Tag: rna sequence

Medical Subject Headings is the National Library of Medicine - controlled vocabulary used for indexing articles for PubMed and other NLM databases.

The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in miRBase represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence ...

The European Genome-phenome Archive (EGA) allows you to explore datasets from genomic studies, provided by a range of data providers. Access to datasets must be approved by the specified Data Access Committee (DAC).

The UCSC Archaeal Genome Browser is a window on the biology of more than 100 microbial species from the domain Archaea. Basic gene annotation is derived from NCBI Genbank/RefSeq entries, with overlays of sequence conservation across multiple species, ...

A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.

ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies. Data is collected to MIAME and MINSEQE standards. Expe ...

Gramene's purpose is to provide added value to plant genomics data sets available within the public sector, which will facilitate researchers' ability to understand the plant genomes and take advantage of genomic sequence known in one species for ide ...

The Expression Atlas is a free resource providing information on gene expression patterns under different biological conditions in a variety of species. Gene expression data is re-analysed in-house to detect genes showing interesting baseline and dif ...

Database of RNA interactions in post-transcriptional regulation.

NONCODE is a database of noncoding RNAs (except tRNAs and rRNAs), including long noncoding (lnc) RNAs. Information contained within the database includes human lncRNA–disease relationships and single nucleotide polymorphism-lncRNA–disease relationshi ...

The Integrated Microbial Genomes (IMG/M) aims to support the annotation, analysis and distribution of microbial genome and microbiome datasets sequenced at DOE's Joint Genome Institute (JGI). It also serves as a community resource for analysis and an ...

Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis which was created to improve knowledge of developmental and disease processes. Through curation and automated data provisioning from various sources, Xenbase aims ...

The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes ...

The ENCODE (Encyclopedia of DNA Elements) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements ...

Encyclopedia of DNA Elements (ENCODE) has created a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which ...

DRSC Functional Genomics Resources (DRSC-FGR) began as the Drosophila RNAi Screening Center (DRSC), founded by Prof. Norbert Perrimon in 2003, and the Transgenic RNAi Project (TRiP), founded by Prof. Perrimon in 2008. DRSC-FGR has been previously kno ...

NCBI Virus is a community portal for viral sequence data from RefSeq, GenBank and other NCBI repositories.

FlyAtlas 2 is the RNA-Seq successor to the original FlyAtlas (which was based on microarray analysis). Specifically, FlyAtlas 2 now provides access to: transcript information, sex-specific data for adult somatic tissues, and micro-RNA genes. FlyAtlas ...

The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the Solanaceae family, which includes species such as tomato, potato, pepper, petunia and eggplant.

MODOMICS is the first comprehensive database system for biology of RNA modification. It integrates information about the chemical structure of modified nucleosides, their localization in RNA sequences, pathways of their biosynthesis and enzymes that ...

As a database, miRTarBase has accumulated more than fifty thousand miRNA-target interactions (MTIs), which are collected by manually surveying pertinent literature after data mining of the text systematically to filter research articles related to fu ...

LNCipedia is a database for human long non-coding RNA (lncRNA) transcripts and genes. In addition to basic transcript information and gene structure, several statistics are determined for each entry in the database, such as secondary structure inform ...

The Aspergillus Genome Database is a resource for genomic sequence data as well as gene and protein information for Aspergilli. This publicly available repository is a central point of access to genome, transcriptome and polymorphism data for the fun ...

The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of multi-omics data ...

The Ribosomal Database Project - II (RDP-II)(1) provides data, tools and services related to ribosomal RNA sequences to the research community. Through its website (http://rdp.cme.msu.edu), RDP-II offers aligned and annotated rRNA sequence data, anal ...

DIANA-LncBase v3.0 (www.microrna.gr/LncBase) is a reference repository with experimentally supported miRNA targets on non-coding transcripts. Its third version provides approximately half a million entries, corresponding to ∼240 000 unique tissue a ...

The Gene Expression Database (GXD) is a community resource for gene expression information from the laboratory mouse. GXD stores and integrates different types of expression data and makes these data freely available in formats appropriate for compre ...

miRNA target prediction and functional annotation

GWIPS-viz is a freely available on-line genome browser which provides pre-populated ribosome profiling (Ribo-seq) and mRNA-seq tracks from published studies.

ATTED-II is a coexpression database for plant species with parallel views of multiple coexpression data sets and network analysis tools. The user can find functional gene relationships and design experiments to identify gene functions by reverse gene ...

microRNA-mRNA interaction maps

ToxoDB is a free online resource that provides access to genomic and functional genomic data for Toxoplasma and related organisms. The resource contains over 30 fully sequenced and annotated genomes, with genomic sequence from multiple strains availa ...

RNAcentral is a free, public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of databases representing a broad range of organisms and RNA types.

The LINCS Data Portal provides a unified interface for searching LINCS dataset packages and reagents. LINCS data are being made openly available as a community resource through a series of data releases, so as to enable scientists to address a broad ...

Long Non-Coding RNA Database

Predicted structures of internal transcribed spacer 2 (ITS2)

FungiDB is an integrated genomic and functional genomic database for the kingdom Fungi. The database integrates whole genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes compara ...

