Tag: rna sequence


Found 287 sources
Source Match ReputationScore*

Kyoto Encyclopedia of Genes and Genomes


Medical Subject Headings is the National Library of Medicine - controlled vocabulary used for indexing articles for PubMed and other NLM databases.
100%

miRBase


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 ...
95%

The European Genome-phenome Archive


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).
77%

The UCSC Archaeal Genome Browser


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, ...
73%

Greengenes


A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.
71%

ArrayExpress


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 ...
71%

Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants


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 ...
66%

Expression Atlas


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 ...
65%

doRiNA


Database of RNA interactions in post-transcriptional regulation.
63%

NONCODE


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 ...
61%

Integrated Microbial Genomes And Microbiomes


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 ...
61%

Xenopus laevis and tropicalis biology and genomics resource


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 ...
59%

Rfam


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 ...
58%

Encyclopedia of DNA Elements at UCSC


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 ...
57%

ENCODE Project


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 ...
57%

DRSC Functional Genomics Resources


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 ...
57%

FlyAtlas 2


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 ...
54%

MODOMICS


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 ...
54%

NCBI Virus


NCBI Virus is a community portal for viral sequence data from RefSeq, GenBank and other NCBI repositories.
54%

Sol Genomics Network


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.
54%

miRTarBase


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 ...
52%

LNCipedia


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 ...
51%

Aspergillus Genome Database


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 ...
50%

Ribosomal Database Project (RDP-II)


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 ...
50%

BIG Data Center


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 ...
50%

DIANA-LncBase


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 ...
49%

MGI Mouse Gene Expression Database


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 ...
49%

miRDB


miRNA target prediction and functional annotation
48%

GWIPS-viz


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.
48%

StarBASE


microRNA-mRNA interaction maps
48%

ToxoDB


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 ...
47%

lncRNAdb


Long Non-Coding RNA Database
46%

Arabidopsis Thaliana Trans-factor and cis-Element prediction Database


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 ...
46%

RNAcentral


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.
46%

ITS2


Predicted structures of internal transcribed spacer 2 (ITS2)
46%

Library of Integrated Network-Based Cellular Signatures Data Portal


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 ...
45%

Fungal and Oomycete genomics resource


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 ...
45%

CellPhoneDB


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 ...
45%

Bgee DataBase for Gene Expression Evolution


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 ...
44%

TISSUES


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 ...
44%

miRNEST


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 ...
44%

IRESite


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 ...
43%

Extracellular RNA Atlas


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 ...
43%

PolyASite


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 ...
43%

The Improved Database Of Chimeric Transcripts and RNA-Seq Data


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 ...
42%

Tomato Functional Genomics Database


The Tomato Functional Genomics Database integrates several prior databases including the Tomato Expression Database and Tomato Metabolite Database, and the Tomato Small RNA Database.
42%

Panzea


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.
42%

CODEX


ChIP-Seq, RNA-Seq and DNase-Seq data for haematopoietic and embryonic stem cells
42%

RMBase


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).
42%

mirEX


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.
42%

Database of small human non-coding RNAs


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.
41%

A database for spatially resolved transcriptomes


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 ...
41%

PseudoBase


PseudoBase is a collection of RNA pseudoknots that have been made available for retrieval to the scientific community.
41%

Information Commons for Rice


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 ...
41%

Nucleic Acid Phylogenetic Profile


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 ...
40%

CRAM


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 ( ...
40%

RNAJunction: A Database of RNA Junction and Kissing loop Structure


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.
40%

GeneProf


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 ...
40%

expVIP


Customizable RNA-seq Data Analysis and Visualization Platform.
40%

Quality Control Markup Language


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 ...
40%

FaceBase


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 ...
40%

PlantRNA


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 ...
40%

T-psi-C


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.
40%

BSRD


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 ...
39%

VIRsiRNAdb


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 ...
39%

Plant Genome Integrative Explorer


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- ...
39%

Mammalian Transcriptomic Database


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 ...
38%

snOPY


Small nucleolar RNA orthological gene database.
38%

tRNADB-CE


tRNA Gene DataBase Curated by Experts
38%

Minimal Information about a high throughput SEQuencing Experiment


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 ...
38%

Alternative Poly(A) Sites database


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 ...
38%

miRPathDB


Dictionary on miRNAs and their putative target pathways
38%

circAtlas


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 ...
38%

Soybean Knowledge Base


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 ...
38%

LungGENS


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 ...
38%

LincSNP


Association of human lncRNAs with disease-related SNPs
37%

ncRNAs database


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 ...
36%

RepTar


Predicted targets of host and viral miRNAs
36%

XenMine


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 ...
36%

PmiRKB


Plant microRNA knowledge base
36%

Heart Diseases related Noncoding RNA Database


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 ...
36%

lnc2cancer


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 ...
36%

siRNAdb


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 ...
36%

AraPheno


Phenotypic data for Arabidopsis thaliana
36%

LncExpDB


Human lncRNA expression database
36%

SalmoBase


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 ...
36%

Aging Atlas


Aging related omics data
36%

KnockTF


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 ...
35%

mESAdb


microRNA Expression and Sequence Analysis Database
35%

rPredictor


rPredictorDB is a predictive database of secondary structures of individual RNAs and their formatted plots.
35%

