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Aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 24 release contains 19,815 protein-coding, 19,941 long noncoding RNA loci and 79,930 coding transcripts. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons.
LNCediting / Long Non Coding editing
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A database of comprehensive information about Adenosine-to-Inosine editing sites in long non-coding RNAs (lncRNAs) across human, rhesus, mouse, and fly, to explore their potential functions. LNCediting contains editing sites in lncRNAs, structure change by editing and the binding sites of lncRNA:miRNA which may be impacted by editing sites. LNCediting provides customized tools to predict functional effects of novel editing sites in lncRNAs.
A database for human long non-coding RNA (lncRNA) transcripts and genes. In addition to basic transcript information and structure, several statistics are calculated for each entry in the database, such as secondary structure information, protein coding potential and microRNA binding sites. The database is publicly available and allows users to query and download lncRNA sequences and structures based on different search criteria. The database may serve as a source of information on individual lncRNAs or as a starting point for large-scale studies.
A comprehensive bioinformatics resource to archive non-coding RNA (ncRNA)-associated cell death interactions. ncRDeathDB documents a total of more than 4600 ncRNA-mediated programmed cell death (PCD) entries in 12 species. ncRDeathDB provides a user-friendly interface to query, browse and manipulate these ncRNA-associated cell death interactions. Furthermore, this resource will help to visualize and navigate current knowledge of the noncoding RNA component of cell death and autophagy, to uncover the generic organizing principles of ncRNA-associated cell death systems, and to generate valuable biological hypotheses.
PNRD / Plant Non-coding RNA Database
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It is the updated version of PMRD. PNRD mainly focuses on plant species. A total of 25739 entries of 11 different types of ncRNAs from 150 plant species were collected. Targets of miRNAs were extended to 178138 pairs in 46 species, while the number of miRNA expression profiles reached 35. Improvements in PNRD are not only the larger amounts of data, but also better service, such as a more user-friendly interface, more multifunctional and browsing options and more background data for users to download.
GREENC / Green Non-Coding Database
A repository of lncRNAs annotated in 37 plant species and six algae. By using the same pipeline to annotate lncRNAs we make it possible to compare lncRNA sequences and distribution from different species. By organizing the sequences in a central database we aim to provide a tool for the scientific community that can boost research on this class of transcripts. The GreeNC database provides information on sequence, genome coordinates, coding potential and folding energy of the lncRNAs. GreeNC includes ∼200 000 pages with information on >190 000 transcripts from 37 plants and six algae. More than 120 000 transcripts were annotated as high confidence lncRNAs, 30% of them from the T. aestivum (17.8%) and Z. mays (8.2%). The lowest number of lncRNAs was annotated in the three algae C. rehinardtii (0.1%), M. pusilla (0.15%) and O. lucimarinus (0.16%). More than 25 000 and 8000 transcripts were annotated as repetitive elements and miRNA precursors, respectively.
NSDNA / Nervous System Disease NcRNAome Atlas
A manually curated database that provides comprehensive experimentally supported associations about nervous system diseases (NSDs) and noncoding RNAs (ncRNAs). NSDNA database documents 24713 associations between 142 NSDs and 8593 ncRNAs in 11 species, curated from more than 1300 articles. This database provides a user-friendly interface for browsing and searching and allows for data downloading flexibility. In addition, NSDNA offers a submission page for researchers to submit novel NSD-ncRNA associations. It represents a useful and valuable resource for researchers who seek to understand the functions and molecular mechanisms of ncRNA involved in NSDs.
A wiki-based platform that is open-content and publicly editable and aimed at community-based curation and collection of information on human lncRNAs. Current related databases are dependent primarily on curation by experts, making it laborious to annotate the exponentially accumulated information on lncRNAs, which inevitably requires collective efforts in community-based curation of lncRNAs. Unlike existing databases, lncRNAWiki features comprehensive integration of information on human lncRNAs obtained from multiple different resources and allows not only existing lncRNAs to be edited, updated and curated by different users but also the addition of newly identified lncRNAs by any user.
