Intron retention in Cathelicidin-4 in river buffalo

Bulletin of the National Research Centre

Table 3 The potential predicted branch point (BP) and polypyrimidine tract (ppt) in buffalo CATH4 unspliced cDNA sequence

seq_id	agez	ss_dist	bp_seq	bp_scr	y_cont	ppt_off	ppt_len	ppt_scr	svm_scr
Intron 1	28	75	aggtgaggg	− 1.5456	0.41	42	20	30	− 2.5503
Intron 1	28	56	agatcagag	− 3.8131	0.49	23	20	30	− 2.1565
Intron 1	28	41	aaatgagcc	− 0.2929	0.67	8	20	30	0.2686
Intron 1	28	35	gcctgaacc	1.3833	0.70	2	20	30	1.3308
Intron 2	13	115	gggtcaatg	− 1.7699	0.50	40	12	27	− 2.5034
Intron 2	13	96	agctgaaca	0.3411	0.51	21	12	27	− 0.4227
Intron 2	13	57	gggtgaggc	− 0.4101	0.52	44	9	22	− 2.2737
Intron 2	13	44	aggttatgg	− 2.4447	0.59	31	9	22	− 2.1868
Intron 2	13	21	gtttgacct	1.4336	0.81	8	9	22	0.9218
Intron 2	13	15	ccttgagcc	0.4239	0.90	2	9	22	0.9529

seq_id - Sequence Identifier, agez AG dinucleotide exclusion zone length, ss_dist distance to 3′ splice site, bp_seq branch point sequence (nonamer; from − 5 to +3 relative to the BP adenine), bp_scr BP sequence score using a variable order Markov model, y_cont pyrimidine content between the BP adenine and the 3′ splice site, ppt_off polypyrimidine tract offset relative to the BP adenine, ppt_len polypyrimidine tract length, ppt_scr polypyrimidine tract score, svm_scr final BP score using the SVM classifier