Evolutionary dynamics of U12-type spliceosomal introns

Table 2 Conservation of Drosophila melanogaster U12-type introns in humans.

	Annotation symbol	Termini	Gene symbol (name) in fruitflies and/or in humans	Intron number	Total number of introns	Fruitflies	Humans
1	CG6323	GT-AG	Tsp97E (Tetraspanin 97E); TSPAN13 (tetraspanin 13)	2	4	U12	U12
2	CG8408	GT-AG	TMEM41B (transmembrane protein 41B)	3	3	U12	U12
3	CG17912	GT-AG	ZNF207 (Zinc finger protein 207)	1	3	U12	U12
4	CG32705	GT-AG	ZDHHC8 (zinc finger, DHHC-type containing 8)	4	11	U12	U12
5	CG33108	GT-AG	C19orf54	2	3	U12	U12
6	CG4894	GT-AG	Ca-α1D (calcium-channel protein); CACNA1D (calcium channel)	3	31	U12	U12
7	CG7892	GT-AG	nmo (nemo); NLK (nemo-like kinase)	6	10	U12	U12
8	CG15735	GT-AG	LSM12	1	4	U12	U12
9	CG3294	GT-AG	ZRSR2 (zinc finger, RNA-binding motif and serine/arginine rich 2); U2AF (small subunit related protein)	3	4	Twintron	U2 only
10	CG16941	GC-AG	SF3A1 (splicing factor 3a, subunit 1, 120 kDa)	1	6	U12	absent
11	CG11839	AT-AC	CCDC16 (coiled-coil domain containing 16); ZNF830 (zinc finger protein 830)	1	1	U12	absent
12	CG11328	AT-AC	Nhe3; SLC9A7 (solute carrier family 9)	5	12	U12	U12
13	CG18177	AT-AC	FLJ14154 hypothetical protein	4	4	U12	U12
14	CG7736	AT-AC	Syx6 (Syntaxin 6); STX6 (syntaxin 6)	1	2	U12	U12
15	CG17228	AT-AC	pros (prospero); PROX1 (prospero homeobox 1)	2	4	Twintron	U12
16	CG15081	AT-AC	l(2)03709 (lethal (2) 03709); PHB2 (prohibitin 2)	3	5	U12	U12
17	CG3427	AT-AC	Epac; RAPGEF3 (Rap guanine nucleotide exchange factor 3)	11	16	U12	U12
18	CG11984	AT-AC	KCMF1 (potassium channel modulatory factor 1)	3	6	U12	U12
19	CG15589	AT-AC	Ca-alphaT-RC (Voltage-dependent T-type calcium channel)	1	23	U12	U12

Depending on the terminal dinucleotides, or termini, U12-type introns are divided into two major subtypes. Of the nineteen fruit fly U12-type introns, ten are GT-AG subtype, including one GC-AG and eight AT-AC. Sixteen have U12-type ortholog in humans. These sixteen human orthologous U12-type introns are of the same subtype as their fruitfly ortholog. The absence of the U12-type intron in the human SF3A1 gene is likely an intron deletion after insects diverged. The CCDC16 gene is intronless in mammals and fish but not in chickens and frogs. Thus, the absence of the U12-type intron in the human CCDC16 gene is presumably due to a retroposition of the gene that occurred in early mammals. The third intron of the fruit fly CG3294 (URP) gene has two pairs of splice sites that form two alternative spliced introns, one of the U12-type and one of the U2-type. The pair of U12-type splice sites is absent in non-diptera species.

ISSN: 2730-7182