ArrayExpress at EBI Any curated MIAME or MINSEQE compliant transcriptomics data
ArrayTrack ArrayTrack hosts both public and private data, including MAQC benchmark data, with integrated analysis tools
caArray at NCI Cancer data, prepared for analysis on caBIG
EBI ArrayExpress
Gene Expression Omnibus (GEO) Any curated MIAME compliant molecular abundance study
GeneNetwork system Open access standard arrays, exons arrays, and RNA-seq data for genetic analysis (eQTL studies) with analysis suite
Genevestigator Gene expression search engine based on manually curated, well annotated public and proprietary microarray and RNA-seq datasets
ImmGen database Open access across all immune system cells; expression data, differential expression, coregulated clusters, regulation
MUSC database The database is a repository for DNA microarray data generated by MUSC investigators as well as researchers in the global research community.
NCI mAdb Hosts NCI data with integrated analysis and statistics tools
NextBio Microarrays analysis
Stanford Microarray database private and published microarray and molecule abundance database (now defunct)
The Cancer Genome Atlas (TCGA) collection of expression data for different cancers
UNC Microarray database provides the service for microarray data storage, retrieval, analysis, and visualization
UNC modENCODE Microarray database Nimblegen customer 2.1 million array
UPenn RAD database MIAME compliant public and private studies, associated with ArrayExpress
UPSC-BASE data generated by microarray analysis within Umeå Plant Science Centre (UPSC).



miRBase The microRNA database
PolymiRTS A database of DNA variations in putative microRNA target sites



ncRNA Noncoding RNAs Database.



Database of RNA-binding Protein Specificities This University of Toronto site page provides a database of RNA-binding protein specificities where you can browse by domain such as RNA Recognition Motif, K Homology, CCCH Zinc Finger and more. Also you can browse by species such as Homo Sapiens, Mus Musculus, Drosophila Melanogaster and Caenorhabditis Elegans.
Extracellular RNA Atlas - GenboreeKB Extracellular RNA Atlas
ExtracellularRNA datasets Extracellular RNA dataset
ExtracellularRNA snapshot Extracellular RNA snapshot
NAR Database Summary Paper Category List Oxford Journals site contains a list of excellent collections of Nucleotide sequence databases, RNA sequence databases, Protein sequence databases, Structure databases, Genomics databases, Metabolic and signaling pathways, Human & other vertebrate genomes, Human genes and diseases, Microarray data & gene expression databases, Protemics resources, Molecular biology databases, Organelle databases, plant databases, Immunological databases and cell biology.
Noncoding RNA Database v2.0 lncRNAdb.org site has a searchable database which provides comprehensive annotations of eukaryotic long non-coding RNAs (lncRNAs). All entries are manually curated from referenced literature and each entry contains references information about the RNA including: Nucleotide sequences, Genomic context, Gene expression data derived from the Illumina Body Atlas, Structural information, Subcellular localization, Conservation, Function with referenced literature.
RNA Databases RNA stands for Ribonucleic acid. The RNA is a polymeric molecule which when teamed with proteins and carbohydrates are considered as three essential macromolecules...
RNA STRAND This site contains known RNA secondary structures of any type and organism. The ultimate goal of this database is to incorporate a comprehensive collection of known RNA secondary structures, and to provide the scientific community with simple yet powerful ways of analyzing, searching and updating the proposed database.
RNABase RNABase is an annotated database of all publicly available RNA structures.
RNA-binding protein database RNA-binding protein database
RNAcentral RNACentral.com is a new resource that provides unified access to the ncRNA sequence data supplied by the Expert Databases.
The RNA Modification Database The RNA modification database provides a comprehensive listing of post transcriptionally modified nucleosides from RNA.



rRNA database The European ribosomal RNA database.
Ribosomal Database Project II The Ribosomal Database Project (RDP) provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences.
5S ribosomal RNA Database The purpose of this database is to provide information on nucleotide sequences of 5S rRNAs and their genes. The sequences for particular organisms can be retrieved as single files using a taxonomic browser or in multiple sequence structural alignments.



siRNA Database Database of siRNA target sequences and other resources for RNA interference studies.


Small RNA

Small RNA database Small RNAs are broadly defined as the RNAs not directly involved in protein synthesis. Small RNAs are usually in the 75-400 nucleotides range, although some are as long as thousand base pairs. They are synthesized by either RNA Polymerase I, II or III. The sequences reported here are based on actual sequence determinations and not on the basis of oligonucleotide catalogs.



AARS DataBase Aminoacyl-tRNA Synthetase Data Bank.
GtRDB: The Genomic tRNA Database This genomic tRNA database contains tRNA identifications made by the program tRNAscan-SE on complete or nearly complete genomes.



The uRNA Database The uRNADB is a tool in the study of the structures and functions of various U RNAs. It provides aligned, annotated and phylogenetically ordered sequences. The alignments of the sequences represent conserved secondary structure elements where each base pair is proven by comparative sequence analysis.