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Subject = Site transfer RNA;
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Displaying Results 1 - 2 of 2 on page 1 of 1
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Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli
(2014)
Sharma, Virag; Prère, Marie-Francoise; Canal, Isabelle; Firth, Andrew E.; Atkins, John ...
Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli
(2014)
Sharma, Virag; Prère, Marie-Francoise; Canal, Isabelle; Firth, Andrew E.; Atkins, John F.; Baranov, Pavel V.; Fayet, Olivier
Abstract:
Programmed ribosomal -1 frameshifting is a non-standard decoding process occurring when ribosomes encounter a signal embedded in the mRNA of certain eukaryotic and prokaryotic genes. This signal has a mandatory component, the frameshift motif: it is either a Z_ZZN tetramer or a X_XXZ_ZZN heptamer (where ZZZ and XXX are three identical nucleotides) allowing cognate or near-cognate repairing to the -1 frame of the A site or A and P sites tRNAs. Depending on the signal, the frameshifting frequency can vary over a wide range, from less than 1% to more than 50%. The present study combines experimental and bioinformatics approaches to carry out (i) a systematic analysis of the frameshift propensity of all possible motifs (16 Z_ZZN tetramers and 64 X_XXZ_ZZN heptamers) in Escherichia coli and (ii) the identification of genes potentially using this mode of expression amongst 36 Enterobacteriaceae genomes. While motif efficiency varies widely, a major distinctive rule of bacterial -1 framesh...
http://hdl.handle.net/10468/5017
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Recode-2: new design, new search tools, and many more genes
(2010)
Bekaert, Michael; Firth, Andrew E.; Zhang, Yan; Gladyshev, Vadim N.; Atkins, John F.; B...
Recode-2: new design, new search tools, and many more genes
(2010)
Bekaert, Michael; Firth, Andrew E.; Zhang, Yan; Gladyshev, Vadim N.; Atkins, John F.; Baranov, Pavel V.
Abstract:
Recoding' is a term used to describe non-standard read-out of the genetic code, and encompasses such phenomena as programmed ribosomal frame-shifting, stop codon readthrough, selenocysteine insertion and translational bypassing. Although only a small proportion of genes utilize recoding in protein synthesis, accurate annotation of 'recoded' genes lags far behind annotation of 'standard' genes. In order to address this issue, provide a service to researchers in the field, and offer training data for developers of gene-annotation software, we have gathered together known cases of recoding within the Recode database. Recode-2 is an improved and updated version of the database. It provides access to detailed information on genes known to utilize translational recoding and allows complex search queries, browsing of recoding data and enhanced visualization of annotated sequence elements. At present, the Recode-2 database stores information on approximately 1500 ge...
http://hdl.handle.net/10468/5029
Displaying Results 1 - 2 of 2 on page 1 of 1
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