Difference between revisions of "Main Page"

From GreeNC
 
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{| style="width: 100%" cellpadding="0"
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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">
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! width="790px" style="text-align: left; font-size: 200%;" | Quick start
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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>.
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! style="text-align: left; font-size: 200%;" | Latest news
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</div>
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{{DISPLAYTITLE:GreeNC}}__NOTOC__
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{| class="wikitable floatleft" style="width: 800px; text-align: center; font-size:85%;"
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==== A Wiki-database of plant lncRNAs (v1.12) ====
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! colspan="2" style="font-style:italic" | Arabidopsis thaliana
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<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>
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! colspan="2" style="font-style:italic" | Brassica rapa
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<div id="main-plants" class="all-width">
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! colspan="2" style="font-style:italic" | Chlamydomonas reinhardtii
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{{Main Plant|Amborella trichopoda|Amborella trichopoda.jpg}}
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! colspan="2" style="font-style:italic" | Cucumis sativus
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{{Main Plant|Ananas comosus|Ananas comosus.jpg}}
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! colspan="2" style="font-style:italic" | Glycine max
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<!--{{Main Plant|Aquilegia coerulea|Aquilegia coerulea.jpg}}-->
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|-
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<!--{{Main Plant|Arabidopsis halleri|Arabidopsis halleri.jpg}}-->
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| colspan="2" | [[File:Ath_155.jpg|155px|link=http://andreupaytuvi.esy.es]]
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{{Main Plant|Arabidopsis lyrata|Arabidopsis lyrata.jpg}}
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| colspan="2" | [[File:Bra_155.jpg|155px|link=http://andreupaytuvi.esy.es]]
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{{Main Plant|Arabidopsis thaliana|Arabidopsis thaliana.jpg}}
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| colspan="2" | [[File:Cre_156.jpg|155px|link=http://andreupaytuvi.esy.es]]
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<!--{{Main Plant|Boechera stricta|Boechera stricta.jpg}}-->
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| colspan="2" | [[File:Csa_155.jpg|155px|link=http://andreupaytuvi.esy.es]]
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{{Main Plant|Brachypodium distachyon|Brachypodium distachyon.jpg}}
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| colspan="2" | [[File:Gma_155.jpg|155px|link=http://andreupaytuvi.esy.es]]
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<!--{{Main Plant|Brassica rapa|Brassica rapa.jpg}}-->
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{{Main Plant|Capsella grandiflora|Capsella grandiflora.jpg}}
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| Genes
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{{Main Plant|Capsella rubella|Capsella rubella.jpg}}
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| Transcripts
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{{Main Plant|Carica papaya|Carica papaya.jpg}}
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| Genes
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{{Main Plant|Chlamydomonas reinhardtii|Chlamydomonas reinhardtii.jpg}}
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| Transcripts
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{{Main Plant|Citrus clementina|Citrus clementina.jpg}}
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| Genes
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{{Main Plant|Citrus sinensis|Citrus sinensis.jpg}}
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| Transcripts
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{{Main Plant|Coccomyxa subellipsoidea C-169|Coccomyxa subellipsoidea C-169.jpg}}
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| Genes
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{{Main Plant|Cucumis sativus|Cucumis sativus.jpg}}
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| Transcripts
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{{Main Plant|Eucalyptus grandis|Eucalyptus grandis.jpg}}
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| Genes
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{{Main Plant|Eutrema salsugineum|Eutrema salsugineum.jpg}}
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| Transcripts
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{{Main Plant|Fragaria vesca|Fragaria vesca.jpg}}
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{{Main Plant|Glycine max|Glycine max.jpg}}
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! colspan="2" style="font-style:italic" | Oryzia sativa
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{{Main Plant|Gossypium raimondii|Gossypium raimondii.jpg}}
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! colspan="2" style="font-style:italic" | Prunus persica
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<!--{{Main Plant|Kalanchoe laxiflora|Kalanchoe laxiflora.jpg}}-->
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! colspan="2" style="font-style:italic" | Solanum lycopersicum
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{{Main Plant|Linum usitatissimum|Linum usitatissimum.jpg}}
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! colspan="2" style="font-style:italic" | Vitis vinifera
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{{Main Plant|Malus domestica|Malus domestica.jpg}}
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! colspan="2" style="font-style:italic" | Zea mays
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{{Main Plant|Manihot esculenta|Manihot esculenta.jpg}}
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|-
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{{Main Plant|Medicago truncatula|Medicago truncatula.jpg}}
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| colspan="2" | [[File:Osa_157.jpg|155px|link=http://andreupaytuvi.esy.es]]
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{{Main Plant|Micromonas pusilla CCMP1545|Micromonas pusilla CCMP1545.jpg}}
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| colspan="2" | [[File:Ppe_155.jpg|155px|link=http://andreupaytuvi.esy.es]]
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{{Main Plant|Micromonas pusilla RCC299|Micromonas pusilla RCC299.jpg}}
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| colspan="2" | [[File:Sly_155.jpg|155px|link=http://andreupaytuvi.esy.es]]
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{{Main Plant|Mimulus guttatus|Mimulus guttatus.jpg}}
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| colspan="2" | [[File:Vvi_155.jpg|155px|link=http://andreupaytuvi.esy.es]]
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{{Main Plant|Musa acuminata|Musa acuminata.jpg}}
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| colspan="2" | [[File:Zma_155.jpg|155px|link=http://andreupaytuvi.esy.es]]
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{{Main Plant|Oryza sativa Japonica Group|Oryza sativa Japonica Group.jpg}}
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|-
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{{Main Plant|Ostreococcus lucimarinus|Ostreococcus lucimarinus.jpg}}
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| Genes
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<!--{{Main Plant|Panicum hallii|Panicum hallii.jpg}}-->
