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Table 3
List of ion channel genes exhibiting alternative splicing in patients with Alzheimer's Disease
Genes by gene class	GenBank accession number (reference transcript*)	GenBank accession number (variant transcript*)	Alternative splicing event: change of mRNA transcript composition in AD^†	Alternatively spliced region	Splice array p value

Calcium channels
CACNA1A	NM_023035	CQ723237	ASA: 23% ↓ reference/total ratio	EXON 23	0.007
	NM_023035	U79668	ASD: 36% ↓ variant/reference ratio	EXON 48	0.022
CACNA1C	NM_000719	CQ722691	ASD: 19% ↑ reference/total ratio	EXON 27	0.033
CACNA1G	NM_018896	NM_198376	PIED: 14% ↓ variant/reference ratio	EXON 36	<0.001
CACNA1I	NM_001003406	AX068892	ASD: 29% ↓ variant/total ratio	EXON 16	0.049
CACNA2D1	NM_000722	BG210356	NE: 55% ↑ reference/total ratio	INTRON 3	0.021

Chloride channels
CLCN2	NM_004366	BC021578	ES: 14% ↓ reference/total ratio	EXON 13	0.041
	NM_004366	BF002578	NE: 38% ↓ variant/total ratio	3' downstream	0.042
CLCN6	NM_001286	NM_021736	ES: 15% ↓ reference/total ratio	EXON 12	0.022
CLCNKA	NM_004070	CQ733615	ASD: 27% ↓ variant/reference	EXON 15	0.039

Sodium channels
SCN2A2	NM_021007	CQ730725	ES: 16% ↓ variant/total ratio	EXON 11	0.023
SCN7A	NM_002976	BC062699	ES: 39% ↓ reference/total ratio	EXON 1	0.027
SCNN1D	NM_002978	AX230571	ASA: 17% ↓ variant/reference ratio	EXON 1	0.045

Potassium channels
KCNAB1	NM_172160	NM_172159	NE: 21% ↓ variant/reference	INITRON 1	0.028
KCNAB2	NM_003636	AI933060	NE: 51% ↓ variant/total ratio	3' downstream	0.017
	NM_003636	AI090677	NEs: 105% ↑ variant/reference ratio	INTRON 7	0.039
	NM_003636	BM925038	PIED: 65% ↑ variant/reference ratio	EXON 16	0.045
KCNF1	NM_002236	AI566537	PIED: 51% ↑ variant/reference ratio	EXON 1	0.045
KCNG1	NM_172318	BF569197	ASD: 23% ↓ variant/reference ratio	EXON 1	0.005
	NM_172318	AI968477	ASD: 28% ↑ reference/total ratio	EXON 1	0.031
KCNH5	NM_172376	NM_139318	ES: 14% ↑ reference/total ratio	EXON 11	0.033
KCNMB2	NM_181361	NM_005832	NEs: 25% ↓ variant/total ratio	INTRON 1	0.030
KCNN1	NM_002248	BX106650	ASD: 47% ↑ reference/total ratio	EXON 6	0.004
	NM_002248	BM718136	ASD: 39% ↑ reference/total ratio	EXON 6	0.015
KCNQ2	NM_004518	NM_172107	NE: 70% ↑ variant/reference ratio	INTRON 10	0.038
	NM_004518	BG772772	NEs: 55% ↑ variant/reference ratio	EXONS 7-9	0.016
KCNQ3	NM_004519	CQ725469	PIED: 47% ↓ reference/total ratio	EXON 15	0.036

GABA receptors
GABRA3	NM_000808	AX897950	ES: 48% ↑ reference/total ratio	EXON 7	0.037
GABRA5	NM_000810	AL035782	EsS: 65% ↑ variant/reference ratio	EXONS 2/3	0.030
GABRA6	NM_000811	AK090735	IR: 72% ↓ variant/total ratio	INTRON 6	0.037

Ionotropic glutamate receptors
GRIK2	NM_021956	CQ715784	ASD: 57% ↓ reference/total ratio	EXON 10	0.007
GRIK4	NM_014619	CQ734018	NEs: 35% ↓ variant/total ratio	INTRON 1	0.006
GRIK5	NM_002088	AJ249209	NE: 52% ↑ variant/reference ratio	INTRON 18	0.037

Transient receptor potential cation channels
TRPM7	NM_017672	CQ728707	ES: 6% ↓ reference/total ratio	EXON 4	0.048

FXYD domain ion transport regulators
FXYD5	NM_014164	BU164524	NE: 36% ↓ variant/reference ratio	INTRON 1	0.030

Inositol triphosphate receptors
ITPR1	NM_002222	CQ719499	ES: 15% ↓ reference/total ratio	EXON 23	0.030

Two pore segment channels
TPCN1	NM_017901	BG899733	NE: 49% ↑ variant/reference ratio	INTRON 1	0.016

Mucolipin
MCOLN1	NM_020533	CA489568	ASD: 95% ↑ variant/reference ratio	EXON 7	0.026
	NM_020533	AJ293659	IR: 33% ↑ variant/total ratio	INTRON 5	0.032

Ryanodine receptors
RYR1	NM_000540	CQ717972	PIED: 30% ↑ reference/total ratio	EXON 91	0.011
	NM_000540	CQ730824	ES: 35% ↑ variant/reference ratio	EXON 35	0.042

Miscellaneous other ion channels/interacting proteins
TM4SF11 (plasmolipin)	NM_015993	R16034	NE: 21% ↑ variant/reference ratio	INTRON 1	0.016
GMRP-1 (potassium channel tetramerization protein)	NM_032320	BG722430	NE: 26% ↑ variant/reference ratio	INTRON 1	0.031

*Reference transcript refers to traditionally splicing gene product, while the variant refers to the alternatively spliced mRNA transcript. ^†Change was quantified using splice array samples (control versus AD temporal cortex, n = 10/group). The ratio selected to quantify event was determined based on best available probe choice (see Materials and methods section). ASA, alternative splice acceptor site; ASD, alternative splice donor site; ES, exon skipped; EsS, exons skipped; IR, intron retention; NE, novel exon; NEs, novel exons; PIED, partial internal exon deletion.
Heinzen et al. Genome Biology 2007 8:R32 doi:10.1186/gb-2007-8-3-r32

Table 3