumipatula (Ensembl Plants 51)|Unknown.png}} | ||
| + | {{Main Plant|Oryza longistaminata (Ensembl Plants 51)|Unknown.png}} | ||
| + | {{Main Plant|Oryza meridionalis (Ensembl Plants 51)|Unknown.png}} | ||
| + | {{Main Plant|Oryza nivara (Ensembl Plants 51)|Unknown.png}} | ||
| + | {{Main Plant|Oryza punctata (Ensembl Plants 51)|Unknown.png}} | ||
| + | {{Main Plant|Oryza rufipogon (Ensembl Plants 51)|Unknown.png}} | ||
| + | {{Main Plant|Oryza sativa (Phytozome 13)|Oryza sativa.jpg}} | ||
| + | {{Main Plant|Panicum hallii (Phytozome 13)|Panicum hallii.jpg}} | ||
| + | {{Main Plant|Panicum virgatum (Phytozome 13)|Panicum virgatum.jpg}} | ||
| + | {{Main Plant|Papaver somniferum (Ensembl Plants 51)|Unknown.png}} | ||
| + | {{Main Plant|Pistacia vera (Ensembl Plants 51)|Unknown.png}} | ||
| + | {{Main Plant|Poncirus trifoliata (Phytozome 13)|Unknown.png}} | ||
| + | {{Main Plant|Porphyra umbilicalis (Phytozome 13)|Unknown.png}} | ||
| + | {{Main Plant|Prunus avium (Ensembl Plants 51)|Unknown.png}} | ||
| + | {{Main Plant|Prunus dulcis (Ensembl Plants 51)|Unknown.png}} | ||
| + | {{Main Plant|Quercus lobata (Ensembl Plants 51)|Unknown.png}} | ||
| + | {{Main Plant|Rosa chinensis (Ensembl Plants 51)|Unknown.png}} | ||
| + | {{Main Plant|Saccharum spontaneum (Ensembl Plants 51)|Unknown.png}} | ||
| + | {{Main Plant|Salix purpurea (Phytozome 13)|Salix purpurea.jpg}} | ||
| + | {{Main Plant|Sesamum indicum (Ensembl Plants 51)|Unknown.png}} | ||
| + | {{Main Plant|Setaria viridis (Phytozome 13)|Unknown.png}} | ||
| + | {{Main Plant|Solanum lycopersicum (Phytozome 13)|Solanum lycopersicum.jpg}} | ||
| + | {{Main Plant|Solanum tuberosum (Phytozome 13)|Solanum tuberosum.jpg}} | ||
| + | {{Main Plant|Sorghum bicolor (Phytozome 13)|Sorghum bicolor.jpg}} | ||
| + | {{Main Plant|Trifolium pratense (Phytozome 13)|Unknown.png}} | ||
| + | {{Main Plant|Triticum aestivum (Ensembl Plants 51)|Triticum aestivum.jpg}} | ||
| + | {{Main Plant|Triticum dicoccoides (Ensembl Plants 51)|Unknown.png}} | ||
| + | {{Main Plant|Triticum spelta (Ensembl Plants 51)|Unknown.png}} | ||
| + | {{Main Plant|Triticum turgidum (Ensembl Plants 51)|Unknown.png}} | ||
| + | {{Main Plant|Triticum urartu (Ensembl Plants 51)|Unknown.png}} | ||
| + | {{Main Plant|Vigna angularis (Ensembl Plants 51)|Unknown.png}} | ||
| + | {{Main Plant|Vigna radiata (Ensembl Plants 51)|Unknown.png}} | ||
| + | {{Main Plant|Vigna unguiculata (Phytozome 13)|Unknown.png}} | ||
| + | {{Main Plant|Vitis vinifera (Phytozome 13)|Vitis vinifera.jpg}} | ||
| + | {{Main Plant|Zea mays (Ensembl Plants 51)|Zea mays.jpg}} | ||
| + | {{Main Plant|Zea mays (Phytozome 13)|Zea mays.jpg}} | ||
| + | |||
| + | </div> | ||
| + | <div id="main-info" class="all-width"> | ||
| + | <div class="cite"> | ||
| + | Di Marsico, M., Paytuvi Gallart, A., Sanseverino, W., & Aiese Cigliano, R. (2021). GreeNC 2.0: a comprehensive database of plant long non-coding RNAs. Nucleic acids research, gkab1014. Advance online publication. [https://doi.org/10.1093/nar/gkab1014 https://doi.org/10.1093/nar/gkab1014] | ||
| + | </div> | ||
| + | |||
| + | <div class="cite" style="margin-top:5px;background-color:#FCF3CF;font-size:1.2em;text-align:center"> | ||
