Table 3.

Positions of positively selected codons in the U2af1-rs1 retrogene lineage

Position in alignment1	Amino acid in retrogene lineage	Amino acid in parent lineage	P value2 in parent lineage	Position in retrogene protein U2af1-rs1 (M. musculus)	Position in parent protein U2af1-rs2 (M. musculus)
38	M	L	0.659	33	38
46	A	L	0.57	41	46
63	L	E	0.996	55	62
154	E	G	0.576	142	154
206	V	I	0.745	192	206
313	V	M	0.678	300	313
355	P	D	0.997	342	355
361	S	F	0.501	348	361
	Y(mouse)
384	H(rat)	R	0.875	371	384
385	H	R	0.965	372	385
388	S	P	0.528	373	388
4803	E	S	0.993	415	475
485	G	R	0.593	420	480
491	H	R	0.942	426	486
493	T	R	0.802	428	488

¹The position differs from alignment to protein as the alignment file contains sequence gaps.

²Our confidence in each of these sites being positively selected is calculated using the posterior probability and summarized in the P values shown. P values vary from 0.00 (no evidence for belonging in the positively selected category) to 1.00 (100% confidence of belonging in the positively selected category).

³Dark gray area refers to residues deemed to be false positives due to poor alignment of the U2af1-rs sequences.