TISSUES is a weekly updated web resource that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. All evidence to common protein identifiers and Brenda Tissue O ...

CellPhoneDB is a publicly available repository of curated receptors, ligands and their interactions. Subunit architecture is included for both ligands and receptors, representing heteromeric complexes accurately. This is crucial, as cell-cell communi ...

Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). Bgee is based exclusively on curated "normal", healthy, expr ...

miRNEST is an integrative collection of animal, plant and virus microRNA data. miRNEST is being gradually developed to create an integrative resource of miRNA-associated data. The data comes from our computational predictions (new miRNAs, targets, mi ...

Alternative cleavage and polyadenylation (APA) of RNAs gives rise to isoforms with different terminal exons, which in turn determine the fate of the RNA and the encoded protein. APA has thus been implicated in the regulation of cell proliferation, di ...

The IRESite database presents information about experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract the eukaryotic ribosomal translation initiation complex and thus promote translation initiation ind ...

The exRNA Atlas is the data and metadata repository of the Extracellular RNA Communication Consortium (ERCC), an NIH Common Fund initiative to learn more about exRNAs in a variety of different contexts. The exRNA Atlas includes small RNA sequencing a ...

The ESTs and mRNAs from GenBank have been used to identify chimeric RNAs of two or more different genes. By analyzing thousands of chimeric ESTs by RNA sequencing, we found that the expression level of chimeric ESTs is generally low and they are high ...

Panzea provides information on the connection between phenotypes and genotypes of complex traits in maize and its wild relative, teosinte, and specifically in how rare genetic variations contribute to overall plant function.

The Tomato Functional Genomics Database integrates several prior databases including the Tomato Expression Database and Tomato Metabolite Database, and the Tomato Small RNA Database.

mirEX2 is a comprehensive platform for comparative analysis of primary microRNA expression data. RT–qPCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface.

ChIP-Seq, RNA-Seq and DNase-Seq data for haematopoietic and embryonic stem cells

Spatially resolved transcriptomics providing gene expression profiles with positional information is key to tissue function and fundamental to disease pathology. SpatialDB is the first public database that specifically curates spatially resolved tran ...

Database to integrate epitranscriptome sequencing data for exploring post-transcriptionally modifications of RNAs, as well as their relationships with microRNA binding events, disease-related SNPs and RNA-binding proteins (RBP).

Integrated annotation and sequencing-based expression data for all major classes of human small non-coding RNAs (sncRNAs) for both full sncRNA transcripts and mature sncRNA products derived from these larger RNAs.

PseudoBase is a collection of RNA pseudoknots that have been made available for retrieval to the scientific community.

Information Commons for Rice (IC4R) is a rice knowledgebase that incorporates rice data through multiple modules such as genome-wide expression profiles derived entirely from RNA-Seq data, resequencing-based genomic variations obtained from re-sequen ...

NAPP (Nucleic Acids Phylogenetic Profile) enables users to retrieve RNA-rich clusters from any genome in a list of 1000+ sequenced bacterial genomes. RNA-rich clusters can be viewed separately or, alternatively, all tiles from RNA-rich clusters can b ...

FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them ...

CRAM is a sequencing read file format that is highly space efficient by using reference-based compression of sequence data and offers both lossless and lossy modes of compression. Building on early proof-of-principle for reference-based compression ( ...

Within this database you will to able to find more than 12,000 extracted three-dimensional junction and kissing loop structures as well as detailed annotations for each.

GeneProf Data is an open web resource for analysed functional genomics experiments. We have built up a large collection of completely processed RNA-seq and ChIP-seq studies by carefully and transparently reanalysing and annotating high-profile public ...

T-psi-C is a database of tRNA sequences and 3D tRNA structures. The T-psi-C database can be continuously updated by any member of the scientific community.

An XML format for quality-related data of mass spectrometry and other high-throughput experiments. Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters ...

Customizable RNA-seq Data Analysis and Visualization Platform.

The PlantRNA database compiles tRNA gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. For each tRNA gene, the linear secondary structure is given as well as biological information. This includes 5'- an ...

The Plant Genome Integrative Explorer is a collection of interoperable web resources for searching, visualising and analysing genomics and transcriptomics data for different plant species. Currently, it includes dedicated web portals for enabling in- ...

VIRsiRNAdb contains information on experimentally validated Viral siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic ...

BSRD is a resource for bacterial sRNA sequences with extensive annotation and expression profiles. BSRD provides combinatorial regulatory networks of transcription factors and sRNAs with their common targets. There is also a novel RNA-Seq analysis pl ...

MINSEQE describes the Minimum Information about a high-throughput nucleotide SEQuencing Experiment that is needed to enable the unambiguous interpretation and facilitate reproduction of the results of the experiment. By analogy to the MIAME guideline ...

The Mammalian Transcriptomic Database (MTD) was created to store information on mammalian transcriptomes. The MTD allows browsing of genes based on their neighboring genomic coordinates or joint KEGG pathway and provides expression information on exo ...

