Table 6.
Twenty-seven nucleus-encoded TAIR10 proteins not identified in Araport11 based on at least two distinct peptides supported by at least three MS/MS spectra
| TAIR10 | No. of Unique Matched Peptide Sequences (Includes also Peptides Observed Only 1x or 2x) | No. of Total Frequency of Observation of Matched Peptides | Protein Name | Change in Araport11 as Compared to TAIR10 | Comments | No. of Gene Models in TAIR10 | No. of Gene Models in Araport11 |
|---|---|---|---|---|---|---|---|
| AT1G14070.1 | 12 | 28 | Xyloglucan fucosyltransferase | Removed | 2 exons; very strong support 2nd exon | 1 | N/A |
| AT2G33430.1 | 15 | 1,339 | MORF2 (also DAG protein) – editing factor | Removed | Very strong peptide support for 3 of the 3 exons | 1 | N/A |
| AT3G12012.1 (Figure 8A) | 5 | 39 | Conserved peptide upstream ORF20 | Removed | 3 exons; strong support for 2 exons | 1 | 0 |
| AT4G18120.1 | 22 | 202 | MEI2-like 2 | Removed | Very strong peptide support for 7 of the 10 exons. How are model .1 and .2 different (TAIR10)? | 2 | N/A |
| AT5G25752.1 | 7 | 235 | Rhomboid protease 11/9 (RBL11/9) | Removed | 7 exons (TAIR10). 5 peptides for first exon. One peptide for last exon | 1 | N/A |
| AT1G16780.1 | 3 | 23 | Inorganic H pyrophosphatase | ATG shifted. Araport11 is shorter | 15 (TAIR10) or 14 exons (Ara11). All Araport models start later | 1 | 3 |
| AT5G18280.2 | 3 | 478 | Apyrase 1 | ATG shifted. Araport11 is shorter | 9 exons in model 1 and 11 in model 2 for TAIR10. 9 exons in Araport11. One extra exon in model .2 supported with one short peptide; 2 peptides for first exon | 2 | 1 |
| AT5G52640.1 | 4 | 51 | Heat shock protein (HSP81-1/HSP83) | ATG shifted. Araport11 is shorter | 4 exons in both TAIR10 and araport11; strong support for 1st exon | 1 | 1 |
| AT5G63980.1 | 4 | 54 | SAL1 (FIERY1), 3(2), 5-bisphosphate nucleotidase | ATG shifted. Araport11 is shorter | 7 exons in both TAIR10 and Araport11; 4 peptides for the 1st exon | 1 | 1 |
| AT5G18280.1 | 3 | 478 | Apyrase 2 | ATG. Araport11 is shorter | 9 exons in model 1 and 11 in model 2 for TAIR10. 9 exons in Araport11. One extra exon in model .2 supported with one short peptide; 2 peptides for first exon | 2 | 1 |
| AT1G03495.1 | 4 | 26 | HXXXD-type acyl-transferase | STOP. Araport11 is shorter | One big exon – clear case | 1 | 1 |
| AT1G79920.1 | 26 | 2,006 | Heat shock protein 70 (Hsp 70) | STOP. Araport11 is shorter | 9 exons in TAIR10; 8 exons in Arport11 | 2 | 4 |
| AT4G23000.1 | 5 | 16 | Calcineurin-like metallo-phosphoesterase | STOP. Araport11 is shorter | 15 exons in TAIR10, 14 exons in Araport11. several peptides for both extra exons | 1 | 2 |
| AT5G40780.2 | 3 | 21 | Lysine histidine transporter 1 | Splicing | 8 exons in TAIR10; 8 exons for model 1, but 7 for models 2 and 3 in Araport11 | 2 | 3 |
| AT3G57180.1 | 3 | 28 | BPG2-homolog of YqeH–GTPase | Mismatch–in one exon | 3 overlapping long peptides; sequencing difference? | 1 | 1 |
| AT4G16150.1 | 3 | 18 | Calmodulin-binding transcription activator 5 | Mismatch–in one exon; likely related to a gene duplication At3G16940 and AT4G16150 | 13 exons in both TAIR10 and Araport11. sequencing mismatch in 11th exon | 1 | 1 |
| AT1G52827.1 | 3 | 191 | Cadmium tolerance 1 | ATG+STOP. Big change | 3 nested peptides for exon 1; no peptides for exon 2 | 1 | 1 |
| AT3G52130.1 (Figure 8C) | 7 | 70 | Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin | ATG+STOP+splicing | One exon in TAIR10; 2 exons in Araport–but first new one very short | 1 | 1 |
| AT4G16770.1 | 3 | 66 | 2-Oxoglutarate (2OG) and Fe(II)-dependent oxygenase | ATG+STOP+splicing. Araport11 is shorter | 11 exons in TAIR10 and 8 in Araport11. 2 peptides for extra C-terminal exon; splice difference for exon 7 | 1 | 1 |
| AT5G39570.1 | 172 | 14,860 | Transmembrane protein | ATG+STOP+splicing. Araport11 is shorter | 2 exons in TAIR10; 2 or 3 exons in Araport11 | 1 | 2 |
| AT4G21326.1 | 3 | 12 | Subtilase SBT12 | ATG+splicing. Araport 11 is shorter | 8 exons in TAIR10, 7 exons in Araport11 | 1 | 1 |
| AT1G23580.1 | 10 | 49 | Transmembrane protein with DUF220 | ATG+splicing. Araport11 is shorter | 4 exons in TAIR10; 2 exons in Araport11 | 1 | 1 |
| AT2G38255.1 (Figure 8B) | 5 | 14 | Hypothetical protein (DUF239) | STOP+splicing | 7 exons (TAIR10); 6 exons in (Araport11). Strong support for extra C-term exon | 1 | 1 |
| AT1G17060.1 | 7 | 33 | Cytochrome p450 72c1 | STOP+splicing | 6 exons (TAIR10) or 4 exons (Araport11); Araport 11–antisense gene–overlapping protein coding–AT1G7065) | 1 | 1 |
| AT4G16144.1 | 5 | 46 | JAB1/Mov34/MPN/PAD-1 domain protein | STOP+splicing. Araport11 is shorter | 13 exons in TAIR10 and 13 in Araport11. 4 peptides in extra C-term exon, and 1 for splice junction | 1 | 1 |
| AT4G18260.1 | 11 | 103 | Cytochrome b561/ferric reductase | STOP+splicing. Araport11 is shorter | 7 exons in TAIR10, 4 exons in Araport11. All 3 extra C-terminal exons are supported with peptides | 1 | 1 |
| AT5G02370.1 | 2 | 11 | Kinesin motor protein-related | STOP+splicing. Araport11 is shorter | 1 exons in TAIR10 but 9 in Araport11; 2 nested peptides for the last exon | 1 | 1 |