PATACSDB - The database of polyA translational attenuators in coding sequences
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Abstract
Recent addition to the repertoire of gene expression regulatory mechanisms are polyadenylate (polyA) tracks encoding for poly-lysine runs in protein sequences. Such tracks stall translation apparatus and induce frameshifting independently of the effects of charged nascent poly-lysine sequence on the ribosome exit channel. As such they substantially influence the stability of mRNA and amount of protein produced from a given transcript. Single base changes in these regions are enough to exert a measurable response on both protein and mRNA abundance, and makes each of these sequences potentially interesting case studies for effects of synonymous mutation, gene dosage balance and natural frameshifting. Here we present the PATACSDB, a resource that contain comprehensive list of polyA tracks from over 250 eukaryotic genomes. Our data is based on Ensembl genomic database of coding sequences and filtered with algorithm of 12A-1 which selects sequences of polyA tracks with a minimal length of 12 A's allowing for one mismatched base. The PATACSDB database is accesible at: http://sysbio.ibb.waw.pl/patacsdb. Source code is available for download from GitHub repository at http://github.com/habich/PATACSDB, including the scripts to recreate the database from the scratch on user's own computer.
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2015. PATACSDB - The database of polyA translational attenuators in coding sequences. PeerJ PrePrints 3:e1557v1 https://doi.org/10.7287/peerj.preprints.1557v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
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This is a submission to PeerJ Computer Science for review.
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Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Malgorzata Habich conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, performed the computation work, reviewed drafts of the paper.
Sergej Djuranovic conceived and designed the experiments, wrote the paper, reviewed drafts of the paper.
Pawel Szczesny conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.
Data Deposition
The following information was supplied regarding data availability:
https://github.com/habich/PATACSDB/
Funding
The authors received no funding for this work.