Small nucleolar RNA orthological gene database.

tRNA Gene DataBase Curated by Experts

APASdb can visualize the precise map and usage quantification of different APA isoforms for all genes. The datasets are deeply profiled by the sequencing alternative polyadenylation sites (SAPAS) method capable of high-throughput sequencing 3'-ends o ...

Dictionary on miRNAs and their putative target pathways

Soybean Knowledge Base (SoyKB), is a comprehensive all-inclusive web resource developed for soybean translational genomics and molecular breeding. SoyKB stores information about genes/proteins, miRNAs/sRNAs, metabolites, SNPs, plant introduction (PI ...

circAtlas is an integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes. Existing circular RNA (circRNA) databases have become essential for transcriptomics. However, most are unsuitable for mining in-dept ...

Query single-cell gene expression databases by entering a gene symbol or a list of genes or selecting a cell type of their interest. Gene query provides quantitative RNA expression of the gene of interest in each lung cell type. Cell type query retur ...

Association of human lncRNAs with disease-related SNPs

XenMine has been created to view, search and analyze Xenopus data, and provides essential information on gene expression changes and regulatory elements present in the genome. It contains published genomic datasets from both Xenopus tropicalis and Xe ...

The noncoding RNAs database is a colection of currently available sequence data on RNAs, which do not have protein-coding capacity and have been implicated in regulation of cellular processes. The RNAs included in the database form very heterogenous ...

Predicted targets of host and viral miRNAs

The Heart Disease-related Non-coding RNAs Database (HDncRNA) provides information about common heart diseases and their related noncoding RNAs. The HDncRNA database contains manually annotated associations of ncRNAs with heart disease. Sources of dat ...

Plant microRNA knowledge base

Lnc2Cancer 3.0 includes comprehensive data on experimentally supported long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) associated with human cancers. In addition, web tools for analyzing lncRNA expression by high-throughput RNA sequencing ...

The siRNA database provides a gene-centric view of human siRNA experimental data, including siRNAs of known efficacy and siRNAs predicted to be of high efficacy by siSearch. Linked to these sequences is information including siRNA thermodynamic prope ...

Phenotypic data for Arabidopsis thaliana

SalmoBase is an integrated molecular resource for Salmonid species which includes visualizations and analytic tools. The genome of the Atlantic salmon (Salmo salar) has undergone extensive restructuring since a whole genome duplication event ~80 mill ...

Human lncRNA expression database

Aging related omics data

rPredictorDB is a predictive database of secondary structures of individual RNAs and their formatted plots.

Transcription factors (TFs) and their target genes have important functions in human diseases and biological processes. Gene expression profile analysis before and after knockdown or knockout is one of the most important strategies for obtaining targ ...

microRNA Expression and Sequence Analysis Database

MetaSRA is a database of normalized SRA human sample-specific metadata following a schema inspired by the metadata organization of the ENCODE project. This schema involves mapping samples to terms in biomedical ontologies, labeling each sample with a ...

LiceBase is a database for sea lice genomics. LiceBase provides the genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, Blast functionality and access to related high-thoughput genomics data.

siRecords is a collection of a diverse range of mammalian RNAi experiments . After choosing a gene, researchers can find all siRNA records targeting the gene, design a new siRNA targeting it, or submit siRNAs that have been tested. The resource also ...

Reference human lncRNA sets

H-DBAS is a specialized database for human alternative splicing (AS) based on H-Invitational full-length cDNAs. RNA-Seq tag information is correlated to the AS exons and splice junctions. A total of 148,376,598 RNA-Seq tags have been generated from R ...

TF-target relationsips inferred from single cell and bulk RNA-seq datasets

"iModulons", groups of independently-modulated genes

A database to systematically evaluate the effects of SNPs on non-coding RNA expression across cancer types | Numerous studies indicate that ncRNAs have critical functions across biological processes, and single nucleotide polymorphisms (SNPs) could c ...

an integrated database and analytic platform for de novo mutations in humans. De novo mutations (DNMs) significantly contribute to sporadic diseases, particularly in neuropsychiatric disorders. Whole-exome sequencing (WES) and whole-genome sequencin ...

Identification of tRNA-derived ncRNAs in TCGA and NCI-60 panel cell lines and development of the public database tRFexplorer. tRFexplorer is a public database through which users may display the expression profile of tRNA-derived ncRNAs in every cel ...

RNA Localization in the cell

An atlas of mRNA, lncRNA and circRNA in extracellular vesicles from human biofluids.

CRISPR/Cas9 Off-Target Cleavage Assays

Sciatic Nerve Atlas (SNAT) is a database med transcriptional profiling of mouse peripheral nerves to the single-cell level.

LncRNA Spatial Atlas of Expression across Normal and Cancer Tissues. Knowledge of lncRNA spatial expression patterns across tissues is important for identifying their roles in different tissues that provide important insights into disease mechanisms ...

OmicsDB offers an integrated platform for studying biological networks in multiple organisms, as well as accessing gene expression data. By expanding the classic single species databases across species, it is possible to leverage the amount of inform ...

STOREDB provides infrastructure for sharing data and resources in radiation biology and epidemiology. It is a platform for the archiving and sharing of primary data and outputs of all kinds, including epidemiological and experimental data, from resea ...

