About

CLIPdb: 351 RBPs with their domain (from Pfam), Gene Ontologies, binding sequence motif (from MEME/HOMER), structural preference (from RNApromo/RNAcontext), and binding sites identified from CLIP-seq experiments.

RBP Binding Sites: Curated 1499 public CLIP-seq datasets (including 225 ENCODE eCLIP datasets and 1274 other CLIP-seq datasets) from 7 species (human, mouse, zebrafish, fly, worm, Arabidopsis, yeast) and 10 CLIP-seq technologies (HITS-CLIP, PAR-CLIP, iCLIP, eCLIP, iCLAP, 4SU-iCLIP, urea-iCLIP, BrdU-CLIP, Fr-iCLIP, PIP-seq).

RNA Crosstalk: Post-transcriptional regulation annotation of RBP binding sites, including ~27 million miRNA-binding sites, ~1.1 million RNA modification sites, and ~8.1 million RNA editing sites.

Genomic Variants: Genomic variation annotation of RBP binding sites, including ~778 million SNV from dbSNP for 7 species, ~78 million SNV from 1000 genomes, ~679 million SNV from gnomAD, ~40 million eQTLs, and ~16 million sQTLs from GTEx for human.

Disease Mutations: Disease-associated variant annotation of human RBP binding sites, including ~615k ClinVar variants, ~3.5 million PanTCGA variants, ~23 million PCAWG variants, ~906k CCLE variants, ~127k GWASdb2 variants, ~406k denovodb variants, ~2.4 million COSMIC variants, and ~7k HmtDB mtDNA mutations.

Structurome: Curated 82 public structure-seq datasets (including 16 ENCODE icSHAPE datasets and 66 other structure-seq datasets) from 4 species (human, mouse, Arabidopsis, yeast) and 6 structure-seq methods (PARS, DMS-seq, CIRS-seq, ChemModSeq, DMS-MaPseq, icSHAPE).

Translatome: Curated 300 public Ribo-seq datasets from 6 species (human, mouse, fly, worm, Arabidopsis, yeast) in 101 different conditions/treatments, displaying ORF annotation, translation density, translation efficiency, and ORF score calculated by different algorithms.

Degradome: Curated 83 public degradome-seq datasets and paired sRNA-seq from 4 species (human, mouse, fly, Arabidopsis) using different sequencing methods (degradome-seq, PARE, GMUCT).