Difference between revisions of "Main Page"

Latest revision as of 08:58, 23 September 2024

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A Wiki-database of plant lncRNAs (v1.12)

Amborella trichopoda

Ananas comosus

Arabidopsis lyrata

Arabidopsis thaliana

Brachypodium distachyon

Capsella grandiflora

Capsella rubella

Carica papaya

Chlamydomonas reinhardtii

Citrus clementina

Citrus sinensis

Coccomyxa subellipsoidea C-169

Micromonas pusilla CCMP1545

Micromonas pusilla RCC299

Mimulus guttatus

Musa acuminata

Oryza sativa Japonica Group

Ostreococcus lucimarinus

Phaseolus vulgaris

Physcomitrella patens

Populus trichocarpa

Prunus persica

Ricinus communis

Selaginella moellendorffii

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.

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

@@ Line 1: / Line 1: @@
+<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 database of plants lncRNAs ====
+==== A Wiki-database of plant lncRNAs (v1.12) ====
 <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">
-{{Main Plant|Amborella trichopoda v1.0|Amborella trichopoda v1.0.jpg}}
+{{Main Plant|Amborella trichopoda|Amborella trichopoda.jpg}}
-{{Main Plant|Aquilegia coerulea v1.1|Aquilegia coerulea v1.1.jpg}}
+{{Main Plant|Ananas comosus|Ananas comosus.jpg}}
-{{Main Plant|Arabidopsis halleri v1.1|Arabidopsis halleri v1.1.jpg}}
+<!--{{Main Plant|Aquilegia coerulea|Aquilegia coerulea.jpg}}-->
-{{Main Plant|Arabidopsis lyrata v1.0|Arabidopsis lyrata v1.0.jpg}}
+<!--{{Main Plant|Arabidopsis halleri|Arabidopsis halleri.jpg}}-->
-{{Main Plant|Arabidopsis thaliana TAIR10|Arabidopsis thaliana.jpg}}
+{{Main Plant|Arabidopsis lyrata|Arabidopsis lyrata.jpg}}
-{{Main Plant|Boechera stricta v1.2|Boechera stricta v1.2.jpg}}
+{{Main Plant|Arabidopsis thaliana|Arabidopsis thaliana.jpg}}
-{{Main Plant|Brachypodium distachyon v2.1|Brachypodium distachyon v2.1.jpg}}
+<!--{{Main Plant|Boechera stricta|Boechera stricta.jpg}}-->
-{{Main Plant|Brassica rapa FPsc v1.3|Brassica rapa.jpg}}
+{{Main Plant|Brachypodium distachyon|Brachypodium distachyon.jpg}}
-{{Main Plant|Capsella grandiflora v1.1|Capsella grandiflora v1.1.jpg}}
+<!--{{Main Plant|Brassica rapa|Brassica rapa.jpg}}-->
-{{Main Plant|Capsella rubella v1.0|Capsella rubella v1.0.jpg}}
+{{Main Plant|Capsella grandiflora|Capsella grandiflora.jpg}}
-{{Main Plant|Carica papaya ASGPBv0.4|Carica papaya ASGPBv0.4.jpg}}
+{{Main Plant|Capsella rubella|Capsella rubella.jpg}}
-{{Main Plant|Chlamydomonas reinhardtii v5.5|Chlamydomonas reinhardtii.jpg}}
+{{Main Plant|Carica papaya|Carica papaya.jpg}}
-{{Main Plant|Citrus clementina v1.0|Citrus clementina v1.0.jpg}}
+{{Main Plant|Chlamydomonas reinhardtii|Chlamydomonas reinhardtii.jpg}}
-{{Main Plant|Citrus sinensis v1.1|Citrus sinensis v1.1.jpg}}
+{{Main Plant|Citrus clementina|Citrus clementina.jpg}}
-{{Main Plant|Coccomyxa subellipsoidea C-169 v2.0|Coccomyxa subellipsoidea C-169 v2.0.jpg}}
+{{Main Plant|Citrus sinensis|Citrus sinensis.jpg}}
-{{Main Plant|Cucumis sativus v1.0|Cucumis sativus.jpg}}
+{{Main Plant|Coccomyxa subellipsoidea C-169|Coccomyxa subellipsoidea C-169.jpg}}
-{{Main Plant|Eucalyptus grandis v1.1|Eucalyptus grandis v1.1.jpg}}