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| Transcripts
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<!--{{Main Plant|Panicum virgatum|Panicum virgatum.jpg}}-->
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| Genes
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{{Main Plant|Phaseolus vulgaris|Phaseolus vulgaris.jpg}}
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| Transcripts
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{{Main Plant|Physcomitrella patens|Physcomitrella patens.jpg}}
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| Genes
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{{Main Plant|Populus trichocarpa|Populus trichocarpa.jpg}}
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| Transcripts
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{{Main Plant|Prunus persica|Prunus persica.jpg}}
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| Genes
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{{Main Plant|Ricinus communis|Ricinus communis.jpg}}
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| Transcripts
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<!--{{Main Plant|Salix purpurea|Salix purpurea.jpg}}-->
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| Genes
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{{Main Plant|Selaginella moellendorffii|Selaginella moellendorffii.jpg}}
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| Transcripts
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{{Main Plant|Setaria italica|Setaria italica.jpg}}
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{{Main Plant|Solanum lycopersicum|Solanum lycopersicum.jpg}}
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{{Main Plant|Solanum tuberosum|Solanum tuberosum.jpg}}
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<div style="overflow:auto; border: 2px; height: 285">Aquí aniria la extenció de "latest news" que hi ha al http://prgdb.crg.eu/</div>
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{{Main Plant|Sorghum bicolor|Sorghum bicolor.jpg}}
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|-
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{{Main Plant|Spirodela polyrhiza|Spirodela polyrhiza.jpg}}
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! style="text-align: left; font-size: 200%;" | What is GreeNC?
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{{Main Plant|Theobroma cacao|Theobroma cacao.jpg}}
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! style="text-align: left; font-size: 200%;" | Stats
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{{Main Plant|Triticum aestivum|Triticum aestivum.jpg}}
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{{Main Plant|Vitis vinifera|Vitis vinifera.jpg}}
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{{Main Plant|Volvox carteri|Volvox carteri.jpg}}
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<p align="justify">Long non-coding RNAs (lncRNAs) are non-translated molecules longer than 200 nucleotides that have been extensively studied in mammal genomes. Their roles are diverse, involved in chromatin modifications, transcriptional regulation, and conformational changes in proteins. However, this class of RNAs remains still largely uninvestigated in plants with few exceptions. For instance, IPS1 is a lncRNA expressed upon phosphate starvation and it is believed to counteract the activity of the miR399 on PHO2, which in turn regulates the expression of phosphate transporter genes. In Arabidopsis, the lncRNA COLDAIR was showed to be required to establish and maintain a stable silenced state of FLC by recruiting the histone methylase PRC2, thus affecting flowering time. Finally, in Medicago truncatula, the lncRNA Enod40 was showed to participate in the establishment of symbiotic interactions with soil-bacteria by affecting nodule formation. These findings highlight that lncRNA could be of great interest in plant biology and in breeding as regulating important agronomic traits. In order to deepen our understanding of the role of lncRNAs in plant biology, their comprehensive annotation is mandatory. To achieve this goal, we used a computational approach to annotate lncRNAs from RNA-seq data. Our pipeline let to distinguish lncRNA from protein-coding and other classes of non-coding RNAs, such as rRNA, precursors of miRNAs, etc. We identified thousands of putative lncRNAs using publicly available RNA-seq data in 2 monocotyledons, 7 dicotyledons, and a green algae. The identified sequences will be analyzed in order to assign a putative function and to study their conservation among different taxa. With the aim to facilitate the study of lncRNAs for the plant research community, we present the Green Non-Coding Database (GreeNC) that will provide information about sequence, expression levels, genomic context, ontology and phylogeny of lncRNAs in plants.</p>
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{{Main Plant|Zea mays|Zea mays.jpg}}
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{{Main Plant|Zostera marina|Zostera marina.jpg}}
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<div style="overflow:auto; border: 2px;">
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</div>
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<div id="main-info" class="all-width">
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<div class="cite">
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''Andreu Paytuvi Gallart; Antonio Hermoso Pulido; Irantzu Anzar Martinez de Lagran; Walter Sanseverino; Riccardo Aiese Cigliano''.
 +
'''GREENC: a Wiki-based database of plant lncRNAs'''.
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Nucleic Acids Research 2015.
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[http://dx.doi.org/10.1093/nar/gkv1215 doi:10.1093/nar/gkv1215]
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</div>
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<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>
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<div class="infobox">
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<!--{{#ifanon:<center>[[Special:Login|Create an account]] in order to download contents.</center>|}}-->
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<div class="pics">[[File:blast.png|link=BLAST]]</div>
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<div class="pics">[[File:advanced-search.png|link=Search]]</div>
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<div class="pics">[[File:faq.png|link=Help]]</div>
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<div class="pics">[[File:contact.png|link=email]]</div>
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</div>
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</div>
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<div class="right">
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==== Latest news  ====
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{{#ask:[[Category:News]]
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|?Has Title
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|?Publication_date=
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|?Post_Tag=
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|?Has Body=
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|?Has_Summary_Length=
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|sort=Publication_date
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|format=template
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|template=Front_News
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|order=desc
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|limit=2
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|searchlabel= <br />All the news &hellip;
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}}
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</div>
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</div>
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<div id="main-stats" class="all-width">
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==== Statistics ====
 