Breast cancer gene-expression miner (bc-GenExMiner) 4.5 is a mining module computes breast cancer differential gene expression analyses. It is a statistical mining tool of published annotated breast cancer transcriptomic data (DNA microarrays and RNA ...

A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. AppleMDO is a multi-dimensional omics database. Users can submit locus IDs to quickly search for co-expression networks, functional modules, chromatin states a ...

A unified gene expression atlas for the model plant Physcomitrella patens. PEATmoss is an interactive tool to visualize gene expression data. These help pages explain several ways to query the expression data and to visualize the results, enabling t ...

the small RNA Expression Atlas web application. Sign in with Google or with you SEA account below. If you have not created an account yet, then please register first. If you have received an eMail from Oasis 2 that the classification or DE analysis ...

PlantAPAdb provides a comprehensive and manually curated catalog of APA sites in plants based on a large volume of data from diverse biological samples generated by 3′ seq. Currently, PlantAPAdb contains APA sites in seven plant organisms, including ...

Dual RNA-seq host-pathogen sequencing

Alternative splicing during development in 20 species

BuG@Sbase is a microbial gene expression and comparative genomic database containing microarray datasets.

CellO (Cell Ontology-based classification) is a Python package for performing cell type classification of human RNA-seq data. CellO makes hierarchical predictions against the Cell Ontology. These classifiers were trained on nearly all of the human pr ...

SyntDB: defining orthologues of human long noncoding RNAs across primates. SyntDB - the database of human long non-coding RNAs conserved across primates. Comprehensive collection of long noncoding RNAs (lncRNAs) and their evolutionary relationships ...

Construction of complete Tupaia belangeri transcriptome database by whole-genome and comprehensive RNA sequencing | Tupaia belangeri (Family Tupaia, Genus Tupaia) | Tupaia ( Tupaia belangeri ) is a small mammal belonging to the family Tupaiidae, whic ...

The eQTL Catalogue aims to provide uniformly processed gene expression and splicing QTLs from all available public studies on human. Quantitative trait loci (QTL) are genomic variants that are significantly associated to a measurable phenotype. This ...

Chickspress is a gene expression database for chicken tissues. Chickspress incorporates both NCBI and Ensembl gene models and links these gene sets with experimental gene expression data and QTL information. By linking gene models from both NCBI and ...

riboCIRC is a comprehensive database of translatable circRNAs. Translation of circular RNAs (circRNAs) now has drawn increasing attention from researchers due to their emerging roles of the functional peptides encoded by circRNAs as new players invol ...

Cancer-Specific CircRNA Databse(CSCD) is an integrated interactional database of cancer-specific circular RNAs.

Full-Parasites is a transcriptome database of apicomplexa parasites, which include Plasmodium and Toxoplasma species. It contains EST sequences, full length cDNAs, transcription start sites and RNA-seq data sets. Various types of cDNA data resources ...

Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish.

Systematic investigation of cytokine signaling activity at the tissue and single-cell levels.

Tissue-specific circRNA expression profiles and regulatory networks

TarDB is a database for conserved miRNA targets, degradome supported miRNA targets and miRNA-triggered phasiRNAs in plants. TarDB is a plant miRNA target repository, which is based on cross-species conservation filter, degradome PARE-seq, and small R ...

A high-quality genome sequence of alkaligrass provides insights into halophyte stress tolerance. A high-quality chromosome-level genome sequence of alkaligrass assembled from Illumina, PacBio and 10× Genomics reads combined with genome-wide chromosom ...

Plant stress RNA-Seq nexus (PSRN) - stress-specific transcriptome database in plant cells.

A gene Expression Browser for RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics.

Database for ncRNA expression in human extracellular vesicles.

A database for plant circRNAs that act as miRNA decoys. Circular RNAs (circRNAs) are a novel type of RNAs that form covalently closed loop structures with neither 5'- 3' polarities nor polyadenylated tails. GreenCircRNA(v1.0) is the most comprehensi ...

circ2GO is a comprehensive database compiling and analyzing circular RNAs found in lung cancer cell lines providing the data in tables as well as visualizing it in transcript maps and in heatmaps. Importantly, we also provide easy-to-use online tools ...

A database of gene expression patterns in the Drosophila terminalia. An Atlas of Transcription Factors Expressed in Male Pupal Terminalia of Drosophila melanogaster.

The CGDB (Coriander Genome Database) is mainly contained the coriander genome, transcriptome, and metabolome datasets

GenBank Sequence Format (GenBank Flat File Format) consists of an annotation section and a sequence section. The start of the annotation section is marked by a line beginning with the word "LOCUS". The start of sequence section is marked by a line be ...

A CT (Connectivity Table) file contains secondary structure information for a RNA sequence.

MONOCLdb is an integrative and interactive database designed to retrieve and visualize annotations and expression profiles of long-non coding RNAs (lncRNAs) expressed in Collaborative Cross (http://compgen.unc.edu/) founder mice in response to respir ...

Define a GFF3 format for output of small RNA pipelines. Here, we present a community based, open source project to work toward the standardization of miRNA pipelines and encourage the development of downstream tools for visualization, differential ex ...

