Hi, Would anyone happen to know if there is
1) anything such as an RNA-Binding protein database for yeast, which gives the predicted or experimentally found binding positions of these proteins 2) same as one, but for DNA-Binding protein that are NOT transcription factor
and all this, for * yeast (Saccharomyces cerevisiae)
thanks in advance
Benjamin
4 answers
use GOA to download all the RNA binding proteins (see this post: The Quickgo/Gannotation Api )
$ curl -s "http://www.ebi.ac.uk/QuickGO/GAnnotation?tax=4932&relType=IP=&goid=GO:0003723&format=proteinList"
DB ID Symbol Name Synonym Type Taxon
UniProtKB A6ZKQ9 MRPL16 Mitochondrial ribosomal large subunit component A6ZKQ9_YEAS7|SCY_0179|MRPL16 protein 307796
UniProtKB A6ZKR5 HEK2 Heterogeneous nuclear rnp K-like protein 2 HEK2_YEAS7|HEK2|KHD1|SCY_0185 protein 307796
UniProtKB A6ZKS4 NCL1 M5C tRNA methyltransferase A6ZKS4_YEAS7|NCL1|SCY_0194 protein 307796
UniProtKB A6ZL23 RPG1 Translation initiation factor eIF3 subunit A6ZL23_YEAS7|SCY_0293|RPG1 protein 307796
UniProtKB A6ZL27 SCY_4021 Conserved protein A6ZL27_YEAS7|SCY_4021|SCY_0297 protein 307796
UniProtKB A6ZL63 TEF2 Elongation factor 1-alpha A6ZL63_YEAS7|TEF2|SCY_0333|TEF1|SCY_5792 protein 307796
UniProtKB A6ZL64 MUD1 U1 snRNP A protein A6ZL64_YEAS7|MUD1|SCY_0334 protein 307796
UniProtKB A6ZL74 SHE3 SWI5-dependent HO expression protein 3 SHE3_YEAS7|SHE3|SCY_0344 protein 307796
UniProtKB A6ZL85 MAK5 ATP-dependent RNA helicase MAK5 MAK5_YEAS7|MAK5|SCY_0355 protein 307796
for DNA binding proteins: use GO:0003677 and remove transcription factors binding ( GO:0008134 )
Just came out: CISBP-RNA Database: Catalog of Inferred Sequence Binding Preferences of RNA binding proteins
And the paper in Nature: http://www.nature.com/nature/journal/v499/n7457/full/nature12311.html
EuRBPDB (http://eurbpdb.syshospital.org/) may be the RNA-Binding protein database you needed, it provides the complete RBP catalogs of a large amount of eurkaryotes including human and yeast.
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