MetaSRA


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 ...
35%

siRecords


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 ...
35%

LncSEA


Reference human lncRNA sets
35%

LiceBase


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.
35%

H-DBAS


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 ...
34%

GRNdb


TF-target relationsips inferred from single cell and bulk RNA-seq datasets
34%

iModulonDB


"iModulons", groups of independently-modulated genes
34%

ncRNA-eQTL


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 ...
34%

Gene4Denovo


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 ...
34%

tRFexplorer


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 ...
34%

SNAT


Sciatic Nerve Atlas (SNAT) is a database med transcriptional profiling of mouse peripheral nerves to the single-cell level.
33%

LncSpA


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 ...
33%

RNALocate


RNA Localization in the cell
33%

crisprSQL


CRISPR/Cas9 Off-Target Cleavage Assays
33%

bc-GenExMiner


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 ...
33%

AppleMDO


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 ...
33%

PEATmoss


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 ...
33%

OmicsDB


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 ...
33%

STOREDB


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 ...
33%

SEAweb


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 ...
33%

PlantAPAdb


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 ...
33%

DualSeqDB


Dual RNA-seq host-pathogen sequencing
32%

MeDAS


Alternative splicing during development in 20 species
32%

[email protected]


[email protected] is a microbial gene expression and comparative genomic database containing microarray datasets.
32%

CellO


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 ...
32%

SyntDB


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 ...
32%

TupaiaBase


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 ...
32%

riboCIRC


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 ...
32%

eQTL Catalogue


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 ...
32%

CSCD2


Cancer-Specific CircRNA Databse(CSCD) is an integrated interactional database of cancer-specific circular RNAs.
32%

Chickspress


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 ...
32%

Full-parasites


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 ...
32%

RsHSF


Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish.
32%

CytoSig


Systematic investigation of cytokine signaling activity at the tissue and single-cell levels.
32%

TarDB


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 ...
32%

alkaligrass


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 ...
32%

PSRN


Plant stress RNA-Seq nexus (PSRN) - stress-specific transcriptome database in plant cells.
31%

BacHBerryEXP


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.
31%

EVAtlas


Database for ncRNA expression in human extracellular vesicles.
31%

GreenCircRNA


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 ...
31%

circ2GO


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 ...
31%

Fly Terminalia Database


A database of gene expression patterns in the Drosophila terminalia. An Atlas of Transcription Factors Expressed in Male Pupal Terminalia of Drosophila melanogaster.
31%

Coriander Genomics Database


The CGDB (Coriander Genome Database) is mainly contained the coriander genome, transcriptome, and metabolome datasets
31%

SCDevDB


A Database for Insights Into Single-Cell Gene Expression Profiles During Human Developmental Processes. PRESDB:pig RNA Editing database
31%

PlanExp


PlanExp is an intuitive integration of complex RNA-seq datasets with planarian omics resources.
31%

CancerSCEM


Database of single-cell expression map across various human cancers.
31%

ctcRbase


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 ...
31%

CuAS


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.
31%

CeDR Atlas


A knowledgebase of cellular drug response.
31%

LanceletDB


Integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species.
31%

Human Eye Transcriptome Atlas


A Searchable Comparative Transcriptome Database for Healthy and Diseased Human Eye Tissue.
31%

Regeneration Roadmap


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 ...
31%

MSRdb


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 ...
31%

GenBank Sequence Format


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 ...
31%

Connectivity Table file format


A CT (Connectivity Table) file contains secondary structure information for a RNA sequence.
31%

The MOuse NOnCode Lung database


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 ...
31%

mirGFF3


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 ...
31%

GTEx Portal


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 ...
31%

GCGVD


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.
31%

circExp


An online transcriptome platform for human circRNA expressions in cancers.
31%

AtFusionDB


Database of fusion transcripts in Arabidopsis thaliana.
31%

CrustyBase


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 ...
31%

CoralTBase


Transcriptomic database for 14 species of scleractinian corals.
31%

TRANSNAP


TRANSNAP is a web database providing comprehensive information on Japanese pear transcriptome.
31%

CDRgator


Web-based database, CDRgator (Cancer Drug Resistance navigator) for comparative analysis of gene expression signatures of cancer drug resistance.
31%