The Genotype-Tissue Expression (GTEx) project is an ongoing effort to build a comprehensive public resource to study tissue-specific gene expression and regulation. Samples were collected from 53 non-diseased tissue sites across nearly 1000 individua ...

A Database for Insights Into Single-Cell Gene Expression Profiles During Human Developmental Processes. PRESDB:pig RNA Editing database

PlanExp is an intuitive integration of complex RNA-seq datasets with planarian omics resources.

Database of single-cell expression map across various human cancers.

ctcRbase is agene expression database of circulating tumor cells and microemboli Circulating tumor cells/microemboli (CTCs/CTM) are those cells that depart from cancerous lesions and shed into the bloodstream. Enumeration and analysis of CTCs/CTM may ...

CuAS is an integrated database for Cucumber Alternative Splicing, includes genomic annotation, isoform-level functions, isoform-level features and tissue-specific AS events among multiple tissues.

A knowledgebase of cellular drug response.

Integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species.

A Searchable Comparative Transcriptome Database for Healthy and Diseased Human Eye Tissue.

Regeneration Roadmap aims to compile large datasets for gene expression and regulation created by a broad spectrum of high-throughput omics technologies. This one-stop service provides user-friendly functionalities to explore annotated regeneration-r ...

MSRdb (Mycobacterial Systems Resource) is a mycobacterial systems resource for the research community. The Mycobacterial Systems Resource (MSR) is a comprehensive, integrated biological and bioinformatic resource for the research community. The MSR u ...

An informational platform for genome biology of grass carp. Grass carp (Ctenopharyngodon idellus) is a herbivorous, freshwater fish species of the family Cyprinidae, and the only species of the genus Ctenopharyngodon.

An online transcriptome platform for human circRNA expressions in cancers.

Database of fusion transcripts in Arabidopsis thaliana.

CrustyBase is an interactive online database for crustacean transcriptomes. CrustyBase provides an environment for navigating and visualising crustacean transcriptome datasets. Users can search existing transcriptomes or import new datasets of their ...

Transcriptomic database for 14 species of scleractinian corals.

TRANSNAP is a web database providing comprehensive information on Japanese pear transcriptome.

Web-based database, CDRgator (Cancer Drug Resistance navigator) for comparative analysis of gene expression signatures of cancer drug resistance.

A major update of the ruminant functional and evolutionary genomics database.

Database to integrate, analyze and visualize human disease-related circRNA transcriptome.

A comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels.

scAPAdb provides a comprehensive and manually curated atlas of poly(A) sites, APA events and poly(A) signals at the single-cell level in six species based on a large volume of scRNA-seq data. Currently, scAPAdb records APA information in animal speci ...

ViroidDB is the most comprehensive collection of viroid, satellite RNA, retrozyme, and deltavirus genome sequences available on the internet.

ColorCells is a database of expression, classification and functions of lncRNAs in single cells. Single cell RNA sequencing (scRNA-Seq) technology has revealed significant differences in gene expression levels between different cell groups.

A comprehensive database of RNAs involved in liquid-liquid phase separation.

Fusion gene annotation updates aided by deep learning.

A database of human tissue functional gene networks built with a large compendium of curated RNA-seq data.

PopTargs is a database for studying population evolutionary genetics of human microRNA target sites. These are the scripts used to create the MySQL database that is used by PopTargs.essex.ac.uk. The pipeline can be altered to create similar database ...

A database for alternative splicing atlas in livestock animals. The alternative splicing in livestock animals database (ASlive.org) is a collection of alternative splicing events across tissues in livestock animal speceis in including cattle (Bos ta ...

A manually curated database for experimentally validated non-coding RNAs in inflammation. Non-coding RNAs in Inflammation (ncRI) provides a manually curated database for experimentally validated non-coding RNAs in inflammatary disease. Recently, inf ...

An interactive online database for analysis of gene expression and viral infection in cancer.

syngeneic mouse tumor database to model tumor immunity and immunotherapy response.

Integrated multi-omics database of human and mouse early embryo.

A large and standardized collection of transcriptome data sets for human pluripotent stem cell research.

An integrative analysis platform for investigating differentially expressed gene-level and isoform-level human cancer markers

A web service for studying gene expression in human skeletal muscle. MuscleAtlasExplorer(BETA)2.

Human Antigen Receptor Consortium (huARdb) is a comprehensive database of single cell immune profiling and V(D)J T cell and B cell analysis, enhanced with advanced visualization of single-cell data.

ADEx: Autoimmune Diseases Explorer is a comprehensive and centralized database for exploring omics data in Autoimmune Diseases. The database that integrates 82 curated transcriptomics and methylation studies covering 5609 samples for some of the most ...

RASP (RNA Atlas of Structure Probing) is build from 161 deduplicated transcriptome-wide RNA secondary structures from datasets culled from 38 papers. RASP covers 18 species across animals, plants, bacteria, fungi, and also viruses, and categorizes 18 ...

Computational prediction of animal microRNA genes

The 5' and 3' untranslated regions of eukaryotic mRNAs may play a crucial role in the regulation of gene expression controlling mRNA localization, stability and translational efficiency. For this reason we developed UTRdb, a specialized database of 5 ...

