Simona Polo^1,2,†, Stefano Confalonieri^1,†, Anna Elisabetta Salcini^1,2, and Pier Paolo Di Fiore^1,2,3*

¹Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy.
²Istituto Europeo di Oncologia, Via Ripamonti 435, 20141 Milan, Italy.
³University of Milan, Medical School, 20122 Milan, Italy.
^†S. P. and S. C. contributed equally.

*Corresponding author. E-mail: difiore{at}ifom-firc.it

Tables 1 through 5. UIM-containing proteins and their functions. UIM-containing proteins were collected both from literature and protein databases searches using a HMM profile for the UIM domain, built starting from a collection of known UIM domains (1). We searched the SwissProt (release 41) and TrEMBL (release 24) protein databases. The identified proteins were made nonredundant using the nrdb90 program (2) and by visual inspection. The protein list was compared and integrated, where necessary, with the one generated automatically at the SMART website (3). Functional annotations, interactors, knock-out (KO) and RNA interference (RNAi) phenotypic information were collected from the WormBase (4) for Caenorhabditis elegans, FlyBase (5) for Drosophila melanogaster, and The Saccharomyces Genome Database (6) for Saccharomyces cerevesiae. Annotations for the mammalian proteins were collected from literature (7-9). Results include proteins from Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus, D. melanogaster, C. elegans, S. cerevisiae, and Schizosaccharomyces pombe. All files are available as Microsoft Excel spreadsheets and include the organism, EMBL-SwissProt accession number, the EMBL-SwissProt ID number, the NCBI accession number, the number of UIM domains, the name of the encoding gene, a brief description (from the TrEMBL database), other domains present (from the SMART website), any known interactors, the ability to interact with ubiquitin or monoubiquitin, and knock-out (KO) phenotypic information.

Table 1. UIM domain-containing proteins in several species. [Access Excel File]

Table 2. UIM domain-containing proteins C. elegans. Phenotype abbreviations of KO by RNA interference (RNAi): Dpy, dumpy; Emb, embryonic lethal; Gro, slow growth; Unc, uncoordinated; WT, wild type. [Access Excel File]

Table 3. UIM domain-containing proteins in D. melanogaster. [Access Excel File]

Table 4. UIM domain-containing proteins in yeast. [Access Excel File]

Table 5. UIM domain-containing proteins in mammals. [Access Excel File]

References