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5'-UTR Sequence Parameters Utilized for Analyses by the Classification Tree |
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| Parameters |
Description |
Range |
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| Consensus Sequence Patterns |
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| Pattern #1 (G/C, C) |
Position -6/-7 |
Yes/No |
| Pattern #2 (Kozak) |
Position -3/+4 |
Yes/No |
| 5'-UTR Sequence Parameters |
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| 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 |
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| IRES |
UTRScan/NCBI |
Yes/No |
| GLUT1 |
UTRScan/NCBI |
Yes/No |
| TOP |
UTRScan/NCBI |
Yes/No |
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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). | ||
Wegrzyn et al. BMC Bioinformatics 2008 9:232 doi:10.1186/1471-2105-9-232 |
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