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. 2001 Jan 1;29(1):264-7.
doi: 10.1093/nar/29.1.264.

RECODE: a database of frameshifting, bypassing and codon redefinition utilized for gene expression

P V Baranov  1 , O L Gurvich, O Fayet, M F Prère, W A Miller, R F Gesteland, J F Atkins, M C Giddings
Affiliations

RECODE: a database of frameshifting, bypassing and codon redefinition utilized for gene expression

P V Baranov et al. Nucleic Acids Res. .

Abstract

The RECODE database is a compilation of 'programmed' translational recoding events taken from the scientific literature and personal communications. The database deals with programmed ribosomal frameshifting, codon redefinition and translational bypass occurring in a variety of organisms. The entries for each event include the sequences of the corresponding genes, their encoded proteins for both the normal and alternate decoding, the types of the recoding events involved, trans-factors and cis-elements that influence recoding. The database is freely available at http://recode.genetics. utah.edu/.

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Figures

Figure 1
Figure 1
Three examples of recoding events. (A) Antizyme frameshifting. The +1 shift at the last codon (UCC) before the termination codon of ORF1 of human antizyme 1 is stimulated by polyamines and by a 5′ mRNA element and a 3′ pseudoknot. (B) Gene 60 bypassing. Fifty nucleotides between codons 47 and 48 of phage T4 gene 60 coding sequence are bypassed by half the ribosomes in response to matched takeoff and landing site codons, a stop codon directly after the take-off site in a stem–loop structure and a nascent peptide signal that acts within the ribosome. (C) Procaryotic selenocysteine insertion—redefinition. UGA codons in procaryotes that specify selenocysteine are directly followed by a stem structure whose apical loop is bound by a selenocysteine tRNA specific elongation factor SELB, resulting in a tethered aminoacylated tRNA poised for the oncoming ribosome. These figures are adapted from Atkins et al. (8).
Figure 1
Figure 1
Three examples of recoding events. (A) Antizyme frameshifting. The +1 shift at the last codon (UCC) before the termination codon of ORF1 of human antizyme 1 is stimulated by polyamines and by a 5′ mRNA element and a 3′ pseudoknot. (B) Gene 60 bypassing. Fifty nucleotides between codons 47 and 48 of phage T4 gene 60 coding sequence are bypassed by half the ribosomes in response to matched takeoff and landing site codons, a stop codon directly after the take-off site in a stem–loop structure and a nascent peptide signal that acts within the ribosome. (C) Procaryotic selenocysteine insertion—redefinition. UGA codons in procaryotes that specify selenocysteine are directly followed by a stem structure whose apical loop is bound by a selenocysteine tRNA specific elongation factor SELB, resulting in a tethered aminoacylated tRNA poised for the oncoming ribosome. These figures are adapted from Atkins et al. (8).
Figure 1
Figure 1
Three examples of recoding events. (A) Antizyme frameshifting. The +1 shift at the last codon (UCC) before the termination codon of ORF1 of human antizyme 1 is stimulated by polyamines and by a 5′ mRNA element and a 3′ pseudoknot. (B) Gene 60 bypassing. Fifty nucleotides between codons 47 and 48 of phage T4 gene 60 coding sequence are bypassed by half the ribosomes in response to matched takeoff and landing site codons, a stop codon directly after the take-off site in a stem–loop structure and a nascent peptide signal that acts within the ribosome. (C) Procaryotic selenocysteine insertion—redefinition. UGA codons in procaryotes that specify selenocysteine are directly followed by a stem structure whose apical loop is bound by a selenocysteine tRNA specific elongation factor SELB, resulting in a tethered aminoacylated tRNA poised for the oncoming ribosome. These figures are adapted from Atkins et al. (8).
Figure 2
Figure 2
Logo of the database.
See this image and copyright information in PMC

References

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