Table IV. Novel EPT clusters with full-length gene model predictions.
Genomic regions containing clustered nEPTs and 10,000 bp of flanking sequence were fed into the AUGUSTUS gene prediction software along with EPT-based coding hints. Predicted gene models were then searched against the RefSeq database using NCBI BLAST. Shown are gene models predicted by AUGUSTUS with both annotated start and stop codons and similarity in overall size to the top BLAST hit. Gene models were reported by AUGUSTUS for an additional 99 novel EPT clusters but are likely to be incomplete due to missing genomic sequence.
| Locus | Contained uniquely mapped nEPTs | All contained nEPTs | Description of top RefSeq hit | Percent identity | E-value |
|---|---|---|---|---|---|
| Cluster_149 | 29 | 29 | Nephrocystin-3-like [Glycine max] | 87.1 | 0.00E+000 |
| Cluster_189 | 24 | 24 | Subtilisin-like protease-like [Glycine max] | 82.3 | 0.00E+000 |
| Cluster_162 | 17 | 17 | Reticuline oxidase [Medicago truncatula] | 78.8 | 0.00E+000 |
| Cluster_102 | 11 | 11 | Conserved oligomeric Golgi complex subunit 1-like [Glycine max] | 84.9 | 0.00E+000 |
| Cluster_033 | 10 | 10 | UDP-glycosyltransferase 84B1-like [Glycine max] | 71.5 | 0.00E+000 |
| Cluster_141 | 8 | 8 | S-adenosylmethionine synthase-like isoform 1 [Glycine max]# | 96.4 | 0.00E+000 |
| Cluster_167 | 8 | 8 | Probable glutathione S-transferase-like [Glycine max] | 77.4 | 4.00E−128 |
| Cluster_184 | 8 | 8 | ruBisCO large subunit-binding protein subunit alpha, chloroplastic-like [Glycine max] | 91.1 | 0.00E+000 |
| Cluster_043 | 7 | 7 | Uncharacterized protein LOC100306450 [Glycine max] | 80.2 | 9.00E−053 |
| Cluster_010 | 6 | 6 | Ubiquinone biosynthesis protein COQ9, mitochondrial-like [Glycine max] | 75.6 | 1.00E−161 |
| Cluster_140 | 6 | 6 | Uncharacterized protein LOC100818804 [Glycine max] | 72.6 | 1.00E−101 |
| Cluster_006 | 5 | 5 | NADP-dependent malic enzyme, chloroplastic-like [Glycine max] | 89.3 | 0.00E+000 |
| Cluster_173 | 5 | 5 | Uncharacterized protein LOC100244411 [Vitis vinifera] | 49.7 | 3.00E−076 |
| Cluster_007 | 4 | 5 | Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial-like [Glycine max] | 89.8 | 0.00E+000 |
| Cluster_001 | 4 | 4 | Uncharacterized protein LOC100788250 [Glycine max] | 81.2 | 0.00E+000 |
| Cluster_039 | 4 | 4 | Uncharacterized protein LOC100527685 [Glycine max] | 65.8 | 1.00E−021 |
| Cluster_081 | 4 | 4 | Uncharacterized protein LOC100805605 [Glycine max] | 61.8 | 3.00E−129 |
| Cluster_094 | 4 | 4 | Poly(A) polymerase-like [Glycine max] | 80.2 | 0.00E+000 |
| Cluster_096 | 4 | 4 | Chlorophyll a-b binding protein 21, chloroplastic-like [Glycine max] | 91.7 | 6.00E−177 |
| Cluster_169 | 4 | 4 | Predicted protein [Populus trichocarpa] | 69.4 | 2.00E−114 |
| Cluster_160 | 2 | 4 | Probable methyltransferase PMT8-like [Glycine max] | 82.9 | 0.00E+000 |
| Cluster_121 | 3 | 3 | Expansin-A4-like [Glycine max] | 88.1 | 4.00E−171 |
| Cluster_134 | 3 | 3 | Em-like protein GEA1-like [Glycine max] | 79.1 | 3.00E−048 |
| Cluster_029 | 2 | 2 | Uncharacterized protein LOC100306283 isoform 2 [Glycine max] | 73.0 | 1.00E−029 |
| Cluster_067 | 2 | 2 | Hypothetical protein MTR_6g034800 [Medicago truncatula] | 36.2 | 1.00E−033 |
| Cluster_097 | 2 | 2 | LRR receptor-like serine/threonine-protein kinase FLS2-like [Glycine max] | 78.1 | 0.00E+000 |
| Cluster_111 | 2 | 2 | Uncharacterized protein LOC100527746 [Glycine max] | 80.0 | 8.00E−065 |
| Cluster_129 | 2 | 2 | Uncharacterized protein LOC100811471 isoform 1 [Glycine max] | 85.4 | 0.00E+000 |
| Cluster_136 | 2 | 2 | Uncharacterized protein LOC100794459 [Glycine max] | 62.2 | 7.00E−053 |
| Cluster_138 | 2 | 2 | Zinc finger CCCH domain-containing protein 32-like [Glycine max] | 75.5 | 0.00E+000 |
| Cluster_168 | 2 | 2 | Transcription factor RF2b-like [Glycine max] | 73.7 | 0.00E+000 |
| Cluster_186 | 2 | 2 | Octanoyltransferase-like [Glycine max] | 86.2 | 8.00E−138 |
| Cluster_194 | 2 | 2 | Uncharacterized protein LOC100526970 precursor [Glycine max] | 68.3 | 1.00E−101 |
| Cluster_002 | 1 | 2 | Uncharacterized protein LOC100788250 [Glycine max] | 81.2 | 0.00E+000 |