+{{Main Plant|Cucumis sativus|Cucumis sativus.jpg}}
-{{Main Plant|Eucalyptus grandis v2.0|Eucalyptus grandis v2.0.jpg}}
+{{Main Plant|Eucalyptus grandis|Eucalyptus grandis.jpg}}
-{{Main Plant|Eutrema salsugineum v1.0|Eutrema salsugineum v1.0.jpg}}
+{{Main Plant|Eutrema salsugineum|Eutrema salsugineum.jpg}}
-{{Main Plant|Fragaria vesca v1.1|Fragaria vesca v1.1.jpg}}
+{{Main Plant|Fragaria vesca|Fragaria vesca.jpg}}
-{{Main Plant|Glycine max Wm82.a2.v1|Glycine max.jpg}}
+{{Main Plant|Glycine max|Glycine max.jpg}}
-{{Main Plant|Gossypium raimondii v2.1|Gossypium raimondii v2.1.jpg}}
+{{Main Plant|Gossypium raimondii|Gossypium raimondii.jpg}}
-{{Main Plant|Kalanchoe laxiflora v1.0|Kalanchoe laxiflora v1.0.jpg}}
+<!--{{Main Plant|Kalanchoe laxiflora|Kalanchoe laxiflora.jpg}}-->
-{{Main Plant|Linum usitatissimum v1.0|Linum usitatissimum v1.0.jpg}}
+{{Main Plant|Linum usitatissimum|Linum usitatissimum.jpg}}
-{{Main Plant|Malus domestica v1.0|Malus domestica v1.0.jpg}}
+{{Main Plant|Malus domestica|Malus domestica.jpg}}
-{{Main Plant|Manihot esculenta v4.1|Manihot esculenta v4.1.jpg}}
+{{Main Plant|Manihot esculenta|Manihot esculenta.jpg}}
-{{Main Plant|Manihot esculenta v6.1|Manihot esculenta v6.1.jpg}}
+{{Main Plant|Medicago truncatula|Medicago truncatula.jpg}}
-{{Main Plant|Medicago truncatula Mt4.0v1|Medicago truncatula Mt4.0v1.jpg}}
+{{Main Plant|Micromonas pusilla CCMP1545|Micromonas pusilla CCMP1545.jpg}}
-{{Main Plant|Micromonas pusilla CCMP1545 v3.0|Micromonas pusilla CCMP1545 v3.0.jpg}}
+{{Main Plant|Micromonas pusilla RCC299|Micromonas pusilla RCC299.jpg}}
-{{Main Plant|Micromonas sp. RCC299 v3.0|Micromonas sp. RCC299 v3.0.jpg}}
+{{Main Plant|Mimulus guttatus|Mimulus guttatus.jpg}}
-{{Main Plant|Mimulus guttatus v2.0|Mimulus guttatus v2.0.jpg}}
+{{Main Plant|Musa acuminata|Musa acuminata.jpg}}
-{{Main Plant|Musa acuminata v1|Musa acuminata v1.jpg}}
+{{Main Plant|Oryza sativa Japonica Group|Oryza sativa Japonica Group.jpg}}
-{{Main Plant|Oryza sativa v7.0|Oryza sativa Japonica Group.jpg}}
+{{Main Plant|Ostreococcus lucimarinus|Ostreococcus lucimarinus.jpg}}
-{{Main Plant|Ostreococcus lucimarinus v2.0|Ostreococcus lucimarinus v2.0.jpg}}
+<!--{{Main Plant|Panicum hallii|Panicum hallii.jpg}}-->
-{{Main Plant|Panicum hallii v2.0|Panicum hallii v2.0.jpg}}
+<!--{{Main Plant|Panicum virgatum|Panicum virgatum.jpg}}-->
-{{Main Plant|Panicum virgatum v1.1|Panicum virgatum v1.1.jpg}}
+{{Main Plant|Phaseolus vulgaris|Phaseolus vulgaris.jpg}}
-{{Main Plant|Phaseolus vulgaris v1.0|Phaseolus vulgaris v1.0.jpg}}
+{{Main Plant|Physcomitrella patens|Physcomitrella patens.jpg}}
-{{Main Plant|Physcomitrella patens v3.1|Physcomitrella patens v3.1.jpg}}
+{{Main Plant|Populus trichocarpa|Populus trichocarpa.jpg}}
-{{Main Plant|Populus trichocarpa v3.0|Populus trichocarpa v3.0.jpg}}
+{{Main Plant|Prunus persica|Prunus persica.jpg}}
-{{Main Plant|Prunus persica v2.1|Prunus persica.jpg}}
+{{Main Plant|Ricinus communis|Ricinus communis.jpg}}
-{{Main Plant|Ricinus communis v0.1|Ricinus communis v0.1.jpg}}
+<!--{{Main Plant|Salix purpurea|Salix purpurea.jpg}}-->
-{{Main Plant|Salix purpurea v1.0|Salix purpurea v1.0.jpg}}
