About CLIPdb Module

The CLIPdb module provides various annotations for the RNA-binding proteins, including RNA recognition domains, Gene Ontology, sequence motifs, and structural preferences. All the binding sites for the query RNA-binding protein and expression level for the target genes are also included.

1. GENCODE annotations: Adam F, Mark D, Anne-Maud F, et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. 2019;47(D1):D766-D773.
2. ZFIN: Howe DG, Ramachandran S, Bradford YM, et al. The Zebrafish Information Network: major gene page and home page updates. Nucleic Acids Res. 2021;49(D1):D1058-D1064.
3. Flybase: Drysdale R; FlyBase Consortium. FlyBase : a database for the Drosophila research community. Methods Mol Biol. 2008;420:45-59.
4. WormBase: Harris TW, Antoshechkin I, Bieri T, et al. WormBase: a comprehensive resource for nematode research. Nucleic Acids Res. 2010;38(Database issue):D463-D467.
5. TAIR: Lamesch P, Berardini TZ, Li D, et al. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res. 2012;40(Database issue):D1202-D1210.
6. SGD: Weng S, Dong Q, Balakrishnan R, et al. Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003;31(1):216-218.
7. Gene Ontologies: Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25(1):25-29.
8. Pfam (domain): El-Gebali S, Mistry J, Bateman A, et al. The Pfam protein families database in 2019. Nucleic Acids Res. 2019;47(D1):D427-D432.
9. MEME: Bailey TL, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol. 1994;2:28-36.
11. Weblogo: Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res. 2004;14(6):1188-1190.
12. RNApromo: Rabani M, Kertesz M, Segal E. Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes. Proc Natl Acad Sci U S A. 2008;105(39):14885-14890.
13. RNAcontext: Kazan H, Ray D, Chan ET, Hughes TR, Morris Q. RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins. PLoS Comput Biol. 2010;6(7):e1000832.
15. CircInteractome circRNA binding: Dudekula DB, Panda AC, Grammatikakis I, De S, Abdelmohsen K, Gorospe M. CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs. RNA Biol. 2016;13(1):34-42.
16. RBP category: Van Nostrand EL, Freese P, Pratt GA, et al. A large-scale binding and functional map of human RNA-binding proteins. Nature. 2020;583(7818):711-719.

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Note: You can download positions of ALL binding sites of RBPs from this link.