Skip to main content

Table 1 Glossary of abbreviations

From: Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes

Abbreviation

Explanation

APE

AUG proximal element: control sequences that flank the iAUG

dAPE

Downstream APE: that part of the APE located downstream (3′) of the iAUG

uAPE

Upstream APE: that part of the APE located upstream (5′) of the iAUG

5′ofAPE

The 5′UTR sequences that lie 5′ of the APE

iAUG

Initiating AUG: the AUG codon at the 5′ end of the CDS

uAUG

Upstream AUG: an AUG codon in the 5′ UTR, i.e., an AUG at the 5′ end of an uORF

BIC

Bayesian Information Criteria: a method to select an efficient set of model features

5′ cap

The 5′ most nucleotide of the mRNA

CDS

Coding sequence: the protein coding portion of the mRNA

CDS 3′ofAPE

That part of the CDS that lies 3′ of the APE

MFE

Minimum free energy: the Gibbs free energy of folding for a defined segment of RNA

uORF

Upstream open reading frame: an uAUG containing open reading frame in the 5′UTR

PWM

Position Weight Matrix: the fraction of A, U, G, and Cs at each nucleotide position

5′region

The region spanning the 5′UTR and the 5′ most ~ 30 nucleotides of the CDS

5′UTR

5′ Untranslated region: all mRNA nucleotides 5′ of the CDS

TR

Translation rate: rate of translation per mRNA molecule at steady state

high TR

A cohort of genes with the highest translation rates

low TR

A cohort of genes with the lowest translation rates