GreeNC

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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.


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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.

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.


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

Actinidia chinensis (Ensembl Plants 51) Red5_PS1_1.69.0 960 961 591 370 146 10
Aegilops tauschii (Ensembl Plants 51) v4 15463 34092 18060 16032 6749 958
Amaranthus hypocondriacus (Phytozome 13) v2.1 2075 2083 1476 607 103 25
Aquilegia coerulea (Phytozome 13) v3.1 4321 4868 3545 1323 447 46
Arabidopsis halleri (Ensembl Plants 51) v2.2 2448 2508 1814 694 251 73
Arabidopsis lyrata (Phytozome 13) v2.1 2593 2676 1831 845 280 38
Arabidopsis thaliana (Phytozome 13) v11 1772 2254 1602 652 271 14
Arabis alpina (Ensembl Plants 51) v4 1857 1919 1304 615 198 22
Beta vulgaris (Phytozome 13) v1.2 4843 4980 3538 1442 574 93
Boechera stricta (Phytozome 13) v1.2 1932 2019 1416 603 192 16
Brachypodium stacei (Phytozome 13) v1.1 2986 3195 2332 863 496 104
Brassica napus (Ensembl Plants 51) v1 9060 9060 6554 2506 526 70
Brassica rapa (Phytozome 13) v1.3 2563 2674 1889 785 209 33
Camelina sativa (Ensembl Plants 51) v1 6099 6200 4072 2128 477 59
Capsella rubella (Phytozome 13) v1.1 1720 1812 1294 518 127 23
Capsicum annuum (Ensembl Plants 51) v2 2124 2124 1154 970 417 6
Chara braunii (Ensembl Plants 51) v1 595 596 269 327 171 31
Chenopodium quinoa (Phytozome 13) v1 1935 1935 1279 656 214 6
Chondrus crispus (Ensembl Plants 51) v2 1465 1465 1293 172 24 31
Chromochloris zofingiensis (Phytozome 13) v5.2.3.2 1457 1457 1186 271 113 11
Cicer arietinum (Phytozome 13) v1 2004 2004 1663 341 82 7
Cinnamomum kanehirae (Phytozome 13) v3 1237 1237 806 431 74 5
Citrullus lanatus (Ensembl Plants 51) v1 2471 2471 2112 359 76 22
Coffea canephora (Ensembl Plants 51) v1 1861 1861 1319 542 149 16
Corchorus capsularis (Ensembl Plants 51) v1 2210 2210 1680 530 80 11
Cucumis melo (Ensembl Plants 51) v4 5001 5001 3921 1080 414 19
Cucumis sativus (Ensembl Plants 51) v2 3459 3459 2465 994 118 22
Cyanidioschyzon merolae (Ensembl Plants 51) v1 141 141 77 64 7 1
Cynara cardunculus (Ensembl Plants 51) v1 1756 1756 1034 722 115 14
Dioscorea alata (Phytozome 13) v2 1531 1728 1016 712 244 15
Eragrostis curvula (Ensembl Plants 51) v1 6042 6042 4712 1330 509 30
Eragrostis tef (Ensembl Plants 51) v1 2437 2437 1701 736 97 14
Glycine max (Phytozome 13) A4v1 5137 5978 4246 1732 625 76
Gossypium barbadense (Phytozome 13) v1.1 7619 8720 6146 2574 731 72
Gossypium darwinii (Phytozome 13) v1.1 8569 9299 6811 2488 639 60
Gossypium hirsutum (Phytozome 13) v2.1 8006 9222 6461 2761 787 81
Gossypium mustelinum (Phytozome 13) v1.1 7953 9233 6467 2766 793 77
Gossypium raimondii (Ensembl Plants 51) v6 3800 4555 3000 1555 461 53
Gossypium tomentosum (Phytozome 13) v1.1 9009 10090 7504 2586 681 77
Helianthus annuus (Phytozome 13) r1.2 8197 8197 5580 2617 795 67
Hordeum vulgare (Phytozome 13) r1 12659 23867 11477 12390 5740 872
Juglans regia (Ensembl Plants 51) v2 662 664 404 260 102 3
Kalanchoe fedtschenkoi (Phytozome 13) v1.1 3206 3568 2428 1140 368 66
Lactuca sativa (Phytozome 13) v5 4949 5395 4095 1300 150 24
