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. 2008 Jan;36(Database issue):D137-40.
doi: 10.1093/nar/gkm959. Epub 2007 Nov 4.

ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse

Anason S Halees  1 , Rashad El-Badrawi, Khalid S A Khabar
Affiliations

ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse

Anason S Halees et al. Nucleic Acids Res. 2008 Jan.

Abstract

ARED Organism represents the expansion of the adenylate uridylate (AU)-rich element (ARE)-containing human mRNA database into the transcriptomes of mouse and rat. As a result, we performed quantitative assessment of ARE conservation in human, mouse and rat transcripts. We found that a significant proportion ( approximately 25%) of human genes differ in their ARE patterns from mouse and rat transcripts. ARED-Integrated, another updated and expanded version of ARED, is a compilation of ARED versions 1.0 to 3.0 and updated version 4.0 that is devoted to human mRNAs. Thus, ARED-Integrated and ARED-Organism databases, both publicly available at http://brp.kfshrc.edu.sa/ARED, offer scientists a comprehensive view of AREs in the human transcriptome and the ability to study the comparative genomics of AREs in model organisms. This ultimately will help in inferring the biological consequences of ARE variation in these key animal models as opposed to humans, particularly, in relationships to the role of RNA stability in disease.

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Figures

Figure 1.
Figure 1.
AUUUA pentamer count-difference distribution among ARE genes in the orthologs. X-axis denotes score differences in pentamers between orthologs in each organism pair and Y-axis denotes the observed frequency of each difference.
See this image and copyright information in PMC

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