PrimateDatabase.com, a publicly available web-accessible archive of intracellular patch clamp recordings and highly detailed three-dimensional digital reconstructions of neuronal morphology. PrimateDatabase.com is unique because it is currently the l ...

Human RNA-RNA and RNA-protein interactions

Naturally modified nucleosides in RNA

A database of 3D RNA fragments within known RNA structures

Database of RNA Editing

A Rigorously Annotated Database of A-to-I RNA editing

Database of RNA Base-Pair Structures

small regulatory RNA in microbial genomes

A-to-I RNA editing events in human

Post-transcriptional regulation by RNA-binding proteins

RNA MEthylation by SEquencing databaSe

RNA editing sites in lncRNAs from human, monkey, mouse and fly

Noncoding RNA Expression Database

Ribosome profiling database

Clusters of piRNAs

5S ribosomal RNA is an integral component of the large subunit of all cytoplasmic and most organellar ribosomes. Its small size and association with ribosomal as well as non-ribosomal proteins made it an ideal model RNA molecule for studies of RNA st ...

Somatic mutations that impact microRNA targeting in cancer

smRNA-seq database for miRNA research

Compilation of tRNA sequences and tRNA genes

RNA SSTRAND contains known secondary structures of any type and organism. The ultimate goal of this database is to incorporate a comprehensive collection of known secondary structures, and to provide the scientific community with simple yet powerful ...

microRNA precursors and their mapping to targets in vertebrate genomes

Functional RNA Database (fRNAdb) is a database service that hosts a large collection of non-coding transcripts including annotated/un-annotated sequences from H-inv database, NONCODE, and RNAdb. A set of computational sequence analyses are performed ...

microRNA target predictions and expression profiles

microRNA target prediction, functional analysis, and gene expression data

Short (14-32 nt) tRNA-related fragments

Sequences and properties of Piwi-interacting RNAs (piRNAs) in human, mouse and rat

Literature-curated database for validatedly or potentially pathogenic roles of dysregulated miRNAs in human disease

All complete or nearly complete rRNA sequences

Although a large amount of experimentally-derived information about RNA editing sites currently exists, this information has remained scattered in a variety of sources and in diverse data formats. Availability of standard collections for high-quality ...

Yeast small nucleolar RNAs

snoRNA genes in plant species

Prediction of viral microRNA candidate hairpins

Locations of modified rRNA nucleotides within the 3D structure of the ribosome

Here, we have predicted CasRx guide efficiency for all human and mouse RefSeq genes. We have also enabled custom sequence input for CasRx guide design.

Modified nucleosides in small subunit rRNA

Small RNAs (smRNAs), which include microRNAs (miRNAs), small-interfering RNAS (siRNAs) and trans-acting siRNAs (ta-siRNAs) are ~19-24 nt RNAs that are important negative regulators of nucleotide sequences involved in development, homeostasis and in t ...

The RNA G-quadruplex and RG4-binding proteins database.

The known occurrences of non-canonical base-base interactions in RNA are tabulated in the NCIR (http://prion.bchs.uh.edu/bp_type/) database. Currently, there are over 1700 entries including those from the crystal and NMR structures of RNAs published ...

rPanglaoDB is an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database. A meta-analysis database for single cell RNA sequencing data. Search across datasets, studies, download data, and perform advanced visualiz ...

Access to the expanded versions of the 16S and 23S Ribosomal RNA Mutation Databases has been improved to permit searches of the lists of alterations for all the data from (1) one specific organism, (2) one specific nucleotide position, (3) one specif ...

A Web-Server of tRNA Expression Profiles from Small RNA Sequencing Data in Humans.

GRSDB: ‘G’-Rich Sequences DataBase contains information on composition and distribution of putative Quadruplex forming 'G'-Rich Sequences (QGRS) in the alternatively processed (alternatively spliced or alternatively polyadenylated) mamma ...

miRecords is a resource for animal miRNA-target interactions. miRecords consists of two components. The Validated Targets component is a large, high-quality database of experimentally validated miRNA targets resulting from meticulous literature curat ...

Plant transfer RNA-derived non-coding RNAs (tncRNAs) database.

This genomic tRNA database contains tRNA identifications made by the program tRNAscan-SE (Lowe & Eddy, Nucl Acids Res 25: 955-964, 1997) on complete or nearly complete genomes. Unless otherwise noted, all annotation is automated, and has not been ins ...

Signal recognition particle (SRP) is an ribonucleoprotein particle designed to recognize secretory signal sequences as they emerge from the ribosome. SRP associates with the SRP-receptor in the ER membrane, is released from the ribosome, and recycled ...

A database of pan-cancer analysis and systematic functional annotation for lncRNAs from RNA-sequencing data.

Sequence conservation in non-coding, upstream regions of orthologous genes from man and mouse is likely to reflect common regulatory DNA sites. Motivated by this assumption we have delineated a catalogue of conserved non-coding sequence blocks and pr ...

MVIP provides a large number of available multi-omics data under viral infection in various species.