| + | If you want to access to the previous GreeNC database (v1.12), please click [http://greenc.sequentiabiotech.com/wiki/Main_Page here]. | ||
| + | </div> | ||
| + | |||
| + | <div class="left"><div class="justify"> | ||
| + | <p>Long non-coding RNAs (lncRNAs) are functional non-translated molecules longer than 200 nucleotides with diverse roles, such as chromatin modifications, transcriptional regulation, and conformational changes in proteins. The Green Non-Coding Database (GreeNC) is a repository of lncRNAs annotated in plants and algae. By using the same pipeline to annotate lncRNAs and organizing them in a central database we aim to provide a tool for the scientific community that can boost the research on this class of transcripts. The GreeNC database provides information about sequence, genomic coordinates, coding potential and folding energy for all the identified lncRNAs.</p> | ||
| + | </div> | ||
| + | |||
| + | <hr> | ||
| + | |||
| + | <div class="infobox" style="width:100%"> | ||
| + | <!--{{#ifanon:<center>[[Special:Login|Create an account]] in order to download contents.</center>|}}--> | ||
| + | <div class="pics">[[File:blast.png|link=BLAST]]</div> | ||
| + | <div class="pics">[[File:advanced-search.png|link=Search]]</div> | ||
| + | <div class="pics">[[File:faq.png|link=Help]]</div> | ||
| + | <div class="pics">[[File:contact.png|link=email]]</div> | ||
| + | <div class="pics">[[File:downloads.png|link=Downloads]]</div> | ||
| + | </div> | ||
| + | |||
| + | <!--<div style="clear:both;font-size:0.8em;padding-top:10px" class="justify"> | ||
| + | <p>You can <strong>download</strong> the lncRNA sequences from each species page, from the "Advanced search" section, or you can download all lncRNAs clicking [http://greenc.sequentiabiotech.com/api2/downloadalllncrnas here].</p> | ||
| + | </div>--> | ||
| + | |||
| + | </div> | ||
| + | |||
| + | <div class="right"> | ||
| + | |||
| + | ==== Latest news ==== | ||
| + | {{#ask:[[Category:News]] | ||
| + | |?Has Title | ||
| + | |?Publication_date= | ||
| + | |?Post_Tag= | ||
| + | |?Has Body= | ||
| + | |?Has_Summary_Length= | ||
| + | |?Has Author= | ||
| + | |link=none | ||
| + | |sort=Publication_date | ||
| + | |format=template | ||
| + | |template=Front_News | ||
| + | |order=desc | ||
| + | |limit=2 | ||
| + | |searchlabel= <br />All the news … | ||
| + | }} | ||
| + | |||
| + | </div> | ||
| + | </div> | ||
| + | |||
| + | <div id="main-stats" class="all-width"> | ||
| + | |||
| + | ==== Statistics ==== | ||
| + | <div class="justify" style="font-size:0.8em"> | ||
| + | In the following table the genome and gene annotation version is displayed together with the number of genes transcribing lncRNAs and the total number of lncRNAs for each species.The high-confidence lncRNAs are those lncRNAs without hits in SwissProt, described as non-coding by the CPC and considered non-precursors of miRNA. Otherwise, the lncRNAs are classified as low-confidence. The column "Repetitive elements" shows the number of lncRNAs having repetitive elements predicted by RepeatMasker, while the column "miRNA precursors" shows the number of lncRNAs identified as putative precursors of miRNAs. | ||
| + | </div> | ||
| + | |||
{{#BioDB:stats|null}} | {{#BioDB:stats|null}} | ||