FARNA / Function Annotation of human non-coding RNA transcripts
Integrates ncRNA information related to expression, pathways and diseases in a large number of human tissues and primary cells. FARNA is a knowledgebase of inferred functions of 10,289 human ncRNA transcripts (2,734 microRNA and 7,555 long ncRNA) in 119 tissues and 177 primary cells of human. It ranks annotated functions of ncRNA based on statistical enrichment of mapped terms from Gene Ontology (GO), pathways, diseases and parts of their regulatory networks that control activation of the ncRNA transcripts.
EVLncRNAs / Experimentally Validated lncRNAs
Provides all species and covers functional and disease-specific roles for all long non-coding RNAs (lncRNAs) validated. EVLncRNAs contains about 1543 lncRNAs from 77 species along with their annotated functions, interaction partners and relevant diseases. The database allows users to submit novel experimentally validated lncRNAs and related diseases or associated components. It can be searched by any keywords, such as lncRNA name, alias, disease name, experimental methods, associated components and level of interaction.
PLncDB / Plant long non-coding RNA database
Attempts to provide the following functions related to long non-coding RNAs (lncRNAs): (i) Genomic information for a large number of lncRNAs collected from various resources; (ii) an online genome browser for plant lncRNAs based on a platform similar to that of the UCSC Genome Browser; (iii) Integration of transcriptome datasets derived from various samples including different tissues, developmental stages, mutants and stress treatments; and (iv) A list of epigenetic modification datasets and small RNA datasets. PLncDB provides a comprehensive genomic view of Arabidopsis lncRNAs for the plant research community.
An online database of long non-coding RNAs (lncRNAs) in 10 model plant species. The lncRNAs were identified computationally using dozens of publicly available RNA sequencing (RNA-Seq) libraries. Expression values, coding potential, sequence alignments as well as other types of data provide annotation for the identified lncRNAs. In order to better characterize them, we investigated their potential roles in splicing modulation and deregulation of microRNA functions. The resource offers browsing, searching and downloading options to its users. To the best of our knowledge, the CANTATAdb database is the largest collection of plant lncRNAs.
A comprehensive database for long noncoding RNA (lncRNA) in Human and Mouse. LncRBase hosts information on basic lncRNA transcript features, with additional details on genomic location, overlapping small noncoding RNAs, associated Repeat Elements, associated imprinted genes, and lncRNA promoter information. Users can also search for microarray probes mapped to specific lncRNAs and associated disease information as well as search for lncRNA expression in a wide range of tissues.
DsTRD / Danshen Transcriptional Resource Database
A comprehensive transcript resource for Salvia miltiorrhiza. DsTRD contains 76531 transcribed sequences assembled from the RNA-seq data. DsTRD provides information regarding the sequences and functional annotations of the transcripts, including protein-coding RNAs, lncRNAs, other ncRNA, miRNAs, and phasiRNAs. The database also includes the tissue expression feature for each transcript, which was calculated and shown based on RNA-seq data. As an efficient bioinformatics tool, DsTRD is important in studying various kinds of molecular processes in S. miltiorrhiza.
A living plant endogenous target mimicry dataset. PeTMbase enables a highly flexible user interface to retrieve endogenous Target Mimicry (eTM) sequences by choosing the plant species. It also provides search features: i) to search eTM sequences by miRNA name, ii) to search eTM sequences in selected plant species, iii) to retrieve a comprehensive information such as gene ID, exon number, genomic coordinates of the long non-coding RNA (lncRNA) and detailed information of the corresponding miRNA sequence, iv) to download eTM data per plant species.
BmncRNAdb / Bombyx mori non-coding RNA database
A comprehensive and web-based database of the silkworm lncRNAs and miRNAs. BmncRNAdb offers a user-friendly interface for data browse and online analysis as well as the three online tools for users to predict the target genes of lncRNA or miRNA. This work gives a glimpse into lncRNAs of the silkworm and lays foundations for the ncRNAs study of the silkworm and other insects in the future. The availability of the complete set of lncRNAs from the silkworm will improve the comparative and evolutionary analyses of lncRNAs among different Lepidoptera or other insect species.
