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. 2005 Jan 1;33(Database issue):D116-20.
doi: 10.1093/nar/gki055.

PolyA_DB: a database for mammalian mRNA polyadenylation

Haibo Zhang  1 , Jun Hu, Michael Recce, Bin Tian
Affiliations

PolyA_DB: a database for mammalian mRNA polyadenylation

Haibo Zhang et al. Nucleic Acids Res. .

Abstract

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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Figures

Figure 1
Figure 1
An outline of the polyA_DB building pipeline. The data flow is indicated by arrowed lines. See the main text for details.
Figure 2
Figure 2
Views offered at the web interface of polyA_DB. (A) Gene view: Mouse gene TPM2 is used as an example. The output includes a pictorial representation of gene structure and poly(A) sites as well as two summary tables regarding the gene and the poly(A) sites. Numbers under each poly(A) site in the picture are the number of supporting cDNA/ESTs and the number of heterogeneous cleavage sites. (B) Ortholog view of human and mouse TPM2 genes. (C) Signal views of mouse and human TPM2 genes are shown in the upper panel and lower panel, respectively. The position of a signal is relative to the cleavage site, which is set to 0.
Figure 2
Figure 2
Views offered at the web interface of polyA_DB. (A) Gene view: Mouse gene TPM2 is used as an example. The output includes a pictorial representation of gene structure and poly(A) sites as well as two summary tables regarding the gene and the poly(A) sites. Numbers under each poly(A) site in the picture are the number of supporting cDNA/ESTs and the number of heterogeneous cleavage sites. (B) Ortholog view of human and mouse TPM2 genes. (C) Signal views of mouse and human TPM2 genes are shown in the upper panel and lower panel, respectively. The position of a signal is relative to the cleavage site, which is set to 0.
See this image and copyright information in PMC

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