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Databases used for RRI curations in RISE


RAIN (RNA–protein Associations and Interaction Networks) is a database that contains ncRNA–RNA and ncRNA–protein interactions.

RISE curated 8,953 RNA-RNA interaction entries from RAIN.

RAID v2.0

RAID (RNA-Associated Interaction Database) v2.0 is a database of RNA-RNA and RNA-protein interactions with experimental or computational prediction evidence.

RISE curated 25,992 RNA-RNA interaction entries from RAID v2.0.

NPInter v3.0

NPInter is a database of experimentally-verified interactions between noncoding RNAs (except tRNAs and rRNAs) and biomolecules (proteins, RNAs and DNAs).

RISE curated 4,272 RNA-RNA interaction entries from NPInter v3.0.

Databases used for RRI annotations in RISE


Ensembl is a large-scale collaborative project that collects, annotates and distributes genomes of many different species.

RISE made use of the Ensembl datasets to annotated the genomic locations, context and gene structures for each RNA.


CLIPdb is a database that characterizes interactions between RNA binding proteins (RBPs) and RNA transcripts from datasets of various CLIP-seq experiments.

RISE used CLIPdb for the annotation of RBP binding sites on RNAs.


RMBase (RNA Modification Base) is a database designed for RNA modifications identified from high-throughput sequencing datasets and public resources.

RISE used RMBase for the annotation of RNA modifications including N6-Methyladenosines (m6A), 5-methylcytosine (m5C), pseudouridine (Ψ), as well as others types of modifications.


RADAR (Rigorously Annotated Database of A-to-I RNA editing) is a database of A-to-I editing sites in human, mouse, and fly transcripts.

RISE used RADAR for the annotation of RNA A-to-I editing sites.


DARNED (DAtabase of RNa EDiting in humans) is a database of published RNA editing events in human.

RISE also used DARNED for the annotation of RNA editing sites.


dbSNP (The Single Nucleotide Polymorphism Database) is a database of genetic variations within and across different species.

RISE used dbSNP for the annotation of SNP sites on RNAs.


TCGA (The Cancer Genome Atlas) is a collaborative project that generates a comprehensive catalogue of genetic mutations in many types of cancer, using large-scale genome sequencing and analysis techniques.

RISE used the TCGA's project datasets for the annotation of cancer-related mutations in human RNAs.

Other related RNA databases


NONCODE is an integrated knowledge database dedicated to non-coding RNAs (excluding tRNAs and rRNAs).

starBase v2.0

starBase v2.0 is a database decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data.