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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__ | {{DISPLAYTITLE:GreeNC}}__NOTOC__ | ||
==== A Wiki-database of plant lncRNAs (v2.0) ==== | ==== 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> | <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"> | + | <div id="main-plants" class="all-width" style="font-size:0.9em"> |
| − | {{Main Plant|Actinidia chinensis | + | |
| − | {{Main Plant|Aegilops tauschii | + | {{Main Plant|Actinidia chinensis (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Amaranthus hypocondriacus | + | {{Main Plant|Aegilops tauschii (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Aquilegia coerulea | + | {{Main Plant|Amaranthus hypocondriacus (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Arabidopsis halleri | + | {{Main Plant|Aquilegia coerulea (Phytozome 13)|Aquilegia coerulea.jpg}} |
| − | {{Main Plant|Arabidopsis lyrata | + | {{Main Plant|Arabidopsis halleri (Ensembl Plants 51)|Arabidopsis halleri.jpg}} |
| − | {{Main Plant|Arabidopsis thaliana | + | {{Main Plant|Arabidopsis lyrata (Phytozome 13)|Arabidopsis lyrata.jpg}} |
| − | {{Main Plant|Arabis alpina | + | {{Main Plant|Arabidopsis thaliana (Phytozome 13)|Arabidopsis thaliana.jpg}} |
| − | {{Main Plant|Beta vulgaris | + | {{Main Plant|Arabis alpina (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Boechera stricta | + | {{Main Plant|Beta vulgaris (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Brachypodium stacei | + | {{Main Plant|Boechera stricta (Phytozome 13)|Boechera stricta.jpg}} |
| − | {{Main Plant|Brassica napus | + | {{Main Plant|Brachypodium stacei (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Brassica oleracea capitata | + | {{Main Plant|Brassica napus (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Brassica rapa | + | {{Main Plant|Brassica oleracea capitata (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Camelina sativa | + | {{Main Plant|Brassica rapa (Phytozome 13)|Brassica rapa.jpg}} |
| − | {{Main Plant|Capsella rubella | + | {{Main Plant|Camelina sativa (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Capsicum annuum | + | {{Main Plant|Capsella rubella (Phytozome 13)|Capsella rubella.jpg}} |
| − | {{Main Plant|Chara braunii | + | {{Main Plant|Capsicum annuum (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Chenopodium quinoa | + | {{Main Plant|Chara braunii (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Chondrus crispus | + | {{Main Plant|Chenopodium quinoa (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Chromochloris zofingiensis | + | {{Main Plant|Chondrus crispus (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Cicer arietinum | + | {{Main Plant|Chromochloris zofingiensis (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Cinnamomum kanehirae | + | {{Main Plant|Cicer arietinum (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Citrullus lanatus | + | {{Main Plant|Cinnamomum kanehirae (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Coffea canephora | + | {{Main Plant|Citrullus lanatus (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Corchorus capsularis | + | {{Main Plant|Coffea canephora (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Cucumis melo | + | {{Main Plant|Corchorus capsularis (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Cucumis sativus | + | {{Main Plant|Cucumis melo (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Cyanidioschyzon merolae | + | {{Main Plant|Cucumis sativus (Ensembl Plants 51)|Cucumis sativus.jpg}} |
| − | {{Main Plant|Cynara cardunculus | + | {{Main Plant|Cyanidioschyzon merolae (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Dioscorea alata | + | {{Main Plant|Cynara cardunculus (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Eragrostis curvula | + | {{Main Plant|Dioscorea alata (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Eragrostis tef | + | {{Main Plant|Eragrostis curvula (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Glycine max | + | {{Main Plant|Eragrostis tef (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Gossypium barbadense | + | {{Main Plant|Glycine max (Phytozome 13)|Glycine max.jpg}} |
| − | {{Main Plant|Gossypium darwinii | + | {{Main Plant|Gossypium barbadense (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Gossypium hirsutum | + | {{Main Plant|Gossypium darwinii (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Gossypium mustelinum | + | {{Main Plant|Gossypium hirsutum (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Gossypium raimondii | + | {{Main Plant|Gossypium mustelinum (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Gossypium tomentosum | + | {{Main Plant|Gossypium raimondii (Ensembl Plants 51)|Gossypium raimondii.jpg}} |
| − | {{Main Plant|Helianthus annuus | + | {{Main Plant|Gossypium tomentosum (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Hordeum vulgare | + | {{Main Plant|Helianthus annuus (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Juglans regia | + | {{Main Plant|Hordeum vulgare (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Kalanchoe fedtschenkoi | + | {{Main Plant|Juglans regia (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Lactuca sativa | + | {{Main Plant|Kalanchoe fedtschenkoi (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Leersia perrieri | + | {{Main Plant|Lactuca sativa (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Lupinus albus | + | {{Main Plant|Leersia perrieri (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Lupinus angustifolius | + | {{Main Plant|Lupinus albus (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Manihot esculenta | + | {{Main Plant|Lupinus angustifolius (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Marchantia polymorpha | + | {{Main Plant|Manihot esculenta (Phytozome 13)|Manihot esculenta.jpg}} |
| − | {{Main Plant|Medicago truncatula | + | {{Main Plant|Marchantia polymorpha (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Musa acuminata | + | {{Main Plant|Medicago truncatula (Ensembl Plants 51)|Medicago truncatula.jpg}} |
| − | {{Main Plant|Nicotiana attenuata | + | {{Main Plant|Musa acuminata (Ensembl Plants 51)|Musa acuminata.jpg}} |
