A comprehensive knowledge of all the factors involved in splicing, both proteins and RNAs, and of their interaction network is crucial for reaching a better understanding of this process and its functions. A large part of relevant information is buried in the literature or collected in various different databases. By hand-curated screenings of literature and databases we retrieved experimentally assessed data on 71 human RNA-binding splicing regulatory proteins and organized them into a database called “SpliceAid-F”. For each splicing factor (SF) the database reports its functional domains and its protein and chemical interactors. Furthermore, we collected experimentally validated RNA-SF interactions, including relevant information on the RNA binding sites such as the genes where these sites lie, their genomic coordinates, the splicing effects, experimental procedures, as well as the corresponding bibliographic references. We also collected information from experiments showing no RNA-SF binding, at least in the assayed conditions. In total, SpliceAid-F contains 4227 interactions, 2622 RNA binding sites and 1170 no-binding sites, including information on binding and no-binding specificity in different cellular contexts. Data collected in SpliceAid-F can provide significant information to explain an observed splicing pattern as well as the effect of mutations in functional regulatory elements. ... [Information of the supplier]
ChIPBase, an integrated resource and platform for decoding transcription factor binding maps, expression profiles and transcriptional regulation of long non-coding RNAs (lncRNAs, lincRNAs), microRNAs, other ncRNAs(snoRNAs, tRNAs, snRNAs, etc.) and protein-coding genes from ChIP-Seq data. ChIPBase currently includes millions of transcription factor binding sites (TFBSs) among 6 species. ChIPBase provides several web-based tools and browsers to explore TF-lncRNA, TF-miRNA, TF-mRNA, TF-ncRNA and TF-miRNA-mRNA regulatory networks. ... [Information of the supplier]
In bacteria, small (~30-500 nt) non-coding RNAs (sRNAs) are the most abundant class of post-transcriptional regulators that are involved in diverse processes including quorum sensing, stress response, virulence and carbon metabolism. Based on the target molecules, sRNAs can be divided into two major groups: (i) mRNA-binding antisense sRNAs and (ii) protein-binding sRNAs. The antisense RNAs can further be categorized as cis-encoded antisense sRNAs, which are completely complementary to their targets, and trans-encoded antisense sRNAs, which are only partially complementary to their targets. In any case, the interaction between antisense RNAs and target mRNAs could direct a plethora of biological regulatory circuits. Recent developments in high-throughput techniques, such as genomic tiling arrays and RNA-Seq have provided invaluable insights into the detection and characterization of bacterial sRNAs. However, a comprehensive bacterial sRNA database is not yet available, especially for integrating and analyzing high-throughput sequencing data. Here, we have designed and constructed BSRD (Bacterial Small regulatory RNA Database) which hosts sRNAs collected from over 783 bacterial species and 957 strains. ... [Information of the supplier]
LncBase hosts elaborated information for, both predicted and experimentally verified, miRNA-lncRNA interactions. The database consists of two distinct modules. The Experimental Module contains detailed information for more than 5,000 interactions, between 2,958 lncRNAs and 120 miRNAs, ranging from miRNA and lncRNA related facts to information specific to their interaction, the experimental validation methodologies and their outcomes. The Prediction Module, which is based on the latest version of DIANA-microT target prediction algorithm (DIANA-microT-CDS), contains detailed information for more than 10 million interactions, between 56,097 lncRNAs and 3,078 miRNAs, ranging from miRNA and lncRNA related details to specific information regarding their interaction sites, graphical representation of their binding and the predicted score. This module exhibits a unique feature for searching the database. Users are able to add genomic locations to their queries thus browsing every miRNA-lncRNA interaction that has at least one MRE located inside the queried locus. ... [Information of the supplier]
MODOMICS and RNApathwaysDB are two complementary resources which present RNA metabolism at different levels. While MODOMICS presents RNA modification pathways on the level of nucleosides, RNApathwaysDB deals with RNA metabolism with respect to whole RNA molecules. Our ultimate goal is to integrate these databases, however at the moment the users are invited to consult both of these complementary resources, depending on their needs and interests. ... [Information of the supplier]
The Protist Ribosomal Reference Database provides an access to unicellular eukaryotes Small SubUnit rRNA and rDNA sequences with curated taxonomy. The database is focused on nuclear-encoded sequences of protists. However, Metazoa, land plants and macrosporic fungi, as well as eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for Next Generation Sequencing dataset analyses. The PR2 database can be downloaded or searched by similarity as explained below. Because of their tremendous diversity, taxonomy of protists is still under progress. ... [Information of the supplier]
YM500 is an Integrative small RNA Sequencing (smRNA-seq) database for miRNA research and provides an integrative web interface for miRNA quantification (for known miRNAs in the miRBase R19), isomiR identification (incl. RNA editing), arm switching discovery, and, most of all, novel miRNA predictions. [Information of the supplier]
This symposium assembles approximately 50 experts from different fields to discuss a fundamental new understanding of genetic novelty, code-generating, genome-formatting factors, multi-use nature for RNAgents and behavioral motifs of RNA-consortia. The small number of participants guarantees a relaxed and inspiring atmosphere for presentation and discussion. The Proceedings will be published. ... [Information of the supplier]
snOPY is the snoRNA orthological gene database. snOPY provides comprehensive information about snoRNAs, snoRNA gene loci and target RNAs. Small nucleolar RNAs (snoRNAs) are a class of non-coding RNAs that guide the modification of specific nucleotides in ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). Although most non-coding RNAs undergo post-transcriptional modifications prior to maturation, the functional significance of these modifications remains unknown. The snoRNA orthological gene database (snOPY) is a tool for studying RNA modifications. ... [Information of the supplier, modified]
The second Computational RNA Biology conference will bring together computational researchers with experimentalists interested in non-coding RNA biology to discuss the latest developments in this fast moving field. In recent years, there have been important advances in identifying and understanding non-coding RNAs. They are involved in many biological processes and are increasingly seen as important in disease. Computational approaches greatly assist our understanding of how to characterise and understand the biological functions of these molecules. This meeting will cover all aspects of RNA biology with a focus on computational methods to elucidate structure, function and interactions of non-coding RNAs across different species. We expect to see many new exciting results unveiled through the application of high-throughput sequencing as well as single sequence approaches. This meeting follows on from the successful first conference held in 2014, which was characterised by excellent presentations and vibrant discussions. ... [Information of the supplier]
