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PolyA_DB: a database for mammalian mRNA polyadenylation

Haibo Zhang1, Jun Hu, Michael Recce

  • 1Center for Computational Biology and Bioengineering, New Jersey Institute of Technology, Newark, NJ 07102, USA.

Nucleic Acids Research
|December 21, 2004
PubMed

Insights

Messenger RNA polyadenylation is crucial for gene expression. The new polyA_DB database offers comprehensive data on mammalian polyadenylation sites and regulation, filling a critical gap for researchers.

Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Messenger RNA (mRNA) polyadenylation is a critical post-transcriptional regulatory mechanism in eukaryotic gene expression.
  • Alternative polyadenylation (APA) generates mRNA variants with different 3' ends, impacting mRNA stability, localization, and translation.
  • Existing biological databases lack systematic, comprehensive information on polyadenylation and APA.

Purpose of the Study:

  • To establish polyA_DB, a centralized database for mammalian polyadenylation information.
  • To provide detailed data on polyadenylation sites, associated cis-elements, and APA regulation.
  • To facilitate research on mRNA metabolism and its implications in various biological contexts.

Main Methods:

  • Compilation of polyadenylation site data from human and mouse genes.
  • Annotation of genomic locations and surrounding cis-regulatory elements for each polyadenylation site.
  • Inclusion of comparative data for orthologous genes and tissue-specific APA information.

Main Results:

  • The polyA_DB database currently houses 45,565 polyadenylation sites for 25,097 human and mouse genes.
  • It provides comprehensive information on polyadenylation sites, cis-elements, orthologous gene comparisons, and tissue-specific APA.
  • Represents the most extensive collection of polyadenylation data available to date.

Conclusions:

  • The polyA_DB database significantly enhances the accessibility of crucial information on mRNA polyadenylation and APA.
  • It serves as a valuable resource for studying gene regulation, mRNA processing, and disease mechanisms.
  • Facilitates future research by providing a unified platform for polyadenylation-related data analysis.

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