Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and DNA are nucleic acids, and, along with lipids, proteins and carbohydrates, constitute the four major macromolecules essential for all known forms of life. Like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA it is more often found in nature as a single-strand folded onto itself, rather than a paired double-strand. Cellular organisms use messenger RNA (mRNA) to convey genetic information that directs synthesis of specific proteins. Many viruses encode their genetic information using an RNA genome.
Rfam is a database containing information about non-coding RNA (ncRNA) families and other structured RNA elements. It is an annotated, open access database originally developed at the Wellcome Trust Sanger Institute in collaboration with Janelia Farm, and currently hosted at the European Bioinformatics Institute. Rfam is designed to be similar to the Pfam database for annotating protein families.
snoRNA U42 is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.
In molecular biology, the small nucleolar RNAs SNORD106 and SNORD12 are two related snoRNAs which belongs to the C/D class of small nucleolar RNAs (snoRNAs). Both contain the conserved C (UGAUGA) and D (CUGA) box sequence motifs
An Hfq binding sRNA is an sRNA that binds the bacterial RNA binding protein called Hfq. A number of bacterial small RNAs which have been shown to bind to Hfq have been characterised . Many of these RNAs share a similar structure composed of three stem-loops. Several studies have expanded this list, and experimentally validated a total of 64 Hfq binding sRNA in Salmonella Typhimurium. A transcriptome wide study on Hfq binding sites in Salmonella mapped 126 Hfq binding sites within sRNAs. Genomic SELEX has been used to show that Hfq binding RNAs are enriched in the sequence motif 5′-AAYAAYAA-3′. Genome-wide study identified 40 candidate Hfq-dependent sRNAs in plant pathogen Erwinia amylovora. 12 of them were confirmed by Northern blot.
In bioinformatics, miRBase is a biological database that acts as an archive of microRNA sequences and annotations. As of September 2010 it contained information about 15,172 microRNAs. This number has risen to 38,589 by March 2018. The miRBase registry provides a centralised system for assigning new names to microRNA genes.
This microRNA database and microRNA targets databases is a compilation of databases and web portals and servers used for microRNAs and their targets. MicroRNAs (miRNAs) represent an important class of small non-coding RNAs (ncRNAs) that regulate gene expression by targeting messenger RNAs.
StarBase is a database for decoding miRNA-mRNA, miRNA-lncRNA, miRNA-sncRNA, miRNA-circRNA, miRNA-pseudogene, protein-lncRNA, protein-ncRNA, protein-mRNA interactions and ceRNA networks from CLIP-Seq and degradome sequencing data. starBase provides miRFunction and ceRNAFunction web tools to predict the function of ncRNAs and protein-coding genes from the miRNA and ceRNA regulatory networks.
tRNADB is a curated database of tRNA
The small nucleolar RNAs (snoRNAs) represent an abundant group of small non-coding RNAs (ncRNAs) in eukaryotes. With the exception of RNase MRP, all the snoRNAs fall into two major families, box C/D and box H/ACA snoRNAs, on the basis of common sequence motifs and structural features. They can be divided into guide and orphan snoRNAs according to the presence or absence of antisense sequence to rRNAs or snRNAs. Recently, thousands of novel snoRNAs were identified from small RNA sequencing datasets in human, mouse, chicken, Ciona intestinalis, Drosophila melanogaster, Caenhorhabditis elegans and Arabidopsis thaliana using snoSeekerNGS program.
The NONCODE database is a collection of expression and functional lncRNA data obtained from re-annotated microarray studies.
VIRsiRNAdb is a database of siRNA/shRNA targeting viral genome regions.
Alexander George Bateman is a computational biologist and Head of Protein Sequence Resources at the European Bioinformatics Institute (EBI), part of the European Molecular Biology Laboratory (EMBL) in Cambridge, UK. He has led the development of the Pfam biological database and introduced the Rfam database of RNA families. He has also been involved in the use of Wikipedia for community-based annotation of biological databases.
RNA modification occurs in all living organisms, and is one of the most evolutionarily conserved properties of Ribonucleic acid or RNAs. It can affect the activity, localization as well as stability of RNAs, and has been linked with human diseases.
In bioinformatics, The Green Non-Coding Database, GreeNC, is a biological database that acts as an archive of plant lncRNAs and annotations. Started on 2015, the GreeNC database provides information on sequence, genome coordinates, coding potential and folding energy of lncRNAs. GreeNC includes about 200.000 pages with information on more than 190.000 transcripts from 37 plants and six algae. According to Paytuví and collaborators, by using the same pipeline to annotate lncRNAs GreeNC make it possible to compare lncRNA sequences and distribution from different species.
