This section contains databases of RNA sequences.

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Displaying 15 links

AREsiteDatabase Content

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AREsite is an online resource for the detailed investigation of AU-rich elements (ARE) in vertebrate mRNA 3'-untranslated regions (UTRs). AREsite allows one to quantify the structuredness of ARE motif sites in terms of opening energies and accessibility probabilities. A detailed phylogenetic analysis of ARE motifs and incorporate information about experimentally validated targets of the ARE-binding proteins TTP, HuR and Auf1 is also provided.


CellBaseTool Content

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CellBase is a relational database that contains relevant biological information about genomic features and proteins, gene expression regulation, functional annotation, genomic variation and systems biology information. Integrated are the most relevant repositories such as Ensembl, Uniprot, Omim, COSMIC, IntAct, HapMap, Reactome, and others.

This content is being maintained by imedina.

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TitlePublication YearGoogle Scholar Citation Count

CLIPZDatabase Content

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CLIPZ supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other type of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The CLIPZ platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets.

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Database for Bacterial Group 2 IntronsDatabase Content

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Database for Bacterial Group 2 Introns: a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank. General info on group 2 intron properties, structures and classification. Lists info for individual introns (insertion sites, DNA sequences, intron-encoded protein sequences, RNA secondary structure models). Tools fo ridentification and analysis of intron sequences.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
Database for bacterial group II introns20121

deepBaseDatabase Content

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deepBase contains deep sequencing data from 185 small RNA libraries from diverse tissues and cell lines of seven organisms: human, mouse, chicken, Ciona intestinalis, Drosophila melanogaster, Caenhorhabditis elegans and Arabidopsis thaliana. deepBase facilitates the comprehensive annotation and discovery of small RNAs from transcriptomic data such as ncRNA-associated small RNAs (nasRNAs), promoter-associated small RNAs (pasRNAs), exon-associated small RNAs (easRNAs), repeat-associated small RNAs (rasRNAs) and miRNA and snoRNA candidates. For the purpose of comparative analysis, deepBase provides an integrative, interactive and versatile display.

ENCODE DCCDatabase Content

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The ENCODE project has a goal of cataloguing all the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) serves as the central repository for ENCODE data. The DCC contains a collection of high-throughput, genome-wide data generated with technologies such as ChIP-Seq, RNA-Seq, DNA digestion and others. It includes sequences with quality scores, alignments, signals calculated from the alignments, and in most cases, element or peak calls calculated from the signal data. Each data set is available for visualization and download via the UCSC Genome Browser. ENCODE data can also be retrieved using a metadata system that captures the experimental parameters of each assay.

ExoCartaDatabase Content

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ExoCarta: a manually curated database of exosomal proteins, RNA, and lipids. Catalogs information from both published and unpublished exosomal studies. Currently contains info on 11,261 protein entries, 2375 mRNA entries, and 764 miRNA entries obtained from 134 exosomal studies.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
ExoCarta 2012: database of exosomal proteins, RNA and lipids20129

Full-parasitesDatabase Content

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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 were interconnected with our original database functionalities. By providing the largest unique full-length cDNA and dynamic transcriptome data, Full-Parasites is useful for understanding host-parasite interactions.

IRESiteDatabase Content

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The IRESite presents carefully curated experimental evidence of many eukaryotic viral and cellular internal ribosome entry site (IRES) regions. The IRESite tool provides biologically meaningful information regarding the IRESs and their experimental background (including annotation of IRES secondary structures and IRES trans-acting factors). RNA secondary structures and for searching through the structures currently stored in the database can also be done.

lncRNAdbDatabase Content

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lncRNAdb database contains a comprehensive list of long noncoding RNAs (lncRNAs) that have been shown to have, or to be associated with, biological functions in eukaryotes, as well as messenger RNAs that have regulatory roles. Each entry contains referenced information about the RNA, including sequences, structural information, genomic context, expression, subcellular localization, conservation, functional evidence and other relevant information. lncRNAdb can be searched by querying published RNA names and aliases, sequences, species and associated protein-coding genes, as well as terms contained in the annotations, such as the tissues in which the transcripts are expressed and associated diseases. In addition, lncRNAdb is linked to the UCSC Genome Browser for visualization and Noncoding RNA Expression Database (NRED) for expression information from a variety of sources.

This content is being maintained by marceldinger.

links directory index: 31
TitlePublication YearGoogle Scholar Citation Count
lncRNAdb: a reference database for long noncoding RNAs201131

mESAdbDatabase Content

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microRNA expression and sequence analysis database (mESAdb) is a database for the multivariate analysis of sequences and expression of microRNAs from multiple taxa. mESAdb is coupled with statistical analysis and visualization packages written for the R language. The database primarily comprises mature microRNA sequences and their target data, along with selected human, mouse and zebrafish expression data sets. mESAdb analysis modules allow (i) mining of microRNA expression data sets for subsets of microRNAs selected manually or by motif; (ii) pair-wise multivariate analysis of expression data sets within and between taxa; and (iii) association of microRNA subsets with annotation databases, HUGE Navigator, KEGG and GO.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
mESAdb: microRNA expression and sequence analysis database20114

MINASDatabase Content

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A database of metal ions in DNA and RNA. Complies info on innersphere, outsphere, and larger coordination environment of >70,000 metal ions of 36 elements fround in >2000 structures of nucleic acids.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
MINAS--a database of Metal Ions in Nucleic AcidS20122

miRBaseDatabase Content

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miRBase is a repository for all microRNA sequences and annotation. miRBase has mapped reads from short RNA deep-sequencing experiments to microRNAs in miRBase and developed web interfaces to view these mappings. The user can view all read data associated with a given microRNA annotation, filter reads by experiment and count, and search for microRNAs by tissue- and stage-specific expression.

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