Table 1. Sequence reads are predominantly derived from the coding regions of selected gene models for seed storage proteins in the footprint libraries as compared to the control libraries.
| Protein Annotation |
Gene Model |
Library Type |
Reads or Normalized Ratio Per Region | ||
|---|---|---|---|---|---|
| 5' UTR | CDS | 3' UTR | |||
| Soybean Seed Lectin | Glyma.02G012600.1 | C300CT | 977 | 19716 | 1593 |
| C300FP | 36 | 10842 | 22 | ||
| FP/CT* | 0.07 | 1.00 | 0.03 | ||
| Kunitz Trypsin Inhibitor | Glyma.01G095000.1 | C300CT | 449 | 13717 | 2818 |
| C300FP | 37 | 7997 | 64 | ||
| FP/CT* | 0.14 | 1.00 | 0.04 | ||
| Kunitz Trypsin Inhibitor | Glyma.08G341000.1 | C300CT | 43 | 838 | 139 |
| C300FP | 0 | 445 | 4 | ||
| FP/CT* | 0.00 | 1.00 | 0.05 | ||
| Kunitz Trypsin Inhibitor | Glyma.08G341500.1 | C300CT | 2159 | 35460 | 2559 |
| C300FP | 114 | 26440 | 78 | ||
| FP/CT* | 0.07 | 1.00 | 0.04 | ||
| Conglycinin | Glyma.20G148200.1 | C300CT | 1564 | 55629 | 4953 |
| C300FP | 143 | 26172 | 79 | ||
| FP/CT* | 0.19 | 1.00 | 0.03 | ||
| Conglycinin | Glyma.20G148300.1 | C300CT | 4495 | 101409 | 5075 |
| C300FP | 328 | 40697 | 115 | ||
| FP/CT* | 0.18 | 1.00 | 0.06 | ||
| Conglycinin | Glyma.20G148400.1 | C300CT | 4453 | 101409 | 6464 |
| C300FP | 328 | 40697 | 140 | ||
| FP/CT* | 0.18 | 1.00 | 0.05 | ||
| Glycinin | Glyma.19G164900.1 | C300CT | 599 | 22484 | 1286 |
| C300FP | 10 | 10100 | 23 | ||
| FP/CT* | 0.04 | 1.00 | 0.04 | ||
The cDNA transcripts derived from the indicated gene models from the soybean genome were used as individual references to which libraries from the C300 stage of 300–400 mg immature seeds were aligned. The specific libraries used were the control library C300CT (RP3001C) compared to its footprint library C300FP (RP3001T). The non-normalized total numbers of trimmed and processed reads aligning to either the 5’ or 3’ UTR regions compared to the protein coding sequences (CDS) of the indicated gene model are shown.
* represents the ratio of the C300FP/C300CT read counts normalized relative to the CDS region as 1.00 and illustrates the dramatic reduction in the representation of the 5’ and 3’ UTR regions in the footprint libraries.