Table 5.1.
List of plant lncRNA databases
| Database | Descriptions/features | Website | Ref |
|---|---|---|---|
| The Arabidopsis Information Resource (TAIR) | Comprehensive database of Arabidopsis thaliana genome, including annotated genome sequences (TAIR10), gene structures, and transcriptome data for coding and nonprotein-coding loci. TAIR has multiple analytical tools: interactive genome browser, BLAST, motif analysis, bulk data retrieval, and a chromosome map tool | https://www.arabidopsis.org/ | [23] |
| Araportll | A comprehensive database based on Arabidopsis Col-0 version 11 (Araport11) includes additional coding and noncoding annotations compared to TAIR10, such as lincRNAs, NATs, and other ncRNAs | https://www.araport.org/ | [24] |
| Plant long noncoding RNA database (PLncDB) | This database includes a curated list of >13,000 lincRNAs identified using RNA-seq and tiling array and their organ-specific expression and the differential expression in RdDM mutants. PLncDB has a genome browser for viewing the association of various epigenetic markers | http://chualab.rockefeller.edu/gbrowse2/homepage.html | [3] |
| Green Non-coding Database (GREENC) |
GREENC has >120,000 annotated lncRNAs from 37 plant species and algae. The user can access the coding potential and folding energy for each lncRNA | http://greenc.sciencedesigners.com/wiki/Main_Page | [25] |
| NONCODE v4.0 | NONCODE includes >500,000 lncRNAs from 16 species. Arabidopsis is the only plant species, as NONCODE focuses on non-plant species, including human and mouse | http://www.noncode.org/index.phphttp://www.noncode.org/index.php | [26] |
| CANTATAdb | CANTATAdb contains >45,000 plant lncRNAs from ten model plant species. In addition to tissue-specific expressions and coding potential, each lncRNA is also evaluated based on potential roles in splicing regulation and miRNA modulations | http://cantata.amu.edu.pl/ | [27] |
| Plant ncRNA database (PNRD) | PNRD has >25,000 ncRNAs of 11 different types and from 150 plant species. It also includes analytical tools, such as an miRNA predictor, coding potential calculator, and customized genome browser | http://structuralbiology.cau.edu.cn/PNRD/ | [28] |
| Plant Natural Antisense Transcripts DataBase (PlantNATsDB) |
A database for natural antisense transcripts (NATs) from 70 plant species, associated gene information, small RNA expression, and GO annotation | http://bis.zju.edu.cn/pnatdb/ | [29] |