GreeNC

From GreeNC

Revision as of 15:19, 14 September 2014 by WikiSysop (Talk | contribs)

A database of plants lncRNAs

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.

News

Aquí aniria la extenció de "latest news" que hi ha al http://prgdb.crg.eu/

Statistics

Taxon Gene number Transcript number High confidence Hits against transposons miRNA precursors

960 961 591 146 10
15463 34092 18060 6749 958
2075 2083 1476 103 25
4321 4868 3545 447 46
2448 2508 1814 251 73
2593 2676 1831 280 38
1772 2254 1602 271 14
1857 1919 1304 198 22
4843 4980 3538 574 93
1932 2019 1416 192 16
2986 3195 2332 496 104
9060 9060 6554 526 70
2563 2674 1889 209 33
6099 6200 4072 477 59
1720 1812 1294 127 23
2124 2124 1154 417 6
595 596 269 171 31
1935 1935 1279 214 6
1465 1465 1293 24 31
1457 1457 1186 113 11
2004 2004 1663 82 7
1237 1237 806 74 5
2471 2471 2112 76 22
1861 1861 1319 149 16
2210 2210 1680 80 11
5001 5001 3921 414 19
3459 3459 2465 118 22
141 141 77 7 1
1756 1756 1034 115 14
1531 1728 1016 244 15
6042 6042 4712 509 30
2437 2437 1701 97 14
5137 5978 4246 625 76
7619 8720 6146 731 72
8569 9299 6811 639 60
8006 9222 6461 787 81
7953 9233 6467 793 77
3800 4555 3000 461 53
9009 10090 7504 681 77
8197 8197 5580 795 67
12659 23867 11477 5740 872
662 664 404 102 3
3206 3568 2428 368 66
4949 5395 4095 150 24
3353 3676 2910 297 37
4869 4869 3179 881 54
1684 1686 1285 102 6
2304 2655 1875 316 55
2896 3196 2665 260 47
8986 9093 5288 2584 102
2091 2214 1592 127 16
3851 3851 2361 924 40
1763 2055 1356 240 26
5516 5516 3140 508 21
4122 4122 3448 54 13
5339 5600 4461 588 51
4575 4575 3454 422 43
4807 4807 3334 1017 29
5402 5837 4536 719 55
3150 3150 2334 74 16
4389 4818 3496 832 67
6077 6586 4875 757 64
3850 4114 3233 440 39
6357 6801 5006 837 66
5395 5724 3788 1435 104
2331 2389 2792 522 37
9607 10438 7543 1958 90
5025 5025 3566 432 50
1360 1360 952 78 7
1660 1795 1233 174 10
934 938 799 20 3
8673 8673 6035 1530 85
4320 4381 2596 1181 109
1873 1873 1011 374 25
11326 11326 6919 2478 104
7488 7488 5252 823 51
3625 4070 2916 396 48
2515 2515 1783 101 12
4897 5427 3948 1025 62
4242 4242 2767 471 29
7181 8005 3302 2022 46
4454 5107 2973 1726 77
5314 5402 3140 830 44
6619 6710 4833 656 78
18737 38102 21006 4356 316
8829 8829 6753 559 37
5523 5870 4166 346 18
4588 4588 3068 281 16
3325 3325 2310 172 31
1255 1268 813 80 21
2719 3083 2270 256 52
2711 2978 2010 243 16
5915 6301 2934 1061 24
4385 7129 4203 252 65
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