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Table 2 Protein structure disruptions in mammalian messenger RNA transcripts

From: Frame disruptions in human mRNA transcripts, and their relationship with splicing and protein structures

Type of initial frame disruption* Alignment verification** Protein structure disruption***   
   Observed [nondisrupting : disrupting] Expected [nondisrupting : disrupting] Significance
Frameshift All cases 293 : 54 272.7 : 74.3 ††
  Cases with verifying alignments 230 : 51 211.3 : 69.7 †††
Stop codon All cases 68 : 5 55.6 : 17.4 †††
  Cases with verifying alignments 34 : 5 27.4 : 11.6
Frameshift or stop codon All cases 360 : 59 327.5 : 91.5 †††
  Cases with verifying alignments 268 : 57 242.2 : 82.8 ††
  Cases with verifying alignments (excluding probable UTR features) 174 : 35 153.6 : 55.4 †††
  1. * For the last row, those with frameshifts and stop codons are pooled together.
  2. ** Verifiying alignments are significant alignments to a rodent or non-mammalian vertebrate protein, as detailed in Methods.
  3. *** The ratio stands for 'the number of frame disruptions not disrupting a protein structure domain assignment versus the number that do'. A margin for ascertaining overlap with a protein domain assignment of 15 nucleotides was used in the calculations. The expectations for the statistical tests (χ2) are calculated by adding up the total amount of coding sequence that can be assigned to a SCOP protein structure domain for the sample of transcripts analysed in each row of the table. † stands for P < 0.05, †† for P < 0.01 and ††† for P < 0.001. The significant results remain significant to at least P < 0.05 when margins for calculating overlap with protein domains of 0, 5, 10, 20 or 25 nucleotides are also used.