msRNAdb for medium-sized RNA

Massive parallel sequencing technologies revealed that large fractions of eukaryotic genomes are transcribed. Interestingly, just a portion of the transcriptome seems to be protein-coding. Many transcripts are considered to encode no protein and are thus referred to as non-coding RNA (ncRNA). Among those ncRNAs exist RNA species with a size of 50 to 300 nts in length. These are referred to as medium-sized ncRNAs (msRNAs). Larger ncRNAs are classified as long ncRNAs (lncRNAs; >200 nts) whereas smaller ncRNAs comprise e.g. miRNAs and piRNAs. Although msRNAs are quite heterogeneous in respect to their biogenesis, cellular localization and functions it is generally accepted that many of these RNAs serve essential cellular roles. For instance, translation of mRNAs into proteins is an example for an msRNA-controlled process. The ribosome itself contains two msRNAs (5S and 5.8s rRNAs) and amino acids are delivered to the translating ribosome by aminoacylated tRNAs, another class of msRNAs. Secreted proteins are co-translationally transported into the endoplasmic reticulum by the action of the signal recognition particle containing the msRNA 7SL. Due to the variety of processes controlled by msRNAs it is important to characterize the expression patterns of msRNAs and how they contribute to cell functions in health and disease.


We focus our research on the identification and characterization of msRNAs. Therefore we use a combination of tight msRNA-purification protocols combined with RNA sequencing to determine msRNA expression in a given cell type or tissue (msRNAseq). We aim at providing this data integrated into this database in an ‘easy access’ mode. For questions and suggestions please contact our staff. If you use data obtained by msRNAdb please cite the following article:

MsRNA-sequencing: Deciphering the middle-class non-coding transcriptome

Marcel Köhn1,2,3, Danny Misiak2, Hendrik Täuber2, Michael Gekle3, Stefan Hüttelmaier2

1 Junior group ‚Non-coding RNAs in human diseases‘, Medical Faculty, University of Halle-Wittenberg
2 Institute of Molecular Medicine, University of Halle-Wittenberg, Germany
3 Julius-Bernstein-Institute of Physiology, University of Halle-Wittenberg, Germany
(Manuscript in preparation)