This is a list of long noncoding RNA databases , which provide information about lncRNAs. [1] [2]
Name | Description | References |
---|---|---|
deepBase | Identification, expression, evolution and function of long non-coding RNAs (LncRNAs), small RNAs and circular RNAs from deep-sequencing data | [3] |
LNCipedia | A comprehensive compendium of human long non-coding RNAs. | [4] [5] |
lncRNAdb | The Reference Database For Functional Long Noncoding RNAs. | [6] |
LncRNAWiki | A wiki-based, publicly editable and open-content platform for community curation of human long non-coding RNAs (lncRNAs) | [7] |
LncBook | A comprehensive collection of 270,044 human lncRNAs and systematic curation of lncRNAs’ annotation by multi-omics data integration, function annotation and disease association | [8] |
MONOCLdb | The MOuse NOnCode Lung database provides the annotations and expression profiles of mouse long non-coding RNAs (lncRNAs) involved in influenza and SARS-CoV infections. | [9] |
NONCODE | An integrated knowledge database dedicated to ncRNAs, especially lncRNAs | [10] |
lncRNome | A comprehensive searchable biologically oriented knowledgebase for long noncoding RNAs in Humans. | |
NRED | A database of long noncoding RNA expression. | [11] |
C-It-Loci | A tool to explore and to compare the expression profiles of conserved loci among various tissues in three organisms | |
MiTranscriptome | A catalog of human long poly-adenylated RNA transcripts derived from computational analysis of high-throughput RNA-Seq data from over 6,500 samples, spanning diverse cancer and tissue types | [13] |
slncky Evolution Browser | This site contains alignments and evolutionary metrics of conserved lncRNAs. | [14] |
Cancer LncRNA Census (CLC) | Database of long-noncoding RNAs causally implicated in cancer through in vivo, in vitro and other evidence. | [15] |
BIGTranscriptome | High-confidence of coding and noncoding transcriptomes assembled with hundreds of pseudo-stranded and stranded RNA-seq datasets. | [16] |
lncRNAKB | A knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA | [17] |
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.
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
Telomerase RNA component, also known as TR, TER or TERC, is an ncRNA found in eukaryotes that is a component of telomerase, the enzyme used to extend telomeres. TERC serves as a template for telomere replication by telomerase. Telomerase RNAs differ greatly in sequence and structure between vertebrates, ciliates and yeasts, but they share a 5' pseudoknot structure close to the template sequence. The vertebrate telomerase RNAs have a 3' H/ACA snoRNA-like domain.
Long non-coding RNAs are a type of RNA, generally defined as transcripts more than 200 nucleotides that are not translated into protein. This arbitrary limit distinguishes long ncRNAs from small non-coding RNAs, such as microRNAs (miRNAs), small interfering RNAs (siRNAs), Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), and other short RNAs. Given that some lncRNAs have been reported to have the potential to encode small proteins or micro-peptides, the latest definition of lncRNA is a class of RNA molecules of over 200 nucleotides that have no or limited coding capacity. Long intervening/intergenic noncoding RNAs (lincRNAs) are sequences of lncRNA which do not overlap protein-coding genes.
The Gene Wiki is a project within Wikipedia that aims to describe the relationships and functions of all human genes. It was established to transfer information from scientific resources to Wikipedia stub articles.
Therapeutic Target Database (TTD) is a pharmaceutical and medical repository constructed by the Innovative Drug Research and Bioinformatics Group (IDRB) at Zhejiang University, China and the Bioinformatics and Drug Design Group at the National University of Singapore. It provides information about known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets. Detailed knowledge about target function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and drug structure, therapeutic class, and clinical development status. TTD is freely accessible without any login requirement at https://idrblab.org/ttd/.
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.
In bioinformatics, lncRNAdb is a biological database of Long non-coding RNAs The database focuses on those RNAs which have been experimentally characterised with a biological function. The database currently holds over 290 lncRNAs from around 60 species. Example lncRNAs in the database are HOTAIR and Xist.
This RNA modification databases are a compilation of databases and web portals and servers used for RNA modification. RNA modification occurs in all living organisms, and is one of the most evolutionarily conserved properties of RNAs. More than 100 different types of RNA modifications have been characterized across all living organisms. It can affect the activity, localization as well as stability of RNAs, and has been linked with human cancer and diseases.
The NONCODE database is a collection of expression and functional lncRNA data obtained from re-annotated microarray studies.
In molecular biology mir-425 microRNA is a short RNA molecule. MicroRNAs function to regulate the expression levels of other genes by several mechanisms.
In molecular biology mir-542 microRNA is a short RNA molecule. MicroRNAs function to regulate the expression levels of other genes by several mechanisms.
Competing endogenous RNAs hypothesis: ceRNAs regulate other RNA transcripts by competing for shared microRNAs. They are playing important roles in developmental, physiological and pathological processes, such as cancer. Multiple classes of ncRNAs and protein-coding mRNAs function as key ceRNAs (sponges) and to regulate the expression of mRNAs in plants and mammalian cells.
Single nucleotide polymorphism annotation is the process of predicting the effect or function of an individual SNP using SNP annotation tools. In SNP annotation the biological information is extracted, collected and displayed in a clear form amenable to query. SNP functional annotation is typically performed based on the available information on nucleic acid and protein sequences.
Model organism databases (MODs) are biological databases, or knowledgebases, dedicated to the provision of in-depth biological data for intensively studied model organisms. MODs allow researchers to easily find background information on large sets of genes, plan experiments efficiently, combine their data with existing knowledge, and construct novel hypotheses. They allow users to analyse results and interpret datasets, and the data they generate are increasingly used to describe less well studied species. Where possible, MODs share common approaches to collect and represent biological information. For example, all MODs use the Gene Ontology (GO) to describe functions, processes and cellular locations of specific gene products. Projects also exist to enable software sharing for curation, visualization and querying between different MODs. Organismal diversity and varying user requirements however mean that MODs are often required to customize capture, display, and provision of data.
Transcription factors are proteins that bind genomic regulatory sites. Identification of genomic regulatory elements is essential for understanding the dynamics of developmental, physiological and pathological processes. Recent advances in chromatin immunoprecipitation followed by sequencing (ChIP-seq) have provided powerful ways to identify genome-wide profiling of DNA-binding proteins and histone modifications. The application of ChIP-seq methods has reliably discovered transcription factor binding sites and histone modification sites.
SHLD1 or shieldin complex subunit 1 is a gene on chromosome 20. The C20orf196 gene encodes an mRNA that is 1,763 base pairs long, and a protein that is 205 amino acids long.
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