PATACSDB-the database of polyA translational attenuators in coding sequences

Malgorzata Habich, Sergej Djuranovic, Pawel Szczesny

Research output: Contribution to journalArticlepeer-review

4 Scopus citations

Abstract

Recent additions to the repertoire of gene expression regulatory mechanisms are polyadenylate (polyA) tracks encoding for poly-lysine runs in protein sequences. Such tracks stall the 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 the 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; this makes each of these sequences a potentially interesting case study for the effects of synonymous mutation, gene dosage balance and natural frameshifting. Here we present PATACSDB, a resource that contain a comprehensive list of polyA tracks from over 250 eukaryotic genomes. Our data is based on the 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 accessible at: http://sysbio.ibb.waw.pl/patacsdb. The source code is available at http://github.com/habich/PATACSDB, and it includes the scripts with which the database can be recreated.

Original languageEnglish
Article numbere45
JournalPeerJ Computer Science
Volume2016
Issue number2
DOIs
StatePublished - Jan 1 2016

Keywords

  • Eukaryotic genomes
  • Gene regulation
  • Ribosome stalling
  • Translation
  • mRNA stability

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