Table 2.
Distribution of Genes and Repeats along the 3.5-Mb Cen8 Virtual Contig
| Feature | Domain C1 | Domain B1 | Domain A | Domain B2 | Domain C2 |
|---|---|---|---|---|---|
| Genetic position (cM) | 54.0–54.3 | 54.3 | 54.3 | 54.3 | 54.3–55.4 |
| Coordinate (kb) | 1–437 | 437–1350 | 1350–2100 | 2100–2749 | 2749–3490 |
| Size (kb) | 437 | 913 | 750 | 649 | 741 |
| Active genes | 28 | 32 | 16 | 38 | 48 |
| Protein homology | 12 | 20 | 7 | 24 | 17 |
| No protein homology | 16 | 12 | 9 | 14 | 31 |
| Gene density (kb per active gene) | 15.6 | 28.5 | 46.9 | 17.1 | 15.4 |
| Active gene coverage | 24.0% | 15.9% | 12.8% | 19.8% | 21.2% |
| Inactive or unanalyzed genes | 15 | 14 | 13 | 7 | 11 |
| Protein homology | 6 | 6 | 10 | 2 | 2 |
| Ab initio prediction | 9 | 8 | 3 | 5 | 9 |
| Total genes | 43 | 46 | 29 | 45 | 59 |
| Retrotransposon (kb) | 135.9 | 390.0 | 277.8 | 214.8 | 209.4 |
| Transposon (kb) | 10.1 | 55.0 | 32.9 | 33.1 | 51.3 |
| MITE (kb) | 10.2 | 15.4 | 8.4 | 20.1 | 17.6 |
| Others or unknown (kb) | 8.1 | 10.9 | 62.2 | 8.4 | 7.1 |
| Total repeats (kb) | 164.2 (37.6%) | 471.3 (51.6%) | 381.3 (50.8%) | 276.3 (42.6%) | 285.4 (38.5%) |
Active genes have matches with rice transcripts and/or are RT-PCR positive. Inactive genes have no matches with rice transcripts and/or are RT-PCR negative. Unanalyzed genes have no matches with rice transcripts and/or RT-PCR was not done. MITE, miniature inverted-repeat transposable element.