Nucleic Acids Research, 2005, Vol. 33, Database issue D116-D120
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
PolyA_DB: a database for mammalian mRNA polyadenylation
1 Center for Computational Biology and Bioengineering, New Jersey Institute of Technology, Newark, NJ 07102, USA and 2 Department of Biochemistry and Molecular Biology and Bioinformatics Center, New Jersey Medical School, UMDNJ, Newark, NJ 07101, USA
* To whom correspondence should be addressed. Tel: +1 973 972 3615; Fax: +1 973 972 5594; Email: btian{at}umdnj.edu
Received August 19, 2004; Revised and Accepted October 1, 2004
Messenger RNA polyadenylation is one of the key post-transcriptional events in eukaryotic cells. A large number of genes in mammalian species can undergo alternative polyadenylation, which leads to mRNAs with variable 3' ends. As the 3' end of mRNAs often contains cis elements important for mRNA stability, mRNA localization and translation, the implications of the regulation of polyadenylation can be multifold. Alternative polyadenylation is controlled by cis elements and trans factors, and is believed to occur in a tissue- or disease-specific manner. Given the availability of many databases devoted to other aspects of mRNA metabolism, such as transcriptional initiation and splicing, systematic information on polyadenylation, including alternative polyadenylation and its regulation, is noticeably lacking. Here, we present a database named polyA_DB, through which we strive to provide several types of information regarding polyadenylation in mammalian species: (i) polyadenylation sites and their locations with respect to the genomic structure of genes; (ii) cis elements surrounding polyadenylation sites; (iii) comparison of polyadenylation configuration between orthologous genes; and (iv) tissue/organ information for alternative polyadenylation sites. Currently, polyA_DB contains 45 565 polyadenylation sites for 25 097 human and mouse genes, representing the most comprehensive polyadenylation database till date. The database is accessible via the website (http://polya.umdnj.edu/polyadb).
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