Table 4. Transcripts involved in seed protein storage or mobilization with high TE values in at least one stage of seed development.
| Gene Model | C25 | C25 | C25 | C100 | C100 | C100 | C300 | C300 | C300 | Annotation Groupa |
|---|---|---|---|---|---|---|---|---|---|---|
| CT | FP | TE | CT | FP | TE | CT | FP | TE | ||
| Glyma.06G272700.1 | 0.1 | 4.02 | 40.21 | 0.1 | 0.16 | 1.58 | 0.52 | 0.16 | 0.31 | A. cysteine proteinases superfamily |
| Glyma.02G213000.1 | 0.1 | 3.57 | 35.67 | 0.1 | 0.1 | 1.00 | 0.1 | 0.1 | 1.00 | A. eukaryotic aspartyl protease |
| Glyma.06G022600.1 | 1.29 | 32.86 | 25.53 | 0.73 | 0.23 | 0.32 | 0.58 | 0.1 | 0.17 | A. subtilisin-like serine endopeptidase |
| Glyma.09G226700.1 | 0.16 | 2.68 | 16.4 | 0.14 | 0.1 | 0.73 | 0.2 | 0.1 | 0.49 | A. serine carboxypeptidase-like 40 |
| Glyma.04G022500.1 | 0.21 | 3.21 | 15.11 | 0.17 | 0.1 | 0.6 | 0.1 | 0.1 | 1.00 | A. subtilisin-like serine endopeptidase |
| Glyma.16G018900.1 | 0.1 | 1.33 | 13.3 | 0.1 | 0.1 | 1.00 | 0.1 | 0.1 | 1.00 | A. subtilisin-like serine endopeptidase |
| Glyma.12G010100.1 | 0.1 | 1.25 | 12.53 | 0.14 | 0.1 | 0.7 | 0.19 | 0.1 | 0.53 | A. serine carboxypeptidase-like 40 |
| Glyma.03G125400.1 | 0.78 | 3.04 | 3.89 | 0.31 | 0.1 | 0.32 | 0.4 | 0.18 | 0.45 | A. serine carboxypeptidase-like 45 |
| Glyma.09G249500.1 | 1.25 | 4.28 | 3.43 | 0.29 | 0.1 | 0.35 | 0.2 | 0.15 | 0.74 | A. serine carboxypeptidase-like 20 |
| Glyma.04G027600.1 | 1.19 | 2.91 | 2.45 | 0.39 | 0.1 | 0.26 | 0.22 | 0.27 | 1.23 | A. papain family cysteine protease |
| Glyma.18G242900.1 | 1 | 1.39 | 1.4 | 0.31 | 0.1 | 0.32 | 0.16 | 0.1 | 0.63 | A. serine carboxypeptidase-like 20 |
| Glyma.06G027700.1 | 2.2 | 2.33 | 1.06 | 0.53 | 0.15 | 0.28 | 0.27 | 0.28 | 1.04 | A. papain family cysteine protease |
| Glyma.19G236600.1 | 0.13 | 0.1 | 0.76 | 13.05 | 6.82 | 0.52 | 130.66 | 212.14 | 1.62 | B. eukaryotic aspartyl protease |
| Glyma.08G116400.1 | 115.99 | 52.91 | 0.46 | 586.73 | 671.26 | 1.14 | 691.81 | 1163.3 | 1.68 | B. xylem bark cysteine peptidase 3 |
| Glyma.03G239700.1 | 0.43 | 0.12 | 0.28 | 32.14 | 19.07 | 0.59 | 194.63 | 281.6 | 1.45 | B. eukaryotic aspartyl protease |
| Glyma.02G281500.1 | 0.25 | 5.02 | 20.28 | 0.59 | 0.51 | 0.86 | 1.6 | 0.1 | 0.06 | C. LTP/seed storage 2S albumin |
| Glyma.01G132500.1 | 1.78 | 34.05 | 19.18 | 1.01 | 0.21 | 0.21 | 1.05 | 0.84 | 0.79 | C. lipid transfer protein 1 |
| Glyma.09G058200.1 | 0.1 | 1.89 | 18.93 | 0.1 | 0.1 | 1.00 | 0.1 | 0.11 | 1.07 | C. LMW cysteine-rich 19 |
| Glyma.05G002200.1 | 0.11 | 1.92 | 17.77 | 0.62 | 0.2 | 0.32 | 0.15 | 0.1 | 0.66 | C. LTP/seed storage 2S albumin |
