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Provides annotation of functional variants involved in post-transcriptional interaction and regulation. RBP-Var provides a user-friendly web interface, allowing users to rapidly find whether SNVs of interest can transform the secondary structure of RNA and identify RBPs whose binding may be subsequently disrupted. Moreover, RBP-Var can assess the impact of each SNV on miRNA–RNA interaction as SNVs may destroy or create miRNA-binding sites, which result in loss-of-function and/or gain-of-function miRNA–RNA interactions. RBP-Var is a useful resource for benchmarking the mutations or RNA-editing events that cause disease by changing post-transcriptional interaction and regulation.

RAID / RNA Association Interaction Database

Provides RNA-associated (RNA-RNA/RNA-protein) interaction database. RAID intends to provide the scientific community with all-in-one resources for efficient browsing and extraction of the RNA-associated interactions. RAID integrates experimental and computational prediction interactions from manually reading literature and other database resources under one common framework. The new developments in RAID include (i) over 850-fold RNA-associated interactions, an enhancement compared to the previous version; (ii) numerous resources integrated with experimental or computational prediction evidence for each RNA-associated interaction; (iii) a reliability assessment for each RNA-associated interaction based on an integrative confidence score; and (iv) an increase of species coverage to 60.

ATtRACT / A daTabase of RNA binding proteins and AssoCiated moTifs

Collects in a unique resource all available information about RNA-binding proteins (RBPs) and their associated motifs. In comparison to other similar databases, ATtRACT adds 192 motifs not present in any other database from 110 different RBPs by retrieving the information buried in the PDB database. In addition, ATtRACT permits to investigate the GO terms associated to the RBPs. To populate ATtRACT we (i) extracted and hand-curated experimentally validated data from CISBP-RNA, SpliceAid–F, RBPDB databases, (ii) integrated and updated the unavailable ASD database and (iii) extracted information from Protein-RNA complexes present in Protein Data Bank database through computational analyses. ATtRACT provides also efficient algorithms to search a specific motif and scan one or more RNA sequences at a time. It also allows discovering de novo motifs enriched in a set of related sequences and compare them with the motifs included in the database.


Contains a collection of z-score based binding sites specific to RNA binding protein (RBP) motifs across the human and mouse genomes. MotifMap-RNA allows user to filter and sort the results based on clustering of local binding sites or evolutionary conservation, quantified by Bayesian branch length scores (BBLS). It provides four major classes of genomic sequences: UTRs, intronic regions, lncRNAs and miRNAs, for all of which we generated class specific model parameters.


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Provides resources to decode Pan-Cancer and Interaction Networks of lncRNAs, miRNAs, competing endogenous RNAs(ceRNAs), RNA-binding proteins (RBPs) and mRNAs from large-scale CLIP-Seq data and tumor samples. starBase deciphers Protein-RNA and miRNA-target interactions, such as protein-lncRNA, protein-sncRNA, protein-mRNA, protein-pseudogene, miRNA-lncRNA, miRNA-mRNA, miRNA-circRNA, miRNA-pseudogene, miRNA-sncRNA interactions and ceRNA networks from 108 CLIP-Seq datasets.


Contains 257 experimentally identified RNA binding proteins (RBPs). For each of the identified proteins, RiceRBP database provides information on transcript and protein sequence, predicted protein domains, details of the experimental identification, and whether antibodies have been generated for public use. In addition, tools are available to analyze expression patterns for the identified genes, view phylogenetic relationships and search for orthologous proteins. RiceRBP is a valuable tool for the community in the study of plant RBPs.


Supplies information about binding sites of RNA-binding proteins. CLIPZ is a database and an analysis environment which supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins to identify the binding sites of these proteins. The platfom allows users to upload their own sequence data sets while being able to limit the access to these data to specific users.


Collects into a unique resource several heterogeneous information about splicing regulatory proteins, their binding sites and context-specific activity. Information of binding sites includes the corresponding genes, their genomic coordinates, the splicing effect, the experimental procedures used to assess binding and the related references. All these data have been manually extracted and collected by extensive database and literature screenings, yielding information on 71 splicing proteins, all those investigated so far to our knowledge for which some information is available on their RNA targets.