An integrated and comprehensive database relating to exploration of the putative regulatory functions of human lncRNAs with two mechanisms of regulation, by encoding siRNAs and by acting as miRNA decoys. To investigate lncRNAs producing siRNAs that regulate protein-coding genes, lncRNAMap integrated small RNAs (sRNAs) that were supported by publicly available deep sequencing data from various sRNA libraries and constructed lncRNA-derived siRNA-target interactions. In addition, lncRNAMap demonstrated that lncRNAs can act as targets for miRNAs that would otherwise regulate protein-coding genes.
Provides regulatory information about lncRNAs, such as targets, regulatory mechanisms, and experimental evidences for regulation and key molecules participating in regulation. LncReg is developed by collecting 1081 validated lncRNA-associated regulatory entries, including 258 non-redundant lncRNAs and 571 non-redundant genes. With regulatory relationships information, LncReg can provide overall perspectives of regulatory networks of lncRNAs and comprehensive data for bioinformatics research, which is useful for understanding the functional roles of lncRNAs.
IRNdb / Immunologically Relevant Non-coding RNAs database
Combines microRNA, PIWI-interacting RNAs, and long non-coding RNA information with immunologically relevant target genes. IRNdb is intended to advance research on the influence of ncRNAs on immunological processes. IRNdb contains information for mouse as it is often used as a model organism for immunological research purposes. We integrated data on predicted and experimentally supported ncRNA-target interactions, ncRNA and gene annotations, biological pathways and processes and experimental data in a uniform format with a user-friendly web interface.
Provides leishmania genomic information. LeishDB contains prediction and annotation of L. braziliensis protein-coding genes and non-coding RNAs. It is able to store a myriad of annotation data from multiple organisms, such as chromosomes, genes, ncRNAs, proteins, gene ontology (GO), associated publications, genomic coordinates, sequences, etc. The database offers about 11500 predicted open reading frames (ORFs), 5300 genes with defined function and 10500 predicted and classified non-coding RNAs.
Allows users to search for functional similar Long non-coding RNAs (lncRNAs) of a selecting lncRNAs. lncRNASim is a database for querying similarity scores of pair-wise lncRNA. Users can choose between several methods for prioritization: SemFunSim_PBPA, Resnik_PBPA, Wang_PBPA, PSB_PBPA, Lin _PBPA, SemFunSim_PBPM, Resnik_PBPM, Wang_PBPM, PSB_PBPM, Lin _PBPM. miRNADis is part of DincRNA, a bioinformatics resource for disease similarity calculation and non-coding RNA functional analysis.
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Provides detailed information for experimentally identified plant lncRNAs. In the current version, PLNlncRbase has manually collected data from nearly 200 published literature, covering a total of 1187 plant lncRNAs in 43 plant species. The user can retrieve plant lncRNA entries from a well-organized interface through a keyword search by using the name of plant species or a lncRNA identifier. Each entry upon a query will be returned with detailed information for a specific plant lncRNA, including the species name, a lncRNA identifier, a brief description of the potential biological role, the lncRNA sequence, the lncRNA classification, an expression pattern of the lncRNA, the tissue/developmental stage/condition for lncRNA expression, the detection method for lncRNA expression, a reference literature, and the potential target gene(s) of the lncRNA extracted from the original reference.
Enables the exploration and comparative analysis of lncRNAs in domestic animals. A user-friendly web interface, integrated information and tools make it valuable to researchers in their studies. ALDB currently archives 12,103 pig intergenic lncRNAs (lincRNAs), 8,923 chicken lincRNAs and 8,250 cow lincRNAs. In addition to the annotations of lincRNAs, it offers related data that is not available yet in existing lncRNA databases (lncRNAdb and NONCODE), such as genome-wide expression profiles and animal quantitative trait loci (QTLs) of domestic animals. Moreover, a collection of interfaces and applications, such as the Basic Local Alignment Search Tool (BLAST), the Generic Genome Browser (GBrowse) and flexible search functionalities, are available to help users effectively explore, analyze and download data related to domestic-animal lncRNAs.
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