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__ | {{DISPLAYTITLE:GreeNC}}__NOTOC__ | ||
| − | ==== A database of | + | ==== 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> | <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"> | ||
| + | {{Main Plant|Amborella trichopoda|Amborella trichopoda.jpg}} | ||
| + | {{Main Plant|Ananas comosus|Ananas comosus.jpg}} | ||
| + | <!--{{Main Plant|Aquilegia coerulea|Aquilegia coerulea.jpg}}--> | ||
| + | <!--{{Main Plant|Arabidopsis halleri|Arabidopsis halleri.jpg}}--> | ||
| + | {{Main Plant|Arabidopsis lyrata|Arabidopsis lyrata.jpg}} | ||
{{Main Plant|Arabidopsis thaliana|Arabidopsis thaliana.jpg}} | {{Main Plant|Arabidopsis thaliana|Arabidopsis thaliana.jpg}} | ||
| − | {{Main Plant|Brassica rapa|Brassica rapa.jpg}} | + | <!--{{Main Plant|Boechera stricta|Boechera stricta.jpg}}--> |
| + | {{Main Plant|Brachypodium distachyon|Brachypodium distachyon.jpg}} | ||
| + | <!--{{Main Plant|Brassica rapa|Brassica rapa.jpg}}--> | ||
| + | {{Main Plant|Capsella grandiflora|Capsella grandiflora.jpg}} | ||
| + | {{Main Plant|Capsella rubella|Capsella rubella.jpg}} | ||
| + | {{Main Plant|Carica papaya|Carica papaya.jpg}} | ||
{{Main Plant|Chlamydomonas reinhardtii|Chlamydomonas reinhardtii.jpg}} | {{Main Plant|Chlamydomonas reinhardtii|Chlamydomonas reinhardtii.jpg}} | ||
| + | {{Main Plant|Citrus clementina|Citrus clementina.jpg}} | ||
| + | {{Main Plant|Citrus sinensis|Citrus sinensis.jpg}} | ||
| + | {{Main Plant|Coccomyxa subellipsoidea C-169|Coccomyxa subellipsoidea C-169.jpg}} | ||
| + | {{Main Plant|Cucumis sativus|Cucumis sativus.jpg}} | ||
| + | {{Main Plant|Eucalyptus grandis|Eucalyptus grandis.jpg}} | ||
| + | {{Main Plant|Eutrema salsugineum|Eutrema salsugineum.jpg}} | ||
| + | {{Main Plant|Fragaria vesca|Fragaria vesca.jpg}} | ||
{{Main Plant|Glycine max|Glycine max.jpg}} | {{Main Plant|Glycine max|Glycine max.jpg}} | ||
| + | {{Main Plant|Gossypium raimondii|Gossypium raimondii.jpg}} | ||
| + | <!--{{Main Plant|Kalanchoe laxiflora|Kalanchoe laxiflora.jpg}}--> | ||
| + | {{Main Plant|Linum usitatissimum|Linum usitatissimum.jpg}} | ||
| + | {{Main Plant|Malus domestica|Malus domestica.jpg}} | ||
| + | {{Main Plant|Manihot esculenta|Manihot esculenta.jpg}} | ||
| + | {{Main Plant|Medicago truncatula|Medicago truncatula.jpg}} | ||
| + | {{Main Plant|Micromonas pusilla CCMP1545|Micromonas pusilla CCMP1545.jpg}} | ||
| + | {{Main Plant|Micromonas pusilla RCC299|Micromonas pusilla RCC299.jpg}} | ||
| + | {{Main Plant|Mimulus guttatus|Mimulus guttatus.jpg}} | ||
| + | {{Main Plant|Musa acuminata|Musa acuminata.jpg}} | ||
{{Main Plant|Oryza sativa Japonica Group|Oryza sativa Japonica Group.jpg}} | {{Main Plant|Oryza sativa Japonica Group|Oryza sativa Japonica Group.jpg}} | ||
| − | {{Main Plant| | + | {{Main Plant|Ostreococcus lucimarinus|Ostreococcus lucimarinus.jpg}} |
| + | <!--{{Main Plant|Panicum hallii|Panicum hallii.jpg}}--> | ||
| + | <!--{{Main Plant|Panicum virgatum|Panicum virgatum.jpg}}--> | ||
| + | {{Main Plant|Phaseolus vulgaris|Phaseolus vulgaris.jpg}} | ||