| − | {| class="wikitable" style="text-align: center; font-size:80 | + | {| class="wikitable sortable" style="text-align: center; font-size:80%" |
| − | ! | + | ! Species |
| + | ! Assembly | ||
! Gene number | ! Gene number | ||
| − | ! | + | ! lncRNAs |
! High confidence | ! High confidence | ||
| − | ! | + | ! Low confidence |
| + | ! Repetitive elements | ||
! miRNA precursors | ! miRNA precursors | ||
{{#BioDB_table:<nowiki /> | {{#BioDB_table:<nowiki /> | ||
{{!}}- | {{!}}- | ||
| − | {{!}} {{{stats.taxon_id}}} | + | {{!}} [[Species:{{{stats.taxon_id}}}|''{{{stats.taxon_id}}}'']] |
| + | {{!}} {{{stats.assembly}}} | ||
{{!}} {{{stats.genes}}} | {{!}} {{{stats.genes}}} | ||
{{!}} {{{stats.transcripts}}} | {{!}} {{{stats.transcripts}}} | ||
{{!}} {{{stats.high_confidence}}} | {{!}} {{{stats.high_confidence}}} | ||
| + | {{!}} {{{stats.low_confidence}}} | ||
{{!}} {{{stats.transposons}}} | {{!}} {{{stats.transposons}}} | ||
{{!}} {{{stats.mirna}}} | {{!}} {{{stats.mirna}}} | ||
}} | }} | ||
|} | |} | ||
| − | |||
</div> | </div> | ||
| − | + | {{#BioDB_clear:}} | |
Latest revision as of 08:31, 23 September 2024
Due to high server resource usage by bots, the database is now restricted to registered users only. Login here and sign up here.
A Wiki-database of plant lncRNAs (v2.0)
Di Marsico, M., Paytuvi Gallart, A., Sanseverino, W., & Aiese Cigliano, R. (2021). GreeNC 2.0: a comprehensive database of plant long non-coding RNAs. Nucleic acids research, gkab1014. Advance online publication. https://doi.org/10.1093/nar/gkab1014
If you want to access to the previous GreeNC database (v1.12), please click here.
Long non-coding RNAs (lncRNAs) are functional non-translated molecules longer than 200 nucleotides with diverse roles, such as chromatin modifications, transcriptional regulation, and conformational changes in proteins. The Green Non-Coding Database (GreeNC) is a repository of lncRNAs annotated in plants and algae. By using the same pipeline to annotate lncRNAs and organizing them in a central database we aim to provide a tool for the scientific community that can boost the research on this class of transcripts. The GreeNC database provides information about sequence, genomic coordinates, coding potential and folding energy for all the identified lncRNAs.
Latest news
Published on 21 November 2018 by Apaytuvi.
Welcome to the Green Non-Coding (GreeNC) database! GreeNC is the major resource of plant lncRNAs tod… Read more.
Published on 19 September 2016 by Apaytuvi.
A recent minor update has been incorporated. Change-log:
- lncRNAs containing undefined nucle… Read more.
All the news …
Statistics
In the following table the genome and gene annotation version is displayed together with the number of genes transcribing lncRNAs and the total number of lncRNAs for each species.The high-confidence lncRNAs are those lncRNAs without hits in SwissProt, described as non-coding by the CPC and considered non-precursors of miRNA. Otherwise, the lncRNAs are classified as low-confidence. The column "Repetitive elements" shows the number of lncRNAs having repetitive elements predicted by RepeatMasker, while the column "miRNA precursors" shows the number of lncRNAs identified as putative precursors of miRNAs.