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Table 3 List of ion channel genes exhibiting alternative splicing in patients with Alzheimer's Disease

From: Alternative ion channel splicing in mesial temporal lobe epilepsy and 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

  1. *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.