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Table 3 Summary of conservation of expression, and of NOLP sequence conservation

From: The distribution and evolution of Arabidopsis thaliana cis natural antisense transcripts

Data set Conserved sequence* Conserved anti-sense transcription in A. lyrata** Conserved sequence and anti-sense transcription*
TAIR set (total 162) 12 57 (35%) 4
55 ¶ (34%) 22
Matsui2008 set (total 3172) 889 1014 (32%) 453 ††
1023 (32%) 350 †
Okamoto2010 set (total 1538) 314 435 (28%) 168 ††
437 (28%) 131
Complete non-redundant NR set (total 4177) 584 1314 (31%) 191
1323 (32%) 427
  1. *The first value is for conserved sequence in A. lyrata and is calculated by pairwise BLASTN alignment (e-value <1e-10 [28]) adjacent to orthologous genes (determined using the bi-directional best hits method applied to the encoded protein sequences). The second value is for overall significant conservation across the nine species as determined by phyloP. Overall significant conservation is calculated as in Table 1.
  2. **Anti-sense transcripts in A. lyrata have no ORF >100 codons and no protein homology in their own sense direction.
  3. † P = 0.03, significant association of transcription and conservation, using hypergeometric test.
  4. †† P ≤ 1x10−25, very significant association of transcription and conservation, using hypergeometric test.
  5. ¶ The total number of conserved are significantly depleted compared to randomly sampled near-gene DNA (P = 0.002, normal statistics). To assess this, for each of the three actual data sets listed, 500 samples of near-gene DNA of the same distribution of sizes and position relative to neighbour genes as the actual set were submitted to PhyloP calculation (as described in the Methods ).