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Cis-regulatory RNA element databases | Gene expression data analysis

Both RNA-binding proteins (RBPs) and non-coding RNAs (ncRNAs) bind mRNAs in the so-called cis-elements, found primarily in 5′ and 3′ UTRs. These elements can be represented as recurring RNA sequences or secondary structures shared by a…
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Ensembl…
Dataset

Ensembl Regulatory Build

Provides a high-level overview of the regulatory activity of the genome. The…

Provides a high-level overview of the regulatory activity of the genome. The Ensembl Regulatory Build offers putative regulatory regions from public experimental data, and associate these regions…

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AREsite
Dataset

AREsite

An online resource for the detailed investigation of AU-rich elements (ARE) in…

An online resource for the detailed investigation of AU-rich elements (ARE) in vertebrate mRNA 3'-untranslated regions (UTRs). The new updated and enhanced version allows detailed investigation…

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SwiSpot
Desktop

SwiSpot

Predicts the two functional conformations of riboswitches, using merely as…

Predicts the two functional conformations of riboswitches, using merely as input the plain RNA nucleotide sequence. The procedure consists in three major steps, including: i) prediction of the…

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uORFdb
Dataset

uORFdb

Serves as a comprehensive literature database on eukaryotic uORF biology. The…

Serves as a comprehensive literature database on eukaryotic uORF biology. The uORFdb was manually curated from all uORF-related literature listed at the PubMed database. It categorizes individual…

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SelenoDB
Dataset

SelenoDB

Aims to provide high-quality annotations of selenoprotein genes, proteins and…

Aims to provide high-quality annotations of selenoprotein genes, proteins and SECIS elements. Selenoproteins are proteins that contain the amino acid selenocysteine (Sec) and the first release of the…

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UTRdb/UTRSite
Dataset

UTRdb/UTRSite

A curated database of 5' and 3' untranslated sequences of eukaryotic…

A curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs, derived from several sources of primary data. Experimentally validated functional motifs are annotated and also…

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RNA workbench
Server

RNA workbench

Establishes a central, redistributable workbench for scientists and programmers…

Establishes a central, redistributable workbench for scientists and programmers working with RNA-related data. The RNA workbench builds a sustainable community around it. This platform is unique in…

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ExportAid
Dataset

ExportAid

Collects information about the RNA elements regulating nuclear export. This…

Collects information about the RNA elements regulating nuclear export. This database could help to understand the RNA export language and to study the possible export efficiency alterations owing to…

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ARED
Dataset

ARED

Offers scientists a comprehensive view of AREs in the human transcriptome and…

Offers scientists a comprehensive view of AREs in the human transcriptome and the ability to study the comparative genomics of AREs in model organisms. This ultimately will help in inferring the…

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Transterm
Dataset

Transterm

A database of regions and elements that affect translation with two major…

A database of regions and elements that affect translation with two major unique components. The first is integrated results of analysis of general features that affect translation (initiation,…

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AURA
Dataset

AURA Atlas of UTR Regulatory Activity

A manually curated and comprehensive catalog of human mRNA untranslated regions…

A manually curated and comprehensive catalog of human mRNA untranslated regions (UTRs) and UTR regulatory annotations. Through its intuitive web interface, it provides full access to a wealth of…

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PTRguide
Dataset

PTRguide

A website listing databases and tools for post-transcriptional regulation of…

A website listing databases and tools for post-transcriptional regulation of gene expression (PTR) analysis. PTRguide provides summary and features for each one and will be regularly updated in the…

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