| + | {{Main Plant|Physcomitrella patens|Physcomitrella patens.jpg}} | ||
| + | {{Main Plant|Populus trichocarpa|Populus trichocarpa.jpg}} | ||
{{Main Plant|Prunus persica|Prunus persica.jpg}} | {{Main Plant|Prunus persica|Prunus persica.jpg}} | ||
| + | {{Main Plant|Ricinus communis|Ricinus communis.jpg}} | ||
| + | <!--{{Main Plant|Salix purpurea|Salix purpurea.jpg}}--> | ||
| + | {{Main Plant|Selaginella moellendorffii|Selaginella moellendorffii.jpg}} | ||
| + | {{Main Plant|Setaria italica|Setaria italica.jpg}} | ||
{{Main Plant|Solanum lycopersicum|Solanum lycopersicum.jpg}} | {{Main Plant|Solanum lycopersicum|Solanum lycopersicum.jpg}} | ||
| + | {{Main Plant|Solanum tuberosum|Solanum tuberosum.jpg}} | ||
| + | {{Main Plant|Sorghum bicolor|Sorghum bicolor.jpg}} | ||
| + | {{Main Plant|Spirodela polyrhiza|Spirodela polyrhiza.jpg}} | ||
| + | {{Main Plant|Theobroma cacao|Theobroma cacao.jpg}} | ||
| + | {{Main Plant|Triticum aestivum|Triticum aestivum.jpg}} | ||
{{Main Plant|Vitis vinifera|Vitis vinifera.jpg}} | {{Main Plant|Vitis vinifera|Vitis vinifera.jpg}} | ||
| + | {{Main Plant|Volvox carteri|Volvox carteri.jpg}} | ||
{{Main Plant|Zea mays|Zea mays.jpg}} | {{Main Plant|Zea mays|Zea mays.jpg}} | ||
| − | + | {{Main Plant|Zostera marina|Zostera marina.jpg}} | |
| − | {{Main Plant| | + | |
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</div> | </div> | ||
| − | |||
<div id="main-info" class="all-width"> | <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 | + | <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> | <hr> | ||
<div class="infobox"> | <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= | + | <div class="pics">[[File:blast.png|link=BLAST]]</div> |
<div class="pics">[[File:advanced-search.png|link=Search]]</div> | <div class="pics">[[File:advanced-search.png|link=Search]]</div> | ||
| − | <div class="pics">[[File:faq.png|link= | + | <div class="pics">[[File:faq.png|link=Help]]</div> |
| − | <div class="pics">[[File:contact.png|link= | + | <div class="pics">[[File:contact.png|link=email]]</div> |
</div> | </div> | ||
</div> | </div> | ||
<div class="right"> | <div class="right"> | ||
| − | ==== | + | |
| + | ==== Latest news ==== | ||
{{#ask:[[Category:News]] | {{#ask:[[Category:News]] | ||
|?Has Title | |?Has Title | ||
| Line 107: | Line 104: | ||
<div id="main-stats" class="all-width"> | <div id="main-stats" class="all-width"> | ||
| + | |||
==== Statistics ==== | ==== Statistics ==== | ||
{{#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%" | ||
! Species | ! Species | ||
| + | ! Assembly | ||
! Gene number | ! Gene number | ||
| − | ! | + | ! lncRNAs |
! High confidence | ! High confidence | ||
| + | ! Low confidence | ||
! Repetitive elements | ! Repetitive elements | ||
! miRNA precursors | ! miRNA precursors | ||
{{#BioDB_table:<nowiki /> | {{#BioDB_table:<nowiki /> | ||
{{!}}- | {{!}}- | ||
| − | {{!}} | + | {{!}} [[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}}} | ||
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.
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
| 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 |