+{{Main Plant|Selaginella moellendorffii|Selaginella moellendorffii.jpg}}
-{{Main Plant|Selaginella moellendorffii v1.0|Selaginella moellendorffii v1.0.jpg}}
+{{Main Plant|Setaria italica|Setaria italica.jpg}}
-{{Main Plant|Setaria italica v2.1|Setaria italica v2.1.jpg}}
+{{Main Plant|Solanum lycopersicum|Solanum lycopersicum.jpg}}
-{{Main Plant|Solanum lycopersicum iTAG2.3|Solanum lycopersicum.jpg}}
+{{Main Plant|Solanum tuberosum|Solanum tuberosum.jpg}}
-{{Main Plant|Solanum tuberosum v3.4|Solanum tuberosum v3.4.jpg}}
+{{Main Plant|Sorghum bicolor|Sorghum bicolor.jpg}}
-{{Main Plant|Sorghum bicolor v2.1|Sorghum bicolor v2.1.jpg}}
+{{Main Plant|Spirodela polyrhiza|Spirodela polyrhiza.jpg}}
-{{Main Plant|Spirodela polyrhiza v2|Spirodela polyrhiza v2.jpg}}
+{{Main Plant|Theobroma cacao|Theobroma cacao.jpg}}
-{{Main Plant|Theobroma cacao v1.1|Theobroma cacao v1.1.jpg}}
+{{Main Plant|Triticum aestivum|Triticum aestivum.jpg}}
-{{Main Plant|Triticum aestivum v2.2|Triticum aestivum v2.2.jpg}}
+{{Main Plant|Vitis vinifera|Vitis vinifera.jpg}}
-{{Main Plant|Vitis vinifera Genoscope.12X|Vitis vinifera.jpg}}
+{{Main Plant|Volvox carteri|Volvox carteri.jpg}}
-{{Main Plant|Volvox carteri v2.0|Volvox carteri v2.0.jpg}}
+{{Main Plant|Zea mays|Zea mays.jpg}}
-{{Main Plant|Zea mays 6a|Zea mays.jpg}}
+{{Main Plant|Zostera marina|Zostera marina.jpg}}
 </div>
 <div id="main-info" class="all-width">
-<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 database of plant lncRNAs that provide information about sequence, expression levels, genomic context, and ontology of lncRNAs in plants.</p></div>
+<div class="cite">
+''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.
+[http://dx.doi.org/10.1093/nar/gkv1215 doi:10.1093/nar/gkv1215]
+</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">
-{{#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=http://greenc.sciencedesigners.com/wiki/BLAST]]</div>
+<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=http://greenc.sciencedesigners.com/wiki/Help]]</div>
+<div class="pics">[[File:faq.png|link=Help]]</div>
-<div class="pics">[[File:contact.png|link=mailto:greenc@sequentiabiotech.com]]</div>
+<div class="pics">[[File:contact.png|link=email]]</div>
 </div>
 </div>
 <div class="right">
-==== Last news  ====
+==== Latest news  ====
 {{#ask:[[Category:News]]
 |?Has Title
@@ Line 94: / Line 104: @@
 <div id="main-stats" class="all-width">
 ==== Statistics ====
 {{#BioDB:stats|null}}
 {| class="wikitable sortable" style="text-align: center; font-size:80%"
 ! Species
+! Assembly
 ! Gene number
-! Transcript number
+! lncRNAs
 ! High confidence
+! Low confidence
 ! Repetitive elements
 ! miRNA precursors
 {{#BioDB_table:<nowiki />
 {{!}}-
-{{!}} ''<span class="getAPI" data-api="http://prgdb.crg.eu/api" data-prefix="Species" data-link="true" data-query="taxon" data-code="{{{stats.taxon_id}}}" data-field="scientific_name" data-print="scientific_name"></span>''
+{{!}} [[Species:{{{stats.taxon_id}}}|''{{{stats.taxon_id}}}'']]
+{{!}} {{{stats.assembly}}}
 {{!}} {{{stats.genes}}}
 {{!}} {{{stats.transcripts}}}
 {{!}} {{{stats.high_confidence}}}
+{{!}} {{{stats.low_confidence}}}
 {{!}} {{{stats.transposons}}}
 {{!}} {{{stats.mirna}}}