Expanded alternative splice isoform profiling of the mouse Cav3.1/α1G T-type calcium channel

BMC Molecular Biology

Table 1 RT-PCR primers for Cacna1g mRNA transcript scanning assay.

Primer and Sequence (5' → 3')		Exons	Splice Isoform(s)	Amplicon(s) (bp)
1F	CGGTTGTGTGAGGACACC	5' UTR→6	*Δ5' E2*	*852*, 900
1R	GAGGCTGAGAGCAGATGAAGG
2F	AGACAGAGAATGAGGACGAGAGC	6→8	*+I6-7*&	*499*, 550,
2R	ATGTACACCAGGTACTTGAGAAGC		*Δ5' E8*	*664, 715*
3F	GTGTACGATTCCTGTCCAATGC	8→9	*Δ3' E8*	*428*, 830
3R	GTCTGAGTCAGGCATTTCATGG
4F	CCATAGCTCCTGCAAAATCTCC	9→13	*ΔE12*	*826*, 951
4R	GCGACAAGCAGGTTAAAGAGC
5F	CTCATGACTTTTGGCAACTACG	13→17	ΔE14 (e)^a	623 (-e),
5R	TCAGGCAGGTCAAAGGAACT			692 (+e)
6F	GTCAGGAGAGCCAGGATGAG	17→25	None	1282
6R	AGCCTCTTTAGTCGCTTCTCC
7F	GCTCTGATGTCCCTGTTTGTG	25→26	Δ3' E25	312 (b),
7R	GGAAGCAATTACATCGTCCAAC		(a/b)^a	333 (a)
8F	TGGAGAAAAAGAGAAGGAGTAAGG	25→28	ΔE26 (c)^a	238 (-c),
8R	ATGACGGTAAAGATGTAGTTGCAG			292 (+c)
9F	GATGGCCATGGAACATTAGG	27→31	None	371
9R	TGAAGAGAAGTCCCAGGTTCC
10F	GCTGTTGAAGATGGCTGTGG	30→33	Δ5' E31^b	561, 610
10R	AAGGGAGAAGCCTGAAGAGG
11F	ACCTGGAAGAGAGCAACAAAGAG	33→35	ΔE34 (f)^a/	256 (-f),
11R	GACAGAGCCTCCATCTCAGC		*Δ5' E34*	*361*, 400 (+f)
12F	AGACAGCTGTTTGACACCATCTC	34→38	ΔE35 (d)^a	732 (-d),
12R	GCTGCTTCTGGTCTCTTGAGG			867 (+d)
13F	AGACAGCTGTTTGACACCATCTC	34→36	ΔE35 (d)^a	215 (-d),
13R	CTGACACCAGACTTCCTCACAG			350 (+d)
14F	CTGACACCAGACTTCCTCACAG	35→38	None	656
14R	GCTGCTTCTGGTCTCTTGAGG
15F	ACCTGTTGTCAGAGGTGAGTGG	38→3' UTR	None	718
15R	CCAGTGGAGAAAGGTGATGG

Analysis of mouse Cacna1g mRNA transcripts by RT-PCR identifies 12 total alternative splicing events. The primer combinations (F, forward; R, reverse) are listed along with the scanned exons, the assayed splice isoforms, and the generated amplicon sizes. Newly-characterized splicing events and amplicon sizes are designated in bold, italic type. Orthologous mouse Cacna1g alternative splice isoforms are comparable to human CACNA1G splice sites, as previously identified by ^aMittman et al. (1999) and ^bEmerick et al. (2006).

ISSN: 1471-2199