HAltORF: a database of predicted out-of-frame alternative open reading frames in human

Database (Oxford). 2012 May 20;2012:bas025. doi: 10.1093/database/bas025. Print 2012.

Abstract

Human alternative open reading frames (HAltORF) is a publicly available and searchable online database referencing putative products of out-of-frame alternative translation initiation (ATI) in human mRNAs. Out-of-frame ATI is a process by which a single mRNA encodes independent proteins, when distinct initiation codons located in different reading frames are recognized by a ribosome to initiate translation. This mechanism is largely used in viruses to increase the coding potential of small viral genomes. There is increasing evidence that out-of-frame ATI is also used in eukaryotes, including human, and may contribute to the diversity of the human proteome. HAltORF is the first web-based searchable database that allows thorough investigation in the human transcriptome of out-of-frame alternative open reading frames with a start codon located in a strong Kozak context, and are thus the more likely to be expressed. It is also the first large scale study on the human transcriptome to successfully predict the expression of out-of-frame ATI protein products that were previously discovered experimentally. HAltORF will be a useful tool for the identification of human genes with multiple coding sequences, and will help to better define and understand the complexity of the human proteome. Database URL: http://haltorf.roucoulab.com/.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Data Mining / methods*
  • Databases, Genetic*
  • Frameshifting, Ribosomal*
  • Humans
  • Molecular Sequence Data
  • Open Reading Frames*
  • Peptide Chain Initiation, Translational
  • Software
  • Transcriptome