| Glyma.02G281400.1 | 0.73 | 12.64 | 17.23 | 2.22 | 0.79 | 0.35 | 3.2 | 1.34 | 0.42 | C. LTP/seed storage 2S albumin |
| Glyma.08G234100.1 | 0.1 | 1.64 | 16.44 | 0.15 | 0.1 | 0.68 | 0.1 | 0.1 | 1.00 | C. LMW cysteine-rich 19 |
| Glyma.19G002300.1 | 0.23 | 3.57 | 15.82 | 0.35 | 0.19 | 0.53 | 0.1 | 0.17 | 1.67 | C. LTP/seed storage 2S albumin |
| Glyma.03G035700.1 | 0.21 | 3.25 | 15.32 | 0.14 | 0.1 | 0.73 | 0.1 | 0.1 | 1.00 | C. lipid transfer protein 5 |
| Glyma.14G032800.1 | 0.16 | 2.16 | 13.65 | 0.11 | 0.1 | 0.94 | 0.1 | 0.1 | 1.01 | C. LTR/seed storage 2S albumin |
| Glyma.08G228400.1 | 0.1 | 1.2 | 11.98 | 0.1 | 0.1 | 1.00 | 0.25 | 0.1 | 0.39 | C. LMW cysteine-rich 56 |
| Glyma.20G248700.1 | 0.18 | 2.01 | 11.19 | 0.19 | 0.34 | 1.8 | 0.1 | 0.59 | 5.87 | C. LTP/seed storage 2S albumin |
| Glyma.10G297600.1 | 0.23 | 1.68 | 7.37 | 1.12 | 0.71 | 0.64 | 0.93 | 1.51 | 1.62 | C. LTP/seed storage 2S albumin |
| Glyma.09G055100.1 | 0.25 | 1.54 | 6.07 | 0.1 | 0.35 | 3.54 | 0.28 | 0.49 | 1.77 | C. LTP/seed storage 2S albumin |
| Glyma.09G055000.1 | 0.34 | 1.63 | 4.83 | 0.1 | 0.38 | 3.82 | 0.3 | 0.53 | 1.77 | C. LTP/seed storage 2S albumin |
| Glyma.05G057800.1 | 0.97 | 1 | 1.03 | 2.75 | 1.27 | 0.46 | 1.96 | 1.58 | 0.8 | C. LTP/seed storage 2S albumin |
| Glyma.06G067000.1 | 0.29 | 0.29 | 1 | 3.13 | 3.36 | 1.07 | 2.04 | 2.29 | 1.12 | C. LTP/seed storage 2S albumin |
| Glyma.09G163900.1 | 0.33 | 0.2 | 0.62 | 1.09 | 0.63 | 0.58 | 1 | 2.05 | 2.05 | D. Kunitz family trypsin inhibitor |
| Glyma.16G211700.1 | 30.04 | 11.64 | 0.39 | 8.11 | 8.55 | 1.05 | 7.52 | 7.23 | 0.96 | D. Kunitz family trypsin inhibitor |
| Glyma.08G341500.1 | 406.43 | 177.39 | 0.44 | 514.57 | 477.37 | 0.93 | 528.44 | 850.64 | 1.61 | D. Kunitz trypsin inhibitor 1 |
| Glyma.13G123500.1 | 59.71 | 21.9 | 0.37 | 1138.1 | 873.26 | 0.77 | 1254.2 | 1748.7 | 1.39 | D. cupins superfamily/glycinin |
RPKMs for control (CT) and footprint (FP) libraries and TE values for the average of the two biological repeats of the indicated stages of development from the early stage C25 cotyledons of 25–50 mg, C100 mid-stage cotyledons of 100–200 mg, and C300 late stage C300 cotyledons of 300–400 mg. Bold type marks the highest TE values for the Glyma model. LTP, lipid transfer protein; LMW, low molecular weight.
aAnnotation groups: A. Proteases and peptidases with high TE in C25; B. Proteases and peptidases high TE in C300; C. Low molecular weight 2S albumin and other storage proteins with high TE in C25; D. Seed storage proteins with high TE in C300.