| − | {{Main Plant|Nymphaea colorata | + | {{Main Plant|Nicotiana attenuata (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Olea europaea | + | {{Main Plant|Nymphaea colorata (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Oropetium thomaeum | + | {{Main Plant|Olea europaea (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Oryza barthii | + | {{Main Plant|Oropetium thomaeum (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Oryza brachyantha | + | {{Main Plant|Oryza barthii (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Oryza glaberrima | + | {{Main Plant|Oryza brachyantha (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Oryza glumipatula | + | {{Main Plant|Oryza glaberrima (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Oryza longistaminata | + | {{Main Plant|Oryza glumipatula (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Oryza meridionalis | + | {{Main Plant|Oryza longistaminata (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Oryza nivara | + | {{Main Plant|Oryza meridionalis (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Oryza punctata | + | {{Main Plant|Oryza nivara (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Oryza rufipogon | + | {{Main Plant|Oryza punctata (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Oryza sativa | + | {{Main Plant|Oryza rufipogon (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Panicum hallii | + | {{Main Plant|Oryza sativa (Phytozome 13)|Oryza sativa.jpg}} |
| − | {{Main Plant|Panicum virgatum | + | {{Main Plant|Panicum hallii (Phytozome 13)|Panicum hallii.jpg}} |
| − | {{Main Plant|Papaver somniferum | + | {{Main Plant|Panicum virgatum (Phytozome 13)|Panicum virgatum.jpg}} |
| − | {{Main Plant|Pistacia vera | + | {{Main Plant|Papaver somniferum (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Poncirus trifoliata | + | {{Main Plant|Pistacia vera (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Porphyra umbilicalis | + | {{Main Plant|Poncirus trifoliata (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Prunus avium | + | {{Main Plant|Porphyra umbilicalis (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Prunus dulcis | + | {{Main Plant|Prunus avium (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Quercus lobata | + | {{Main Plant|Prunus dulcis (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Rosa chinensis | + | {{Main Plant|Quercus lobata (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Saccharum spontaneum | + | {{Main Plant|Rosa chinensis (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Salix purpurea | + | {{Main Plant|Saccharum spontaneum (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Sesamum indicum | + | {{Main Plant|Salix purpurea (Phytozome 13)|Salix purpurea.jpg}} |
| − | {{Main Plant|Setaria viridis | + | {{Main Plant|Sesamum indicum (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Solanum lycopersicum | + | {{Main Plant|Setaria viridis (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Solanum tuberosum | + | {{Main Plant|Solanum lycopersicum (Phytozome 13)|Solanum lycopersicum.jpg}} |
| − | {{Main Plant|Sorghum bicolor | + | {{Main Plant|Solanum tuberosum (Phytozome 13)|Solanum tuberosum.jpg}} |
| − | {{Main Plant|Trifolium pratense | + | {{Main Plant|Sorghum bicolor (Phytozome 13)|Sorghum bicolor.jpg}} |
| − | {{Main Plant|Triticum aestivum | + | {{Main Plant|Trifolium pratense (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Triticum dicoccoides | + | {{Main Plant|Triticum aestivum (Ensembl Plants 51)|Triticum aestivum.jpg}} |
| − | {{Main Plant|Triticum spelta | + | {{Main Plant|Triticum dicoccoides (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Triticum turgidum | + | {{Main Plant|Triticum spelta (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Triticum urartu | + | {{Main Plant|Triticum turgidum (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Vigna angularis | + | {{Main Plant|Triticum urartu (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Vigna radiata | + | {{Main Plant|Vigna angularis (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Vigna unguiculata | + | {{Main Plant|Vigna radiata (Ensembl Plants 51)|Unknown.png}} |
| − | {{Main Plant|Vitis vinifera | + | {{Main Plant|Vigna unguiculata (Phytozome 13)|Unknown.png}} |
| − | {{Main Plant|Zea mays | + | {{Main Plant|Vitis vinifera (Phytozome 13)|Vitis vinifera.jpg}} |
| − | {{Main Plant|Zea mays | + | {{Main Plant|Zea mays (Ensembl Plants 51)|Zea mays.jpg}} |
| + | {{Main Plant|Zea mays (Phytozome 13)|Zea mays.jpg}} | ||
| + | |||
</div> | </div> | ||
<div id="main-info" class="all-width"> | <div id="main-info" class="all-width"> | ||
<div class="cite"> | <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] | |
| − | + | ||
| − | Nucleic | + | |
| − | [ | + | |
</div> | </div> | ||
| Line 111: | Line 114: | ||
</div> | </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> | + | <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> | <hr> | ||
| − | <div class="infobox"> | + | <div class="infobox" style="width:100%"> |
<!--{{#ifanon:<center>[[Special:Login|Create an account]] in order to download contents.</center>|}}--> | <!--{{#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:blast.png|link=BLAST]]</div> | ||
| Line 121: | Line 126: | ||
<div class="pics">[[File:faq.png|link=Help]]</div> | <div class="pics">[[File:faq.png|link=Help]]</div> | ||
<div class="pics">[[File:contact.png|link=email]]</div> | <div class="pics">[[File:contact.png|link=email]]</div> | ||
| + | <div class="pics">[[File:downloads.png|link=Downloads]]</div> | ||
</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> | ||
| Line 149: | Line 160: | ||
==== Statistics ==== | ==== 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 sortable" style="text-align: center; font-size:80%" | {| class="wikitable sortable" style="text-align: center; font-size:80%" | ||
Due to high server resource usage by bots, the database is now restricted to registered users only. Login here and sign up here.
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.
All the news …
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.