{{#BioDB:stats|null}}
 
{{#BioDB:stats|null}}
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{| class="wikitable" style="text-align: center; font-size:80%; width=50%"
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{| class="wikitable sortable" style="text-align: center; font-size:80%"
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! Taxon
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! Species
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! Assembly
 
! Gene number
 
! Gene number
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! Transcript number
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! lncRNAs
 
! High confidence
 
! High confidence
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! Hits against transposons
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! Low confidence
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! Repetitive elements
 
! miRNA precursors
 
! miRNA precursors
 
{{#BioDB_table:<nowiki />
 
{{#BioDB_table:<nowiki />
 
{{!}}-
 
{{!}}-
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{{!}} {{{stats.taxon_id}}}
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{{!}} [[Species:{{{stats.taxon_id}}}|''{{{stats.taxon_id}}}'']]
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{{!}} {{{stats.assembly}}}
 
{{!}} {{{stats.genes}}}
 
{{!}} {{{stats.genes}}}
 
{{!}} {{{stats.transcripts}}}
 
{{!}} {{{stats.transcripts}}}
 
{{!}} {{{stats.high_confidence}}}
 
{{!}} {{{stats.high_confidence}}}
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{{!}} {{{stats.low_confidence}}}
 
{{!}} {{{stats.transposons}}}
 
{{!}} {{{stats.transposons}}}
 
{{!}} {{{stats.mirna}}}
 
{{!}} {{{stats.mirna}}}
 
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{{#BioDB_clear:}}
 
 
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{{#BioDB_clear:}}

Latest revision as of 08:58, 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 (v1.12)

Andreu Paytuvi Gallart; Antonio Hermoso Pulido; Irantzu Anzar Martinez de Lagran; Walter Sanseverino; Riccardo Aiese Cigliano. GREENC: a Wiki-based database of plant lncRNAs. Nucleic Acids Research 2015. doi:10.1093/nar/gkv1215

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.

