| RPFdb |
Ribo-seq data |
RPFdb v3 is a publicly accessible repository dedicated to hosting, analyzing, and visualizing ribosome profiling (Ribo-seq) data. The latest version, RPFdb v3, offers an expansive dataset featuring Ribo-seq data from 5,018 samples across 496 studies, complemented by matched RNA-seq data from 2,343 samples, encompassing 34 distinct species. |
| circBase |
circRNA data |
A database for circular RNAs,hosting data from various Homo sapiens, Mus musculus, Caenorhabditis elegans, and Latimeria samples. |
| CIRCpedia |
circRNA data |
An updated comprehensive database containing circRNA annotations from over 180 RNA-seq datasets across six different species. |
| circAtlas |
circRNA data |
circAtlas 3.0 integrates more than over 3.1 million circRNAs across 10 species (human, macaque, mouse, rat, pig, chicken, dog, sheep, cat, rabbit) and a variety of tissues |
| circBank |
circRNA data |
A database of more than 14,000 human-annotated circRNAs, showing five features of the circRNA, including the miRNA binding site, conservation of circRNAs, m6A modification of circRNAs, mutation of circRNAs and protein-coding potential of circRNAs. |
| circRNADb |
circRNA data |
A database of circular RNA molecules in humans contains 32,914 annotated exonic circRNAs. |
| CSCD |
circRNA data |
An integrated interactional database of cancer-specific circular RNAs includes 1013461 cancer-specific circRNAs, 1533704 circRNAs from only normal samples and 354422 circRNAs from both cancer and normal samples. |
| REPIC |
m6A data |
The REPIC (RNA EPItranscriptome Collection) database records about 10 million peaks called from publicly available m6A-seq and MeRIP-seq data using an unified pipeline. |
| IRESbase |
IRES data |
A comprehensive database of IRESs, by curating the experimentally validated functional minimal IRES elements from literature and annotating their host linear and circular RNAs. The current version of IRESbase contains 1328 IRESs, including 774 eukaryotic IRESs and 554 viral IRESs from 11 eukaryotic organisms and 198 viruses, respectively. |
| POSTAR3 |
RBP data |
A comprehensive database for exploring POST-trAnscriptional Regulation based on high-throughput sequencing data from 7 species, including human, mouse, zebrafish, fly, worm, Arabidopsis, and yeast. POSTAR3 is developed as the updated version of CLIPdb, POSTAR, and POSTAR2, which provides the largest binding sites collection of RNA-binding proteins and their functional annotations. |
| REDIportal |
RNA editing data |
REDIportal V3.0 collects 15,680,833 sites from 9,642 GTEx RNAseq samples (across 31 tissues and 54 body sites) and 9,683 TCGA RNAseq samples (across 31 studies and 24 disease types). |
| CIRCexplorer3 |
circRNA caller |
A computational pipeline for Circular and Linear RNA Expression Analysis from Ribosomal-RNA depleted (Ribo–) RNA-seq (CLEAR/CIRCexplorer3). |