Table 1.
The 19 features used to select the potential non-coding set
| Features | Genes | Peptide detection (%) |
|---|---|---|
| Homology existence [UP] | 131 | 6.87 |
| Pseudogene [E] | 75 | 6.67 |
| PUTATIVE transcripts [G] | 434 | 2.53 |
| Caution—pseudogene [UP] | 79 | 2.53 |
| Caution—dubious CDS [UP] | 47 | 2.13 |
| Poor conservation (MI score) [A] | 987 | 2.03 |
| Predicted existence [UP] | 507 | 1.58 |
| No protein features [A] | 1212 | 1.32 |
| Nonsense-mediated decay [G] | 78 | 1.28 |
| Circular annotation [E/UP] | 336 | 1.19 |
| Uncertain existence [UP] | 100 | 1.00 |
| Primate gene family [E] | 563 | 0.89 |
| Read-through [E/G] | 229 | 0.87 |
| Obsolete [E/UP] | 130 | 0.00 |
| Dubious EST support [E/G] | 98 | 0.00 |
| Non-functional [E] | 44 | 0.00 |
| Non-coding [E] | 38 | 0.00 |
| Antisense/opposite strand [E] | 25 | 0.00 |
| Miscellaneous RNA [E] | 7 | 0.00 |
Each feature is explained in more detail in Materials and methods and Supplementary sections. The source of each feature is indicated in square brackets (A, APPRIS; E, Ensembl; G, GENCODE; UP, UniProt). For each feature, we also show the number of genes with the feature and the proportion that we identify in the seven datasets.