RGD v2.0


A major update of the ruminant functional and evolutionary genomics database.
31%

circMine


Database to integrate, analyze and visualize human disease-related circRNA transcriptome.
31%

GEN


A comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels.
31%

scAPAdb


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 ...
31%

ViroidDB


ViroidDB is the most comprehensive collection of viroid, satellite RNA, retrozyme, and deltavirus genome sequences available on the internet.
30%

ColorCells


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.
30%

RPS


A comprehensive database of RNAs involved in liquid-liquid phase separation.
30%

FusionGDB 2.0


Fusion gene annotation updates aided by deep learning.
30%

TissueNexus


A database of human tissue functional gene networks built with a large compendium of curated RNA-seq data.
30%

PopTargs


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 ...
30%

ASlive


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 ...
30%

ncRI


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 ...
30%

OncoDB


An interactive online database for analysis of gene expression and viral infection in cancer.
30%

TISMO


syngeneic mouse tumor database to model tumor immunity and immunotherapy response.
30%

DevOmics


Integrated multi-omics database of human and mouse early embryo.
30%

SISTEMA


A large and standardized collection of transcriptome data sets for human pluripotent stem cell research.
30%

Cancer DEIso


An integrative analysis platform for investigating differentially expressed gene-level and isoform-level human cancer markers
30%

MuscleAtlasExplorer


A web service for studying gene expression in human skeletal muscle. MuscleAtlasExplorer(BETA)2.
30%

huARdb


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.
30%

RNA Atlas of Structure Probing


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 ...
29%

miROrtho


Computational prediction of animal microRNA genes
29%

UTRdb/UTRsite


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 ...
29%

Primate Cell Type Database


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 ...
29%

RAID


Human RNA-RNA and RNA-protein interactions
27%

RNA Modification Database


Naturally modified nucleosides in RNA
27%

RNA FRABASE


A database of 3D RNA fragments within known RNA structures
27%

DARNED


Database of RNA Editing
27%

RADAR


A Rigorously Annotated Database of A-to-I RNA editing
27%

BPS


Database of RNA Base-Pair Structures
27%

sRNAMap


small regulatory RNA in microbial genomes
27%

PolyA_DB


27%

REDIportal


A-to-I RNA editing events in human
27%

POSTAR


Post-transcriptional regulation by RNA-binding proteins
27%

MeT-DB


RNA MEthylation by SEquencing databaSe
27%

LNCediting


RNA editing sites in lncRNAs from human, monkey, mouse and fly
27%

NRED


Noncoding RNA Expression Database
27%

RPFdb


Ribosome profiling database
27%

5S Ribosomal RNA Database


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 ...
27%

piRNAclusterDB


Clusters of piRNAs
27%

SomamiR


Somatic mutations that impact microRNA targeting in cancer
27%

RNA SSTRAND


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 ...
27%

YM500


smRNA-seq database for miRNA research
27%

CircNet


Tissue-specific circRNA expression profiles and regulatory networks
27%

tRNAdb


Compilation of tRNA sequences and tRNA genes
27%

fRNAdb


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 ...
27%

miRNAMap


microRNA precursors and their mapping to targets in vertebrate genomes
27%

microRNA.org


microRNA target predictions and expression profiles
27%

miRGator


microRNA target prediction, functional analysis, and gene expression data
27%

tRFdb


Short (14-32 nt) tRNA-related fragments
27%

piRNABank


Sequences and properties of Piwi-interacting RNAs (piRNAs) in human, mouse and rat
27%

miR2Disease


Literature-curated database for validatedly or potentially pathogenic roles of dysregulated miRNAs in human disease
27%

European rRNA database


All complete or nearly complete rRNA sequences
27%

dbRES


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 ...
27%

Yeast snoRNA Database


Yeast small nucleolar RNAs
27%

Plant snoRNA DB


snoRNA genes in plant species
27%

Vir-Mir db


Prediction of viral microRNA candidate hairpins
27%

3D rRNA modification maps


Locations of modified rRNA nucleotides within the 3D structure of the ribosome
27%

RNA-targeting


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.
27%

The Small Subunit rRNA Modification Database


Modified nucleosides in small subunit rRNA
27%

Cereal Small RNA Database


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 ...
27%

NCIR - Non-Canonical Interactions in RNA


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 ...
27%

rPanglaoDB


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 ...
27%

DBtRend


A Web-Server of tRNA Expression Profiles from Small RNA Sequencing Data in Humans.
27%

16S and 23S Ribosomal RNA Mutation Database


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 ...
27%

GRSDB


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 ...
27%

miRecords


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 ...
27%

GtRDB - Genomic tRNA 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 ...
27%

lncExplore


A database of pan-cancer analysis and systematic functional annotation for lncRNAs from RNA-sequencing data.
27%

