Table 1 List of ion channel genes exhibiting alternative splicing in patients with mTLE
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 epilepsy†| Alternatively spliced region | Splice array p value |
|---|---|---|---|---|---|
Calcium channels | Â | Â | Â | Â | Â |
   CACNA1A | NM_023035 | U79668 | ES: 26% ↓ variant/reference ratio | EXON 48 | 0.002 |
|  | NM_023035 | CQ723237 | ASA: 24% ↓ reference/total ratio | EXON 23 | 0.003 |
|  | NM_023035 | BE972738 | NE: 36% ↓ variant/total ratio | 3' downstream | <0.001 |
   CACNA1C | NM_000719 | CQ722696 | ASD: 94% ↓ variant/reference ratio | EXON 2 | <0.001 |
|  | NM_000719 | CQ722691 | ASD: 23% ↓ variant/reference ratio | EXON 24 | 0.017 |
   CACNA1H | NM_021098 | CQ730788 | ASA: 25% ↓ variant/reference ratio | EXON 34 | <0.001 |
   CACNA1I | NM_001003406 | AX068892 | NE: 36% ↓ variant/reference ratio | INTRON 1 | 0.012 |
|  | NM_001003406 | AX068892 | NE: 23% ↓ variant/reference ratio | INTRONS 20/21 | 0.009 |
   CACNA2D1 | NM_000722 | BG211441 | ES: 28% ↑ reference/total ratio | EXON 8 | 0.003 |
   CACNB1 | NM_000723 | NM_199247 | NE: 28% ↑ variant/reference ratio | INTRON 6 | <0.001 |
|  | NM_000723 | BP316738 | NE: 28% ↑ variant/reference ratio | INTRON 6 | 0.002 |
   CACNB2 | NM_201596 | AF465485 | ES: 20% ↓ variant/reference ratio | EXON 7 | 0.020 |
   CACNB3 | NM_000725 | AK122911 | NEs: 28% ↓ variant/total ratio | 5' upstream | <0.001 |
   CACNB4 | NM_000726 | AY054985 | NE: 31% ↑ variant/reference ratio | INTRON 2 | 0.012 |
   CACNG4 | NM_014405 | AW134993 | PIED: 45% ↑ reference/total ratio | EXON 4 | 0.009 |
|  | NM_014405 | AI675178 | PIED: 41% ↓ variant/reference ratio | EXON 4 | 0.003 |
Chloride channels | Â | Â | Â | Â | Â |
   CLCN2 | NM_004366 | BC021578 | ES: 38% ↓ reference/total ratio | EXON 13 | <0.001 |
   CLCN3 | NM_001829 | CQ732096 | ASA: 22% ↓ variant/reference ratio | EXON 2 | 0.004 |
|  | NM_001829 | CQ736554 | NE: 32% ↑ reference/total ratio | INTRON 12 | 0.012 |
   CLCN6 | NM_001286 | BC050457 | ASA: 16% ↓ variant/reference ratio | EXON 20 | 0.016 |
   CLCN7 | NM_001287 | AK096963 | IR: 36% ↓ variant/reference ratio | INTRON 18 | <0.001 |
|  | NM_001287 | BQ920088 | ASA: 21% ↓ variant/reference ratio | EXON 12 | 0.004 |
   CLIC5 | NM_016929 | BC039380 | ASA: 20% ↓ reference/total ratio | EXON 5 | 0.013 |
Sodium channels | Â | Â | Â | Â | Â |
   SCN2A2 | NM_021007 | BC029489 | ES: 23% ↑ reference/total ratio | EXON 1 | 0.006 |
   SCN9A | NM_002977 | BG108767 | ASD: 26% ↓ variant/reference ratio | EXON 16 | 0.003 |
   SCNN1A | NM_001038 | BF033087 | PIED: 21% ↓ variant/reference ratio | EXON 13 | <0.001 |
   SCNN1D | NM_002978 | AX230571 | NE: 52% ↑ variant/total ratio | INTRON 2 | 0.012 |
|  | NM_002978 | AK127357 | NE: 77% ↑ variant/total ratio | 5' upstream | 0.002 |
Potassium channels | Â | Â | Â | Â | Â |
   KCNAB2 | NM_003636 | BG720519 | ES: 35% ↑ variant/reference ratio | EXON 1 | 0.014 |
|  | NM_003636 | BM823724 | NEs: 19% ↓ variant/total ratio | 5' upstream | 0.015 |
|  | NM_003636 | CA495339 | IR: 24% ↓ reference/total ratio | INTRON 11 | 0.020 |
   KCNC3 | NM_004977 | AK127492 | ASD: 27% ↓ variant/reference ratio | EXON 5 | 0.020 |
