A database of long non-coding RNAs in plants

How were these lncRNAs discovered?

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:

What's inside the database?

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.

Why we created this database?

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.

Contact information

Any questions, remarks, suggestions? Feel free to contact us:

miszcz [at] amu.edu.pl

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



You might be also interested in other resources from our lab:

HuntMi
RetrogeneDB
ERISdb
miRNEST database