SRPDB


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 ...
27%

MVIP


MVIP provides a large number of available multi-omics data under viral infection in various species.
27%

MetazExp


A database for gene expression and alternative splicing profiles and their analyses based on 53 615 public RNA-seq samples in 72 metazoan species.
27%

CORG - A database for COmparative Regulatory Genomics


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 ...
27%

snoRNA-LBME-db


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 ...
27%

Database for Bacterial Group II Introns


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 ...
27%

piRNAdb


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.
27%

ViRBase


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 ...
27%

RNAi codex


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 ...
27%

HMDD v2.0 - Human microRNA Disease Database version 2.0


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 ...
27%

RNAdb


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 ...
27%

Animal-eRNAdb


A comprehensive animal enhancer RNA database.
27%

T1TAdb


T1TAdb is a database of Type I Toxin-Antitoxin systems.
27%

BaRTv1.0


Barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq.
27%

VastDB


An atlas of alternative splicing profiles in vertebrate cell and tissue types
27%

lncRNASNP


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 ...
27%

NATsDB


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 ...
27%

IPdb


A PIWI-bound piRNAs database to mining NGS sncRNA data and beyond.
27%

FishExp


Database and analysis platform for gene expression and alternative splicing of fish species.
27%

SCMVTDb


Plant virus interaction mechanism and associated pathways in mosaic disease of small cardamom (Elettaria cardamomum Maton) by RNA-Seq approach.
27%

TeaAS


A comprehensive database for alternative splicing in tea plants (Camellia sinensis).
27%

PCaDB


A comprehensive and interactive database for transcriptomes from prostate cancer population cohorts.
27%

ViRBase v3.0


A virus and host ncRNA-associated interaction repository with increased coverage and annotation.
27%

DRscDB


DRscDB is a single-cell RNA-seq resource for data mining and data comparison across species.
27%

PSDX


A Comprehensive Multi-Omics Association Database of Secondary Growth in Response to Stress in Populus trichocarpa.
27%

BrainPalmSeq


A curated RNA-seq database of palmitoylating and de-palmitoylating enzyme expression in the mouse brain.
27%

ARED


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 ( ...
27%

3 aQTL-atlas


An atlas of 3'UTR alternative polyadenylation quantitative trait loci across human normal tissues.
27%

SPICA


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.
27%

LncRNAWiki


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 ...
27%

NPInter


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 ...
27%

LjaFGD


LjaFGD is the Lonicera japonica functional genomics database..
27%

Sno/scaRNAbase


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 ...
27%

CancerCoCoPUTs


Distinct signatures of codon and codon pair usage in 32 primary tumor types in the novel database CancerCoCoPUTs for cancer-specific codon usage.
27%

EVLncRNAs


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 ...
27%

DIANA-miTED


A microRNA tissue expression database.
27%

CancerMIRNome


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 ...
27%

tmRDB


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 ...
27%

CGGA


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 ...
27%

AOE


AOE (All Of gene Expression) - an integrated index for public gene expression databases.
27%

SELEXdb


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 ...
27%

NeuroCirc


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 ...
27%

HpeNet


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 ...
27%

Kiwifruit Genome Database


A comprehensive resource for kiwifruit genomics.
27%

Sex-Associated Gene Database


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 ...
27%

bacteria.guru


Comparative transcriptomics and co-expression database for bacterial pathogens.
27%

PCMDB


A curated and comprehensive resource of plant cell markers.
27%

GEPSdb


The Gene Expression Database of Poplar under Stress.
27%

MISpheroID


A knowledgebase and transparency tool for minimum information in spheroid identity.
27%

GeneMarkeR


A Database and User Interface for scRNA-seq Marker Genes.
27%

AhNGE


AhNGE is a Database for Arachis hypogaea nodule developmental gene expression.
27%

RLBase


Exploration and analysis of R-loop mapping data with RLBase.
27%

Quickomics


Quickomics is a tool for exploring omics data in an intuitive, interactive and informative manner.
27%

RPGD


Rhododendron Plant Genome Database (RPGD) is a comprehensive online omics database for Rhododendron.
27%

RecountDB


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.
27%

MtExpress


MtExpress is a comprehensive and curated RNAseq-based gene expression atlas for the model legume medicago truncatula.
27%

ALEXA


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 ...
27%

BrainEXP-NPD


Database of transcriptomic profiles of human brains of six neuropsychiatric disorders.
27%

ASMdb


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 ...
27%

ADEx: Autoimmune Diseases Explorer


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 ...
27%

BART Cancer


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 ...
27%

PaIntDB


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 ...
27%

FAANG metadata analysis specification


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 ...
27%

iMarmot


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 ...
27%

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