CANTATAdb is a database of lncRNAs identified computationally in ten plant species:
We mapped reads from 107 RNA-Seq libraries to corresponding plant genomes and we re-annotated these genomes using gene prediction software and known annotation data as a reference. Then, we applied several filters to discriminate between non-coding and protein-coding transcripts. Using this approach we obtained the following numbers of lncRNAs:
CANTATAdb collects 45,117 lncRNAs predicted in ten plant species. The database presents their 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 and PNRD databases as well as similarities between lncRNAs, including potential orthologs. We also made an effort to functionally characterize the lncRNAs - we found that a number of them could participate in deregulation of miRNA functions or splicing modulation.
A number of model plant species lack comprehensive datasets of lncRNas and their annotations, which poses a difficulty for their further studies. CANTATAdb is probably the biggest and most comprehensive database of plant lncRNAs. For example, NONCODE v4 collects only data for A. thaliana, lncRNAdb (http://www.lncrnadb.org) collects only a small number of lncRNAs in several plants (though tested experimentally), LNCipedia.org keeps only human lncRNAs, while Plant non-coding RNA Databse (PNRD) contains only lncRNAs from 4 plants. An advantage of CANTATAdb is not only the number of stored lncRNAs but also provided annotation data, including lncRNA expression values and predicted functions in the context of lncRNA-RNA interactions.
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Website of the Laboratory of Functional Genomics
(group of prof. Izabela Makalowska).
Laboratory of Functional Genomics
Department of Bioinformatics
Institute of Molecular Biotechnology and Biotechnology
Adam Mickiewicz University in Poznan
ul. Umultowska 89, 61-674 Poznan, Poland
