GreeNC

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A Wiki-database of plant lncRNAs (v2.0)

Actinidia chinensis (Ensembl Plants 51)

Aegilops tauschii (Ensembl Plants 51)

Amaranthus hypocondriacus (Phytozome 13)

Aquilegia coerulea (Phytozome 13)

Arabidopsis halleri (Ensembl Plants 51)

Arabidopsis lyrata (Phytozome 13)

Arabidopsis thaliana (Phytozome 13)

Arabis alpina (Ensembl Plants 51)

Beta vulgaris (Phytozome 13)

Boechera stricta (Phytozome 13)

Brachypodium stacei (Phytozome 13)

Brassica napus (Ensembl Plants 51)

Brassica oleracea capitata (Phytozome 13)

Brassica rapa (Phytozome 13)

Camelina sativa (Ensembl Plants 51)

Capsella rubella (Phytozome 13)

Capsicum annuum (Ensembl Plants 51)

Chara braunii (Ensembl Plants 51)

Chenopodium quinoa (Phytozome 13)

Chondrus crispus (Ensembl Plants 51)

Chromochloris zofingiensis (Phytozome 13)

Cicer arietinum (Phytozome 13)

Cinnamomum kanehirae (Phytozome 13)

Citrullus lanatus (Ensembl Plants 51)

Coffea canephora (Ensembl Plants 51)

Corchorus capsularis (Ensembl Plants 51)

Cucumis melo (Ensembl Plants 51)

Cucumis sativus (Ensembl Plants 51)

Cyanidioschyzon merolae (Ensembl Plants 51)

Cynara cardunculus (Ensembl Plants 51)

Dioscorea alata (Phytozome 13)

Eragrostis curvula (Ensembl Plants 51)

Eragrostis tef (Ensembl Plants 51)

Glycine max (Phytozome 13)

Gossypium barbadense (Phytozome 13)

Gossypium darwinii (Phytozome 13)

Gossypium hirsutum (Phytozome 13)

Gossypium mustelinum (Phytozome 13)

Gossypium raimondii (Ensembl Plants 51)

Gossypium tomentosum (Phytozome 13)

Helianthus annuus (Phytozome 13)

Hordeum vulgare (Phytozome 13)

Juglans regia (Ensembl Plants 51)

Kalanchoe fedtschenkoi (Phytozome 13)

Lactuca sativa (Phytozome 13)

Leersia perrieri (Ensembl Plants 51)

Lupinus albus (Phytozome 13)

Lupinus angustifolius (Ensembl Plants 51)

Manihot esculenta (Phytozome 13)

Marchantia polymorpha (Phytozome 13)

Medicago truncatula (Ensembl Plants 51)

Musa acuminata (Ensembl Plants 51)

Nicotiana attenuata (Ensembl Plants 51)

Nymphaea colorata (Phytozome 13)

Olea europaea (Phytozome 13)

Oropetium thomaeum (Phytozome 13)

Oryza barthii (Ensembl Plants 51)

Oryza brachyantha (Ensembl Plants 51)

Oryza glaberrima (Ensembl Plants 51)

Oryza glumipatula (Ensembl Plants 51)

Oryza longistaminata (Ensembl Plants 51)

Oryza meridionalis (Ensembl Plants 51)

Oryza nivara (Ensembl Plants 51)

Oryza punctata (Ensembl Plants 51)

Oryza rufipogon (Ensembl Plants 51)

Oryza sativa (Phytozome 13)

Panicum hallii (Phytozome 13)

Panicum virgatum (Phytozome 13)

Papaver somniferum (Ensembl Plants 51)

Pistacia vera (Ensembl Plants 51)

Poncirus trifoliata (Phytozome 13)

Porphyra umbilicalis (Phytozome 13)

Prunus avium (Ensembl Plants 51)

Prunus dulcis (Ensembl Plants 51)

Quercus lobata (Ensembl Plants 51)

Rosa chinensis (Ensembl Plants 51)

Saccharum spontaneum (Ensembl Plants 51)

Salix purpurea (Phytozome 13)

Sesamum indicum (Ensembl Plants 51)

Setaria viridis (Phytozome 13)

Solanum lycopersicum (Phytozome 13)

Solanum tuberosum (Phytozome 13)

Sorghum bicolor (Phytozome 13)

Trifolium pratense (Phytozome 13)

Triticum aestivum (Ensembl Plants 51)

Triticum dicoccoides (Ensembl Plants 51)

Triticum spelta (Ensembl Plants 51)

Triticum turgidum (Ensembl Plants 51)

Triticum urartu (Ensembl Plants 51)

Vigna angularis (Ensembl Plants 51)

Vigna radiata (Ensembl Plants 51)

Vigna unguiculata (Phytozome 13)

Vitis vinifera (Phytozome 13)

Zea mays (Ensembl Plants 51)

Zea mays (Phytozome 13)

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.

Tags: GreeNC, Minorupdate, Update

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