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Table 1 Known and novel ncRNAs and UTR elements in PigEST data

From: Detection of RNA structures in porcine EST data and related mammals

  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
  1. 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.