Spliceosome Database

1. I accessed the Spliceosome Database Spliceosome Database
2. The purpose of this database is to unify and simplify the many (over 200) proteins that spliceosomes are assembled from, to provide a means of searching specifically for spliceosome proteins and components in the literature, and a way to search for homologues of spliceosome components across several species.
3. The database contains the names, orthologs, and gene identifiers of spliceosome proteins, links to gene and protein records for the components of spliceosomes found in other databases, and "tools to compare the association of spliceosome proteins with complexes that form at specific stages of spliceosome assembly based on a compendium of mass spectrometry experiments that identified proteins in purified splicing complexes" (Cvitkovic & Jurica, 2013).
4. The species covered by the database are Homo sapiens (humans), Schizosaccharomyces cerevisiae (yeast), Schizosaccharomyces pombe (yeast), Drosophila melanogaster (fruit fly), Caenorhabditis elegans (nematode), Plasmodium falciparum (malaria causing protozoa), Gallus gallus (chicken), Trypanosoma brucei (trypanosome), Leishmania major (protozoa), and Arabidopsis thaliana (small flowering plant).
5. This database can answer the biological questions "What genes code for spliceosome proteins and RNAs?", "What proteins are involved in the formation of spliceosomes?", and "How do spliceosomes differ across species?".
6. This database is a specialty database that focuses on the genes, proteins, protein conformations, homologues, and small nuclear RNAs (snRNA) that are found in spliceosomes in humans and several model organisms listed above in #4.
7. Ivan Cvitkovic and Melissa S. Jurica maintain the database, though the paper and database website list only Melissa S. Jurica as the contact person and recipient of the NIH grant. Both authors are professors at University of California Santa Cruz.
8. The National Institute of Health provides funding for this database.
9. The Spliceosome Database is free and available to the public.
10. The database is updated automatically from public sources and from mass spectrometer papers concerning spliceosomes. It is updated regularly by scripts (Cvitkovic & Jurica, 2013). However, no date or time for the most recent update could be found on the database page.
11. Yes, there are links to records of proteins and genes of spliceosome components found in other databases.
12. Yes, the information on the database can be downloaded as a spreadsheet. The spreadsheet is formatted as a CSV but can be read by excel.
13. This database is extremely user friendly; while its contents may be arcane to anyone not currently doing specific research on spliceosomes, its navigation is simple and easy to understand quickly.

• The web site is very well organized with multiple search fields displayed in a logical order, and has different pages for the different types of searches (component search, mass spectrometer experiments, and comparison of complexes across species)
• Each type of search has a tutorial/about page as well as a general one for the database as a whole.
• A sample query was run for the U1 snRNP found in H. sapiens. Entries for 11 structures were listed, each of which was a homologue or transitional stage for that particular snRNP in humans. The query results make perfect sense.

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Kmeilak (talk) 21:20, 12 September 2013 (PDT)