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Table 2 5'-UTR Sequence Parameters Utilized for Analyses by the Classification Tree

From: Bioinformatic analyses of mammalian 5'-UTR sequence properties of mRNAs predicts alternative translation initiation sites

Parameters Description Range
Consensus Sequence Patterns
Pattern #1 (G/C, C) Position -6/-7 Yes/No
Pattern #2 (Kozak) Position -3/+4 Yes/No
5'-UTR Sequence Parameters
5'-UTR Length Length of 5'-UTR 80 to 2000 bp
mRNA Sequence Length Full mRNA length 350 to 5000 bp
G/C Ratio Ratio of G to C 0.4 to 3
GC Percentage Percentage of GC content 0.3 to 0.9
A/T Ratio Ratio of A to T 0.2 to 8
Number of AUGs Number of upstream AUGs from first start site. 0 to 19
Codon Bias Codonw 0.02 to 1.0
Secondary Structure
IRES UTRScan/NCBI Yes/No
GLUT1 UTRScan/NCBI Yes/No
TOP UTRScan/NCBI Yes/No
  1. This table illustrates the parameters (properties) of 5'-UTR regions of mRNAs utilizing aTIS with respect to distinct consensus sequence patterns compared to the traditional Kozak pattern, sequence parameters of 5'-UTR regions, and secondary structure features. The distinct consensus sequence pattern consists of C at position -6 and G/C at position -7 (Fig. 2A). 5'-UTR length is defined as the length of the mRNA sequence from the beginning of the 5'-UTR to the translation initiation site and sequence length as annotated in GenBank. Number of AUGs is determined from the start of the 5'-UTR to the first annotated start site. Secondary structure features considered are Internal Ribosome Entry Sites (IRES), Glucose Transporter 1 (GLUT1), and Terminal Oligopyrimidine (TOP).