   KCNH5 | NM_172376 | NM_139318 | NE: 24% ↑ variant/total ratio | 3' downstream | <0.001 |
   KCNJ1 | NM_153767 | NM_000220 | NE: 27% ↓ variant/reference ratio | INTRON 3 | <0.001 |
   KCNJ6 | NM_002240 | CQ738104 | NEs: 24% ↓ variant/total ratio | INTRON 2 | 0.017 |
   KCNJ15 | NM_170736 | NM_002243 | NE: 108% ↑ variant/total ratio | 5' upstream | <0.001 |
|  | NM_170736 | NM_170737 | NE: 2.5x ↑ reference/total ratio | INTRON 2 | <0.001 |
|  | NM_170736 | CQ732921 | NEs: 42% ↓ variant/reference ratio | INTRON 2 | 0.005 |
|  | NM_170736 | BM544058 | NE: 98% ↑ variant/total ratio | 5' upstream | <0.001 |
|  | NM_170736 | BF105170 | NE: 78% ↑ variant/total ratio | 5' upstream | 0.003 |
|  | NM_170736 | BI518753 | NE: 2.5x ↑ reference/total ratio | INTRON 2 | <0.001 |
   KCNK1 | NM_002245 | AV733795 | PIED: 34% ↓ variant/reference ratio | EXON 2 | 0.010 |
|  | NM_002245 | BG699040 | NE: 45% ↓ variant/total ratio | INTRON 1 | 0.009 |
|  | NM_002245 | BF212472 | NEs: 23% ↓ variant/total ratio | INTRON 1 | 0.017 |
|  | NM_002245 | BU661246 | NEs: 48% ↓ variant/total ratio | INTRON 1 | <0.001 |
   KCNK2 | NM_014217 | BU956092 | ES: 62% ↑ reference/total ratio | EXON 4 | 0.008 |
   KCNK4 | NM_016611 | NM_033310 | NE: 102% ↑ variant/total ratio | 5' upstream | 0.005 |
   KCNK12 | NM_022055 | AX302031 | NEs: 20% ↓ variant/total ratio | INTRON 1 | 0.014 |
   KCNMA1 | NM_002247 | CQ870200 | NE: 24% ↓ variant/reference ratio | EXON 20 | 0.006 |
|  | NM_002247 | CQ870204 | PIED: 32% ↓ variant/reference ratio | 3' downstream | 0.020 |
|  | NM_002247 | BG185868 | NE: 28% ↓ variant/reference ratio | EXON 9 | 0.014 |
   KCNN2 | NM_021614 | NM_170775 | NE: 26% ↓ variant/total ratio | INTRON 3 | 0.002 |
   KCNQ2 | NM_004518 | AY358189 | NE: 28% ↓ variant/reference ratio | INTRON 7 | 0.018 |
|  | NM_004518 | BG772772 | NEs: 23% ↓ variant/reference ratio | INTRON 7 | 0.018 |
   HCN3 | NM_020897 | CQ715247 | EsS: 15% ↓ variant/reference ratio | EXONS 3-4 | 0.012 |
   SLICK | NM_198503 | CQ728754 | EsS: 28% ↓ reference/total ratio | EXONS 22-25 | 0.019 |
|  | NM_198503 | CQ728754 | ES: 57% ↑ variant/reference ratio | EXON 15 | 0.003 |
GABA receptors | Â | Â | Â | Â | Â |
   GABRA2 | NM_000807 | CD014113 | ES: 26% ↑ reference/total ratio | EXON 8 | <0.001 |
|  | NM_000807 | CD014116 | EsS: 29% ↑ reference/total ratio | EXONS 4-9 | <0.001 |
|  | NM_000807 | CD014112 | EsS: 35% ↑ reference/total ratio | EXON 4 | <0.001 |
|  | NM_000807 | CD014107 | EsS: 31% ↑ reference/total ratio | EXONS 7/8 | <0.001 |
|  | NM_000807 | CD014110 | EsS: 36% ↑ reference/total ratio | EXONS 6-8 | <0.001 |
|  | NM_000807 | CD014109 | EsS: 40% ↑ reference/total ratio | EXONS 6/7 | <0.001 |
   GABRA3 | NM_000808 | AX897950 | ES: 17% ↓ reference/total ratio | EXON 7 | 0.007 |
   GABRG2 | NM_198904 | NM_198903 | ASA: 22% ↑ reference/total ratio | EXON 4 | 0.005 |
   GABRR1 | NM_002042 | CB959800 | NEs: 17% ↓ variant/total ratio | 5' upstream | 0.007 |
Ionotropic glutamate receptors | Â | Â | Â | Â | Â |
   GRIA1 | NM_000827 | A46050 | NE: 34% ↓ variant/reference ratio | INTRON 14 | 0.012 |
