Table 4

Substitution rates between the intronic and exonic regions of retrogenes and their corresponding regions of parental genes
Retrogene Intronic region Exonic region
Ka Ks Ka/Ks P-value Length Ka Ks Ka/Ks P-value Length
TMEM14Dc 0.062 0.058 1.074 0.936 105 0.006 0.014 0.440 0.570 237
RPS3AP5a NA NA NA NA NA 0.017 0.014 1.210 0.172 780
XXyac-R12DG2.2b 0.024 0.029 0.830 0.892 129 0.008 0.012 0.643 0.631 813
HSP90B2Pac,* 0.823 0.597 1.379 0.526 144 0.045 0.067 0.678 0.091 2163
HSP90AA4Pc,* 0.104 0.277 0.374 0.000 744 0.055 0.085 0.656 0.000 1374
HSP90AA5Pc,* 0.087 0.215 0.406 0.001 672 0.088 0.221 0.400 0.082 897
CSMD3b 0.313 0.575 0.544 0.051 291 0.186 0.282 0.659 0.310 225
WBP2NLb 0.033 0.088 0.373 0.192 177 0.385 0.377 1.021 0.919 684
AC019016.1c 0.083 0.082 1.010 0.978 636 0.081 0.175 0.466 0.084 273

Ka represents the non-synonymous substitution rate and Ks indicates the synonymous substitution rate. The P-value was calculated with the likelihood ratio test and the null hypothesis was Ka/Ks =1. NA: not available (the corresponding parental sequence of the new intron in retrogene RPS3AP5 did not exist, because the intron was created by insertion of an external sequence). ‘a’, The retrogene gained introns by insertion of an external sequence. ‘b’, The retrogene gained introns after transcription in the opposite orientation compared to the parent. ‘c’, The retrogene gained introns by intronization. ‘*’, Evidence at the protein level for transcription of the retrogene was obtained.

Kang et al.

Kang et al. BMC Evolutionary Biology 2012 12:128   doi:10.1186/1471-2148-12-128

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