GreeNC
From GreeNC
A Wiki-database of plant lncRNAs
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 http://dx.doi.org/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 37 plant species and six 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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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 |