Table 1.
A selected list of plant lncRNA databases
| Name | Descriptions/features | Link | Refs |
|---|---|---|---|
| The Arabidopsis Information Resource (TAIR) | TAIR and its latest version (TAIR10) offer a comprehensive database of the Arabidopsis thaliana genome. In addition to gene structures and transcriptome data for coding and nonprotein-coding loci, it offers many analytical tools | https://www.arabidopsis.org/ | [6] |
| Araport11 | Similar to TAIR, Araport11 curates comprehensive genomic information of Arabidopsis thaliana using the ecotype Col-0 version 11 genome | https://www.araport.org/ | [7] |
| Plant long noncoding RNA database (PLncDB) | This is a plant-specific database that has >13,000 lncRNAs. The organ-specific expression and the differential expression in RNA-directed DNA methylation mutants of the curated lncRNAs are provided. A genome browser allows the user to examine the association between lincRNAs and epigenetic markers | http://chualab.rockefeller.edu/gbrowse2/homepage.html | [8] |
| Green Non-coding Database (GreeNC)a | Including lncRNAs from 37 plant species and algae, this database curates a total of >120,000 annotated lncRNAs and offers the coding potential and folding energy for each curated lncRNA | http://greenc.sciencedesigners.com/wiki/Main_Page | [9] |
| NONCODE v4.0 | This database mainly curated noncoding RNAs from metazoans. Although Arabidopsis is the only plant species considered in this database, it has >500,000 lncRNAs from all 17 species and > 3500 Arabidopsis lncRNAs | http://www.noncode.org/index.php | [10] |
| CANTATAdba | This database has >45,000 plant lncRNAs from 10 plant species. Each lncRNA is also evaluated based on potential roles in splicing regulation and miRNA modulations, as well as their tissue-specific expressions and coding potential | http://cantata.amu.edu.pl/ | [11] |
| Plant ncRNA database (PNRD) | Includes lncRNAs from 150 plant species, this database curated a total of >25,000 ncRNAs of 11 types. In addition, this database offers several analytical tools and includes a customized genome browser, a coding potential calculator, and miRNA predictor | http://structuralbiology.cau.edu.cn/PNRD/ | [12] |
| EVLncRNAsa | This database has lncRNAs that are validated by experiments and also integrated information from other databases. The database currently has >1500 lncRNAs from >75 species, including animals, plants, and microbes | http://biophy.dzu.edu.cn/EVLncRNAs/ | [13] |
| Plant Natural Antisense Transcripts DataBase (PlantNATsDB) | This database has the natural antisense transcripts (NATs) of 70 plant species. Other information is housed in the database, including associated gene information, small RNA expression, and GO annotation | http://bis.zju.edu.cn/pnatdb/ | [14] |
a
The descriptions and protocols for how to use them are included in the same book