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NRDR - The Non-coding RNA Databases Resource


Database version: 2.0
RNA Type: Long RNA
Overview: CANTATAdb is a database of 239,631 lncRNAs identified computationally in 36 plant species and 3 algae. They mapped reads from hundreds RNA-Seq libraries to corresponding plant genomes and re-annotated these genomes using gene prediction software and known annotation data as a reference. Then, they applied several filters to discriminate between non-coding and protein-coding transcripts. The database presents, among others, lncRNA sequences, expression values across RNA-Seq libraries, genomic locations, hypothetical peptides encoded by lncRNAs, BLAST search results against Swiss-Prot proteins and non-coding RNAs from NONCODE.
Search Methods:
  • Keyword: Search by lncRNA id, by combining different extra information
  • Similarity: BLAST searches against stored lncRNAs
  • TAG: TAG for selection of the species of interest
Source: RNA-seq, NONCODE,
Information Source: Experimental, In silico annotation.
Information Content: .
Reference: Szcześniak et al. 2015. CANTATAdb: A collection of plant long non-coding RNAs. Plant and Cell Physiology 57(1):pcv201
PubmedID: 26657895.
Year: 2015
Multiple search: Yes
Download: GTF, FASTA.
Genomic Overview: No
Organism: Arabidopsis Thaliana (Thale Cress), Brassica rapa, Glycine Max (Soybean), Medicago truncatula (Barrel Medic), Oryza sativa (Rice), Vitis vinifera, Chlamydomonas reinhardtii (Green Alga), Physcomitrella patens, Selaginella moellendorffii, Arabidopsis lyrata, Brassica napus, Brassica oleracea, Gossypium hirsutum, Theobroma cacao (Cacao), Malus domestica and 28 others.

Url: http://yeti.amu.edu.pl/CANTATA/
June 2018: Release 3.0