Abstract
SyntDB (http://syntdb.amu.edu.pl/) is a collection of data on long noncoding RNAs (lncRNAs) and their evolutionary relationships in twelve primate species, including humans. This is the first database dedicated to primate lncRNAs, thousands of which are uniquely stored in SyntDB. The lncRNAs were predicted with our computational pipeline using publicly available RNA-Seq data spanning diverse tissues and organs. Most of the species included in SyntDB still lack lncRNA annotations in public resources. In addition to providing users with unique sets of lncRNAs and their characteristics, SyntDB provides data on orthology relationships between the lncRNAs of humans and other primates, which are not available on this scale elsewhere. Keeping in mind that only a small fraction of currently known human lncRNAs have been functionally characterized and that lncRNA conservation is frequently used to identify the most relevant lncRNAs for functional studies, we believe that SyntDB will contribute to ongoing research aimed at deciphering the biological roles of lncRNAs.
Highlights
Long non-coding RNAs represent a highly heterogeneous class of RNA molecules arbitrarily defined as transcripts of more than 200 nucleotides in length that are not translated into proteins
A rapidly growing number of studies highlight their essential biological roles in processes such as transcription, splicing, translation, the cell cycle and apoptosis, protein localization, imprinting or stem cell pluripotency [1]. They have been implicated in human diseases; e.g., Long non-coding RNAs (lncRNAs) have been linked to malignant transformation, and a number of them represent diagnostic and prognostic biomarkers for cancers [2]. lncRNAs play these roles in different ways, including through direct RNA:RNA
One should keep in mind that there are plentiful functional, non-conserved lncRNAs, including human-specific lncRNAs, such as MSTRG.141391.4, an isoform of p53induced noncoding RNA (PINCR), which plays a critical prosurvival role in the response to DNA damage [5]
Summary
Long non-coding RNAs (lncRNAs) represent a highly heterogeneous class of RNA molecules arbitrarily defined as transcripts of more than 200 nucleotides in length that are not translated into proteins. Keeping in mind the very limited availability of orthologous relationships for human lncRNAs and the importance of such data in functional studies, we searched for lncRNA orthologues across eleven primate species and classified them into those showing exonic identity, locus identity or only positional conservation (syntologs) [15]. The resulting unique sets of lncRNAs for eleven primates and the identified orthologues with accompanying data are made available in the newly developed online database SyntDB (http://syntdb.amu.edu.pl/).
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