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
