SINE jumping contributes to large-scale polymorphisms in the pig genomes

Table 2 Intersection of SINE RIPs with genic regions

Type of biogenic regions	No. of SINE RIPs	Percentage¹ (%)	Denisty(/Mb)	No. of gene contain SINE RIPs
LncRNA gene	4443	100.00	14.75	2504
LncRNA gene-exon	157	3.53	9.43	154
LncRNA gene-first-exon	68	1.53	10.15	67
LncRNA gene-last-exon	89	2.00	9.44	87
LncRNA gene-intron	4305	96.89	14.98	2389
LncRNA gene-intron1	2900	65.27	15.40	1846
LncRNA gene-intron2	1228	27.64	14.10	631
LncRNA gene-intron3	513	11.55	13.61	284
LncRNA gene-intron4	219	4.93	13.17	137
LncRNA gene-intron5	145	3.26	15.88	66
LncRNA gene- 5’ flank (5 kb)	1007	22.66	14.28	946
LncRNA gene-3’ flank (5 kb)	1116	25.12	15.80	1059
Protein coding gene	16,787	100.00	14.67	6154
Protein coding gene-exon	260	1.55	3.11	245
Protein coding gene-CDS	8	0.05	0.22^a	8
Protein coding gene-5’UTR	98	0.58	4.44^B	93
Protein coding gene-3’UTR	151	0.90	4.39^B	147
Protein coding gene-intron	16,635	99.09	15.41	6070
Protein coding gene-intron1	4954	29.51	15.03	2636
Protein coding gene-intron2	3937	23.45	14.78	2102
Protein coding gene-intron3	2726	16.24	14.24	1546
Protein coding gene-intron4	2156	12.84	14.86	1262
Protein coding gene-intron5	1739	10.36	15.04	1094
Protein coding gene-5’ flank (5 kb)	1589	9.47	15.96	1509
Protein coding gene-3’ flank (5 kb)	1435	8.55	14.77	1400
Intergenic	14,688	40.48	14.41	N
Random5kb (N = 20,000)	1380	N	14.07	N
Intragenic	21,596	59.52	14.57	10,347

Note 1: the values used as the denominator to calculate the percentage of SINE RIPs were 4443 for lncRNA genes, 16,787 for protein coding genes, and 36,284 for intergenic and intragenic regions. a, B: indicates p < 0.01 with Chi-square test

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