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Fig. 3 | Genetics Selection Evolution

Fig. 3

From: Origin, evolution, and tissue-specific functions of the porcine repetitive element 1

Fig. 3

The splicing model of PRE1. a Neighbour-joining tree based on consensus sequences of 15 PRE1 lineages, several affected PRE1, and consensus sequences of CRHS from Sus scrofa, Bos taurus and Capra hircus. The PRE1 shown in black font belong to class I, and those in red belong to class II. b Principal component analysis based on the Needleman–Wunsch genetic distance from PRE1 to the consensus sequences of 15 PRE1 lineages. Red and black dot sets represent class I and class II PRE1, respectively. The small image at the bottom left shows the specular mapping (x = 1) of class I PRE1. c IGV window of the promoter region of the TECA3 gene. The green box shows the PRE1 region in Sus scrofa. The six resequencing reads data downloaded from public databases, Sus barbatus (ERR173177) [16], Sus cebifrons (ERR173209) [16], Sus celebensis (ERR173210) [16], Sus verrucosus (ERR173211) [16], Phacochoerus africanus (ERR173203) [16], Sus scrofa (11-146,206) [36]. d Number of PRE1 that overlap with known exons. e Splicing signals are enriched in direct repeats. The x axis represents the base position on the consensus sequence. The font colour indicates the type of splicing signal, the physical locations of the splicing signals, and the transcript names. Numbers 3 and 5 represent the 3′ splicing signal and 5′ splicing signal in PRE1, respectively, and T represents the 3′ splicing signal in the reverse complementary sequence of PRE1. f Splicing model for the PRE1 body and degenerate sequences

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