| |
Method
|
Contigs
|
Singletons
|
|---|
|
ncRNAs
|
Known by sequence
|
13
|
12
|
| |
Known by structure
|
10
|
16
|
| |
Previously predicted
|
143
|
52
|
| |
Novel predicted
|
549
|
260
|
| |
Total
|
715
|
340
|
|
UTR elements
|
Known by sequence
|
24
|
2
|
| |
Known by structure
|
44
|
16
|
| |
Previously predicted
|
69
|
6
|
| |
Novel predicted
|
174
|
27
|
| |
Total
|
311
|
51
|
|
Sum of all RNA structures
|
1,026
|
391
|
- Table 1: Overview of all conreads in the PigEST data consisting known and putative novel ncRNAs and cis-acting (UTR) regulatory RNA elements. Known RNA families were found through sequence similarity to ncRNA databases and structure similarity to covariance models of Rfam, whereas tRNA candidates are not counted due to a high rate of tRNA pseudogene annotations [see Additional file 1, Table S11 for a similar table inluding the tRNA candidates]. Previously predicted RNA secondary structures overlap with greater than 50% a RNAz or Evofold prediction in human reported in [16] and [17]. Novel predictions comprise the remaining high confidence RNAz candidates. Cis-acting (UTR) elements are predicted RNA structures conserved in an human UTR (no matter if conreads contain an ORF) and ncRNAs represent conserved RNA structures predicted in ORF-free conreads without similarity to annotated UTRs.