A database for gene expression and alternative splicing profiles and their analyses based on 53 615 public RNA-seq samples in 72 metazoan species.

snoRNA-LBME-db is a collection of human small nucleolar RNAs (snoRNAs) and Cajal body-specific RNAs (scaRNAs), that serve to guide modifications in rRNAs or snRNAs. The database can be search by sno/scaRNA name or Accession number, or by the position ...

Group II introns are self-splicing RNAs and retroelements found in bacteria and lower eukaryotic organelles. During the past several years, they have been uncovered in surprising numbers in bacteria due to the genome sequencing projects; however, mos ...

piRNAdb it's a piwi-interacting RNA sequences storage and search system, providing some others relevant information like alignments, clusters, datasets and targets of these piRNAs.

Increasing evidence reveals that diverse non-coding RNAs (ncRNAs) play critically important roles in viral infection [1-3]. Viruses can use diverse ncRNAs to manipulate both cellular and viral gene expression to establish a host environment conducive ...

RNAi Codex consists of a database of shRNA related information and an associated website. It has been developed as a portal for publicly available short-hairpin RNA (shRNA) resources and is accessible at http://codex.cshl.org. RNAi Codex currently ho ...

The HMDD database is a collection of experimentally supported human microRNA (miRNA) and disease associations. Here, we describe the HMDD v2.0 update that presented several novel options for users to facilitate exploration of the data in the database ...

In recent years there have been increasing numbers of transcripts identified that do not encode proteins, many of which are developmentally regulated and appear to have regulatory functions. We have constructed a comprehensive mammalian noncoding RNA ...

T1TAdb is a database of Type I Toxin-Antitoxin systems.

A comprehensive animal enhancer RNA database.

Barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq.

lncRNASNP is an integrated database of SNPs in lncRNAs and their potential functions in human and mouse. It integrated several public databases and tools, including LNCipedia, NONCODE, dbSNP, miRBase, TCGA and so on. Its aim is to provide information ...

An atlas of alternative splicing profiles in vertebrate cell and tissue types

Natural antisense transcripts (NATs) are reverse complementary at least in part to the sequences of other endogenous sense transcripts. Most NATs are transcribed from opposite strands of their sense partners. They regulate sense genes at multiple l ...

Full-length transcripts and conservation of plant circRNAs.

A PIWI-bound piRNAs database to mining NGS sncRNA data and beyond.

A blood platelets-based gene expression database for disease investigation.

Plant virus interaction mechanism and associated pathways in mosaic disease of small cardamom (Elettaria cardamomum Maton) by RNA-Seq approach.

Database and analysis platform for gene expression and alternative splicing of fish species.

A comprehensive database for alternative splicing in tea plants (Camellia sinensis).

A comprehensive and interactive database for transcriptomes from prostate cancer population cohorts.

A virus and host ncRNA-associated interaction repository with increased coverage and annotation.

DRscDB is a single-cell RNA-seq resource for data mining and data comparison across species.

A Comprehensive Multi-Omics Association Database of Secondary Growth in Response to Stress in Populus trichocarpa.

A curated RNA-seq database of palmitoylating and de-palmitoylating enzyme expression in the mouse brain.

The adenylate uridylate-rich elements (AREs) mediate the rapid turnover of mRNAs encoding proteins that regulate cellular growth and body response to exogenuous agents such as microbes,inflammatory and environmental stimuli. The Adenylate Uridylate ( ...

LncRNAWiki (http://lncrna.big.ac.cn) is a wiki-based, open-content, and publicly editable platform aimed at community-based curation and collection of information on human long non-coding RNAs (lncRNAs). Current related databases are dependent primar ...

An atlas of 3'UTR alternative polyadenylation quantitative trait loci across human normal tissues.

The Swiss Portal for Immune Cell Analysis (SPICA) is a web resource dedicated to the exploration and analysis of single-cell RNA-seq data of immune cells.

The Noncoding RNAs and Protein related biomacromolecules Interaction database (NPInter; http://bioinfo.ibp.ac.cn/NPInter or http://www.bioinfo.org.cn/NPInter) is a database that documents experimentally determined functional interactions between nonc ...

EchinoDB is a database consisting of amino acid sequence othoclusters from 42 echinoderm transcriptomes. We sampled taxa to span the deepest divergences within each of the 5 extant echinoderm classes. Data can be searched by keywords such as annotati ...

dbDEMC (database of Differentially Expressed MiRNAs in human Cancers) is an integrated database that designed to store and display differentially expressed microRNAs cancers detected by high-throughput and low-throughput methods.

LjaFGD is the Lonicera japonica functional genomics database..

Sno/scaRNA database (sno/scaRNAbase, http://bioinfo.fudan.edu.cn/snoRNAbase.nsf) was developed to facilitate the research of small nucleolar RNAs (snoRNAs) and cajal body-specific RNAs (scaRNAs) that have been found to play important roles in rRNA, t ...

exRNADisease is a database designed for providing the landscape of different types of extracellular RNAs (mRNAs, lncRNAs, miRNAs, circRNAs, tRFRNAs and piRNAs) from body fluids in human diseases.

