Table 3

Percentile scores [41] of splicing signals of retrogene introns (after retroposition) and their corresponding regions in the parental gene (before retroposition)
Intron symbol Splice sites After retroposition Before retroposition
BS (K) PPT (K) 5′ SS (M) 3′ SS (M) BS (K) PPT (K) 5′ SS (M) 3′ SS (M)
TMEM14D GC-AG 0.14 0.06 0.02 0.02 0.14 0.04 0.01 0.11
(HSP90B2P-1) GT-AG 0.39 0.39 0 0.01 0.39 0.24 0 0
HSP90B2P-2 GT-AG 0.5 0.03 0 0.01 0.5 0.02 0 0.02
HSP90AA4P-1 GT-AG 0.21 0.03 0.04 0.12 0 0 0.04 0
HSP90AA4P-2 GT-AG 0.03 0.06 0.04 0.28 0.03 0.06 0.04 0.25
(HSP90AA4P-3) GT-AG 0.56 0.33 0 0.03 0.56 0.22 0 0.02
(HSP90AA5P-1) TT-AG 0.25 0.27 0 0.54 0 0 0 0
HSP90AA5P-2 GT-AG 0.45 0.45 0.01 0.15 0.12 0.15 0.01 0.21
AC019016.1-1 GT-AG 0.91 0.35 0.11 0.84 0.61 0.35 0.11 0.82
(AC019016.1-2) GT-AG 0.91 0.35 0.47 0.84 0.61 0.35 0 0.82

The higher the score, the stronger the splicing signal is. The scores for BS and PPT were calculated with the ‘K’ algorithms [47], and those for 5′ SS and 3′ SS were calculated with ‘M’ [48] by SROOGLE [41]. The intron symbol is in the format of the gene name plus a serial number following the hyphen. For example, ‘HSP90B2P-1’ indicates the first intron (in the direction from 5′ to 3′) in HSP90B2P. If a retrogene evolved only one intron (TMEM14D), the intron is represented by the gene name. In the column ‘Intron symbol’, parentheses indicate that the splice sites underwent base substitution.

Kang et al.

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

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