Blast.png
Advanced-search.png
Faq.png
Contact.png

Latest news

Welcome to GreeNC!
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.
Tags: GreeNC
Minor update 1.12
Published on 19 September 2016 by Apaytuvi.
A recent minor update has been incorporated. Change-log:
  • lncRNAs containing undefined nucle… Read more.
Tags: GreeNC, Minorupdate, Update

All the news …

Statistics

Species Assembly Gene number lncRNAs High confidence Low confidence Repetitive elements miRNA precursors

Amborella_trichopoda v1.0 5698 5698 4156 1542 103 347
Ananas_comosus v3 3376 3376 1674 1702 163 935
Arabidopsis_lyrata v1.0 4363 4363 2622 1741 158 60
Arabidopsis_thaliana TAIR10 2752 3008 1720 1288 1018 63
Brachypodium_distachyon v3.1 4828 5584 3648 1936 870 1024
Capsella_grandiflora v1.1 1338 1394 1013 381 90 27
Capsella_rubella v1.0 1395 1458 1069 389 100 20
Carica_papaya ASGPBv0.4 3986 3987 2439 1548 980 181
Chlamydomonas_reinhardtii v5.5 583 619 135 484 217 450
Citrus_clementina v1.0 2056 2192 1553 639 149 34
Citrus_sinensis v1.1 2344 2562 1788 774 171 42
Coccomyxa_subellipsoidea_C-169 v2.0 668 668 469 199 33 92
Cucumis_sativus v1.0 1817 1929 1390 539 152 32
Eucalyptus_grandis v2.0 4499 4639 3629 1010 204 103
Eutrema_salsugineum v1.0 1588 1669 1238 431 85 25
Fragaria_vesca v1.1 3503 3503 2412 1091 728 133
Glycine_max Wm82.a2.v1 5974 6689 4749 1940 832 133
Gossypium_raimondii v2.1 3520 4216 3037 1179 256 55
Linum_usitatissimum v1.0 2598 2598 1955 643 37 46
Malus_domestica v1.0 4126 4126 2565 1561 688 83
Manihot_esculenta v6.1 3137 3468 2660 808 266 90
Medicago_truncatula Mt4.0v1 9373 9676 5793 3883 2567 286
Micromonas_pusilla_CCMP1545 v3.0 651 651 230 421 19 300
Micromonas_pusilla_RCC299 v3.0 351 351 199 152 6 48
Mimulus_guttatus v2.0 2169 2333 1591 742 186 59
Musa_acuminata v1 4071 4071 2525 1546 170 90
Oryza_sativa_Japonica_Group v7.0 4995 5237 3601 1636 1148 119
Ostreococcus_lucimarinus v2.0 501 501 209 292 9 128
Phaseolus_vulgaris v1.0 1838 1946 1450 496 152 30
Physcomitrella_patens v3.3 6888 9690 8390 1300 907 299
Populus_trichocarpa v3.0 4997 5569 4111 1458 434 124
Prunus_persica v2.1 2803 3301 2216 1085 526 85
Ricinus_communis v0.1 4198 4198 3127 1071 174 215
Selaginella_moellendorffii v1.0 906 906 409 497 28 26
Setaria_italica v2.2 3240 3492 2159 1333 507 669
Solanum_lycopersicum ITAG2.4 3440 3440 2448 992 423 60
Solanum_tuberosum v3.4 5974 6680 2976 3704 2682 184
Sorghum_bicolor v3.1 4624 5305 2682 2623 1737 1057
Spirodela_polyrhiza v2 2111 2111 1536 575 86 174
Theobroma_cacao v1.1 4137 4268 3306 962 461 59
Triticum_aestivum v2.2 23359 38820 21132 17688 5714 1039
Vitis_vinifera Genoscope.12X 2526 2526 1624 902 296 23
Volvox_carteri v2.1 1097 1134 592 542 222 371
Zea_mays 6a 16857 18110 10229 7881 4004 2192
Zostera_marina v2.2 1393 1393 1014 379 55 23
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