Long non-coding RNAs (lncRNAs) play important functional roles in various biological processes. Early databases were utilized to deposit all lncRNA candidates produced by high-throughput experimental and/or computational techniques to facilitate clas ...

Distinct signatures of codon and codon pair usage in 32 primary tumor types in the novel database CancerCoCoPUTs for cancer-specific codon usage.

A microRNA tissue expression database.

CancerMIRNome is a web server for cancer miRNome interactive analysis and visualization based on the huamn miRNome data of 33 cancer types from The Cancer Genome Atlas (TCGA), and 40 public cancer circulating miRNome profiling datasets from NCBI Gene ...

tmRNA is a molecule that combines functions of tRNA and mRNA in a process called trans-translation [see 1, for review] to rescue ribosomes that are stalled at the end of broken mRNA. tmRNA-like sequences have been identified in all bacteria analyzed ...

The Chinese Glioma Genome Atlas (CGGA) is a user-friendly web application for data storage and analysis to explore brain tumors datasets. This database includes the whole-exome sequencing, DNA methylation, mRNA sequencing, mRNA microarray and microRN ...

SELEX_DB is an online resource containing both the experimental data on in vitro selected DNA/RNA oligomers (aptamers) and the applets for these oligomers recognition. In vitro selection of oligomers binding target proteins is a novel technology inte ...

AOE (All Of gene Expression) - an integrated index for public gene expression databases.

NeuroCirc is an integrative web-based resource of circRNA expression in the human brain, which allows interactive exploration of circRNA expression across multiple datatsets, including circRNA expression in bulk brain tissue, circQTLs, circRNA expres ...

Co-expression Network Database for <i>de novo</i> Transcriptome Assembly of <i>Paeonia lactiflora</i> Pall. Paeonia lactiflora Pall., commonly known as the herbaceous peony, is an ornamental flowering plant known around the world. Its oil contains a ...

A comprehensive resource for kiwifruit genomics.

A curated repository of cell types with multifaceted characterization.

Many animal species present sex differences. Sex-associated genes (SAGs), which have female-biased or male-biased expression, have major influences on the remarkable sex differences in important traits such as growth, reproduction, disease resistance ...

Comparative transcriptomics and co-expression database for bacterial pathogens.

Sepsis single-cell whole gene expression database.

Multi-omics molecular biomarkers and database of osteoarthritis.

A curated and comprehensive resource of plant cell markers.

The Gene Expression Database of Poplar under Stress.

A knowledgebase and transparency tool for minimum information in spheroid identity.

A Database and User Interface for scRNA-seq Marker Genes.

Fully-automated and ultra-fast cell-type identification using specific marker combinations from single-cell transcriptomic data.

A manually curated resource for multi-omics level evidence integration of fibrosis research

AhNGE is a Database for Arachis hypogaea nodule developmental gene expression.

A manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication.

Quickomics is a tool for exploring omics data in an intuitive, interactive and informative manner.

Exploration and analysis of R-loop mapping data with RLBase.

Rhododendron Plant Genome Database (RPGD) is a comprehensive online omics database for Rhododendron.

A secondary database derived from primary data in NCBI's short read archive. Database for corrected read counts and genome mapping on NCBI's transcriptomics archives.

MtExpress is a comprehensive and curated RNAseq-based gene expression atlas for the model legume medicago truncatula.

COGVIC(Catalogue Of Germline Variants In Cancer). A comprehensive database of germline pathogenic variants in East Asian pan-cancer patients.

ALEXA is a microarray design platform for 'alternative expression analysis'. This platform facilitates the design of expression arrays for analysis of mRNA isoforms generated from a single locus by the use of alternative transcription initiation, spl ...

An atlas of intronic polyadenylation quantitative trait loci across human tissues.

Database of transcriptomic profiles of human brains of six neuropsychiatric disorders.

The CerealESTdb, a user-friendly, searchable, and interactive database has been developed with a primary goal to provide information on assembled and annotated ESTs from four major crop plants, namely wheat, rice, maize, and sorghum under multiple en ...

Allele-Specific DNA Methylation Databases (ASMdb) is a comprehensive database for allele-specific DNA methylation in diverse organisms. ASMdb is aiming to provide a comprehensive resource and a web tool for showing the DNA methylation level and diffe ...

BART Cancer Database is a web resource designed to display putative transcriptional regulators (TRs) that are responsible for up and downregulation of genes in 15 different cancer types in The Cancer Genome Atlas. BART Cancer uses BART (Binding Analy ...

PaIntDB (Pseudomonas aeruginosa Interactions Database) is a tool for network-based omics integration and visualization using protein–protein interactions in Pseudomonas aeruginosa. PaIntDB contains more than 150K protein-protein (PPI) and protein-met ...

The FAANG metadata analysis specification describes the specification for all analysis metadata as part of the larger FAANG metadata guidance project. Analysis metadata needs to contain the following process attributes: input data (a list of files us ...

An integrative platform for comparative and functional genomics of marmots. iMarmot: an integrative Marmot database. Marmots are large Holarctic rodents in the genus Marmota with 14 living species. Most marmot species occupy a harsh environment cha ...