Leersia perrieri (Ensembl Plants 51) v1.4 3353 3676 2910 766 297 37
Lupinus albus (Phytozome 13) v1 4869 4869 3179 1690 881 54
Lupinus angustifolius (Ensembl Plants 51) v1 1684 1686 1285 401 102 6
Manihot esculenta (Phytozome 13) v8.1 2304 2655 1875 780 316 55
Marchantia polymorpha (Phytozome 13) v3.1 2896 3196 2665 531 260 47
Medicago truncatula (Ensembl Plants 51) v4 8986 9093 5288 3805 2584 102
Musa acuminata (Ensembl Plants 51) v2 2091 2214 1592 622 127 16
Nicotiana attenuata (Ensembl Plants 51) r2 3851 3851 2361 1490 924 40
Nymphaea colorata (Phytozome 13) v1.2 1763 2055 1356 699 240 26
Olea europaea (Phytozome 13) v1 5516 5516 3140 2376 508 21
Oropetium thomaeum (Phytozome 13) v1 4122 4122 3448 674 54 13
Oryza barthii (Ensembl Plants 51) v1 5339 5600 4461 1139 588 51
Oryza brachyantha (Ensembl Plants 51) v1.4b 4575 4575 3454 1121 422 43
Oryza glaberrima (Ensembl Plants 51) v1 4807 4807 3334 1473 1017 29
Oryza glumipatula (Ensembl Plants 51) v1.5 5402 5837 4536 1301 719 55
Oryza longistaminata (Ensembl Plants 51) v1 3150 3150 2334 816 74 16
Oryza meridionalis (Ensembl Plants 51) v1.3 4389 4818 3496 1322 832 67
Oryza nivara (Ensembl Plants 51) v1 6077 6586 4875 1711 757 64
Oryza punctata (Ensembl Plants 51) v1.2 3850 4114 3233 881 440 39
Oryza rufipogon (Ensembl Plants 51) w1943 6357 6801 5006 1795 837 66
Oryza sativa (Phytozome 13) v7 5395 5724 3788 1936 1435 104
Panicum hallii (Phytozome 13) v3.2 2331 2389 2792 -403 522 37
Panicum virgatum (Phytozome 13) v5.1 9607 10438 7543 2895 1958 90
Papaver somniferum (Ensembl Plants 51) v1 5025 5025 3566 1459 432 50
Pistacia vera (Ensembl Plants 51) v2 1360 1360 952 408 78 7
Poncirus trifoliata (Phytozome 13) v1.3.1 1660 1795 1233 562 174 10
Porphyra umbilicalis (Phytozome 13) v4.1 934 938 799 139 20 3
Prunus avium (Ensembl Plants 51) r1 8673 8673 6035 2638 1530 85
Prunus dulcis (Ensembl Plants 51) v2 4320 4381 2596 1785 1181 109
Quercus lobata (Ensembl Plants 51) v3 1873 1873 1011 862 374 25
Rosa chinensis (Ensembl Plants 51) v2 11326 11326 6919 4407 2478 104
Saccharum spontaneum (Ensembl Plants 51) v1 7488 7488 5252 2236 823 51
Salix purpurea (Phytozome 13) v1 3625 4070 2916 1154 396 48
Sesamum indicum (Ensembl Plants 51) v1 2515 2515 1783 732 101 12
Setaria viridis (Phytozome 13) v2.1 4897 5427 3948 1479 1025 62
Solanum lycopersicum (Phytozome 13) v3.2 4242 4242 2767 1475 471 29
Solanum tuberosum (Phytozome 13) v4.03 7181 8005 3302 4703 2022 46
Sorghum bicolor (Phytozome 13) v3.1.1 4454 5107 2973 2134 1726 77
Trifolium pratense (Phytozome 13) v2 5314 5402 3140 2262 830 44
Triticum aestivum (Ensembl Plants 51) IWGSC 6619 6710 4833 1877 656 78
Triticum dicoccoides (Ensembl Plants 51) v1 18737 38102 21006 17096 4356 316
Triticum spelta (Ensembl Plants 51) v2 8829 8829 6753 2076 559 37
Triticum turgidum (Ensembl Plants 51) v1 5523 5870 4166 1704 346 18
Triticum urartu (Ensembl Plants 51) v1 4588 4588 3068 1520 281 16
Vigna angularis (Ensembl Plants 51) v1.1 3325 3325 2310 1015 172 31
Vigna radiata (Ensembl Plants 51) v6 1255 1268 813 455 80 21
Vigna unguiculata (Phytozome 13) v1.1 2719 3083 2270 813 256 52
Vitis vinifera (Phytozome 13) v2.1 2711 2978 2010 968 243 16
Zea mays (Ensembl Plants 51) v5 5915 6301 2934 3367 1061 24
Zea mays (Phytozome 13) v4 4385 7129 4203 2926 252 65