A database of human long non-coding RNAs conserved across primates
What is SyntDB?
SyntDB is a database of human long non-coding RNAs conserved across primates.
What is a long non-coding RNA?
Long non-coding RNAs (lncRNAs) are usually defined as transcripts longer than 200 nucleotides that do not encode proteins.
LncRNAs participate in a wide range of processes in a cell, including regulation of transcription and translation, RNA stability, chromatin remodeling, scaffolding, but the function of the vast majority of lncRNAs remains unknown.
Why we created this repository?
Evolutionary conservation is one of the most significant signs of functional importance. Comparative conservation studies based on comprehensive catalogs are essential to understand their evolutionary dynamics and biological roles. Due to the lack of comprehensive lncRNA catalogs in primates and fairly close evolutionary distances between species, we developed a pipeline to identify, study and characterize conserved counterparts of human lncRNAs.
Search
Use ENSEMBL IDs or FASTA sequence to find conserved counterparts of human lncRNAs across primates
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We believe that the scientific data should be freely distributed, thus we provide all the data available for download
DownloadUpdates
Render of the expression table improved, also we removed a bug which sometimes leads to displaying of the wrong expression values for some of the transcripts
Implementation
We’ve developed a pipeline for evolutionary analyses of lncRNAs. It consists of two parts. The first part enables ab initio transcriptome assembly from RNA-Seq data, followed by identification of lncRNAs, using a number of commonly accepted criteria. The second module, based on slncky (reference) and a set of Python and R scripts, serves as a tool for identification of conserved lncRNAs, utilizing both synteny and sequence identities across species of interest.
How search for conserved lncRNAs works?
As the core of conserved lncRNA search module we used custom modification of slncky. Slncky provides an efficient, sensitive, and accessible method for detecting and characterizing orthologous lncRNAs across any pair of species, providing an important tool for studying lncRNA evolution. For detailes please visit slncky webpage.
The main concept is represented in the figure below.
What the data can tell us?
The obtained results allow tracking the evolution of human lncRNAs across eleven primate species.
Additional analyses have been applied to characterizen lncRNA transcripts on multiple levels, including genomic context and expression.
Identification of syntenic/orthologous lncRNAs
