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

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

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

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).

ISSN: 1471-2105