49266 Bos taurus sequence windows
comprising 3305 of 9187 genes.

0 Caenorhabditis elegans sequence windows
comprising 0 of 28211 genes.

25836 Danio rerio sequence windows
comprising 1929 of 6197 genes.

102404 Homo sapiens sequence windows
comprising 6732 of 17893 genes.

86837 Mus musculus sequence windows
comprising 5933 of 15620 genes.

26979 Rattus norvegicus sequence windows
comprising 1959 of 5341 genes.

71433 Saccharomyces bayanus sequence windows
comprising 2951 of 4970 genes.

73836 Saccharomyces castellii sequence windows
comprising 2964 of 4681 genes.

150045 Saccharomyces cerevisiae sequence windows
comprising 4128 of 6352 genes.

48447 Saccharomyces kudriavzevii sequence windows
comprising 2212 of 3778 genes.

9700 Saccharomyces paradoxus sequence windows
comprising 436 of 8955 genes.

79485 Xenopus laevis sequence windows
comprising 4808 of 9325 genes.

44299 Xenopus tropicalis sequence windows
comprising 2663 of 5126 genes.

The last update was a Virus-human adenovirus sequence at 2009-06-29 16:18:02.

NCI

Cis-acting mRNA elements that program ribosomes to shift translational reading frame were first discovered in viruses. These programmed -1 ribosomal frameshift (-1 PRF) signals are composed of a heptameric "slippery site" followed by an mRNA pseudoknot secondary structure. ¹

Viruses typically use -1 PRF as a genome condensation strategy; enabling them to encode multiple proteins from a single unaltered mRNA. Historically, because of their relative simplicity, many molecular regulatory elements have been first discovered in viruses: -1 PRF is no different.

We developed a computational method to identify putative -1 PRF signals in eukaryotic genomic sequences. Subsets of these sequences were shown to stimulate significant -1 programmed frameshifting using dual-luciferase reporter constructs. ²

Analysis of these signals suggests that, after a frameshifting event, ribosomes would be directed to translate premature termination codons. These should promote mRNA destabilization via the nonsense-mediated mRNA decay (NMD) pathway. We previously showed that a viral -1 PRF signal cloned in a similar context can function as an mRNA destabilizing element. ³ This suggests that regulation of -1 PRF may be used to regulate cellular gene expression by controlling mRNA stability. In addition, ribosome stalling induced by strong mRNA structures can also promote mRNA degradation via 'No-go decay,' suggesting that our computational approach may be capable of identifying a class of mRNA destabilizing elements independent of -1 PRF.

This online database is focused on cataloging programmed ribosomal frameshift signals (PRF) in eukaryotic genomes. Please search for a gene of interest or select one of the links above to get started. Most of the sequence information from this database came from either the Yeast Genome Project or the Mammalian Gene Collection.

It is possible to search for any word(s) from the NCBI or SGD gene description as well as the canonical gene name. Thus searching for 'RPL' or 'ribosome' are likely candidates for looking at ribosomal genes.

1. Plant, E.P., Muldoon Jacobs, K.L., Harger, J.W., Meskauskas, A., Jacobs, J.L., Baxter, J.L., Petrov, A.N., Dinman, J.D. The 9-Å solution: How mRNA pseudoknots promote efficient programmed -1 ribosomal frameshifting. RNA (9), 168-174 (2003).
2. Jacobs JL, Belew AT, Rakauskaite R, Dinman JD. Identification of functional, endogenous programmed -1 ribosomal frameshift signals in the genome of Saccharomyces cerevisiae NAR 2006 Dec7
3. Plant EP, Wang P, Jacobs JL and Dinman JD. A programmed –1 ribosomal frameshift signal can function as a cis-acting mRNA destabilizing element. NAR (32), 784-790 (2004).