|  | NM_000827 | M64752 | NE: 39% ↓ variant/reference ratio | INTRON 14 | 0.008 |
   GRIA2 | NM_000826 | BC010574 | NE: 44% ↓ variant/reference ratio | INTRON 13 | 0.007 |
|  | NM_000826 | AX147452 | NE: 61% ↓ variant/reference ratio | INTRON 13/EXON14 | 0.005 |
|  | NM_000826 | AV748963 | NE: 44% ↓ variant/reference ratio | EXON 14 | 0.015 |
   GRIA3 | NM_007325 | NM_181894 | NEs: 19% ↑ variant/reference ratio | INTRON 2 | 0.006 |
   GRIK2 | NM_021956 | CQ715784 | ASD: 65% ↓ reference/total ratio | EXON 10 | <0.001 |
   GRIK4 | NM_014619 | CQ869986 | NEs: 29% ↓ variant/total ratio | 5' upstream | 0.006 |
|  | NM_014619 | CQ715345 | NE: 31% ↓ variant/total ratio | INTRON 4 | 0.015 |
|  | NM_014619 | CQ715345 | ES: 23% ↑ reference/total | EXON 7 | 0.005 |
   GRIK5 | NM_002088 | CQ719647 | ASD: 24% ↓ reference/total ratio | EXON 16 | 0.008 |
|  | NM_002088 | AX665460 | ASD: 23% ↓ variant/reference ratio | EXON 18 | 0.004 |
|  | NM_002088 | CN420154 | EsS: 27% ↓ variant/reference | EXONS 12-14 | 0.020 |
FXYD domain ion transport regulators | Â | Â | Â | Â | Â |
   FXYD1 | NM_021902 | BQ181273 | IR: 51% ↓ variant/reference ratio | INTRON 7 | <0.001 |
   FXYD6 | NM_022003 | AX430335 | NE: 31% ↓ variant/total ratio | 5' upstream | <0.001 |
|  | NM_022003 | AX892598 | NE: 35% ↓ variant/total ratio | 5' upstream | <0.001 |
|  | NM_022003 | BC018652 | NEs: 38% ↓ variant/reference ratio | EXON 1/INTRON 1 | <0.001 |
|  | NM_022003 | AL832811 | NE: 33% ↓ variant/reference ratio | INTRON 1 | <0.001 |
|  | NM_022003 | AW270073 | ES: 34% ↓ variant/reference ratio | EXON 9 | <0.001 |
|  | NM_022003 | BI823239 | NE: 48% ↓ variant/reference ratio | INTRON 1 | <0.001 |
|  | NM_022003 | BF527041 | NE: 36% ↓ variant/reference ratio | INTRON 1 | 0.002 |
|  | NM_022003 | BP372334 | NE: 45% ↓ variant/reference ratio | INTRON 1 | <0.001 |
|  | NM_022003 | BE263758 | NE: 37% ↓ variant/reference ratio | EXON 2 | <0.001 |
|  | NM_022003 | BX488702 | ASA: 50% ↓ variant/reference ratio | INTRON 2 | <0.001 |
|  | NM_022003 | BI598749 | NE: 40% ↓ variant/reference ratio | INTRON 1 | 0.006 |
   FXYD7 | NM_022006 | CQ722304 | ES: 21% ↓ variant/reference ratio | EXON 4 | 0.007 |
Transient receptor potential cation channels | Â | Â | Â | Â | Â |
   TRPA1 | NM_007332 | BF570694 | ASD: 37% ↓ reference/total ratio | EXON 25 | <0.001 |
   TRPC4 | NM_016179 | AF421362 | ES: 24% ↓ reference/total ratio | EXON 3 | 0.004 |
   TRPM1 | NM_002420 | AX480882 | ASD:43% ↓ variant/reference ratio | EXON 17 | <0.001 |
   TRPM7 | NM_017672 | CQ728707 | EsS: 35% ↑ variant/reference ratio | EXONS 7-11 | <0.001 |
   TRPV1 | NM_080704 | NM_080705 | NE: 31% ↑ variant/total ratio | INTRON 1 | 0.007 |
|  | NM_080704 | AX686983 | ES: 35% ↑ variant/reference ratio | EXON 8 | 0.005 |
   TRPV2 | NM_016113 | BQ645005 | ASD: 25% ↓ variant/reference ratio | EXON 15 | 0.005 |
Glycine receptors | Â | Â | Â | Â | Â |
   GLRB | NM_000824 | CD013911 | ES: 31% ↑ variant/reference ratio | EXON 9 | 0.004 |
Inositol triphosphate receptors | Â | Â | Â | Â | Â |
   ITPR1 | NM_002223 | CQ727353 | EsS: 22% ↑ variant/reference ratio | EXONS 52-54 | 0.020 |
Purinergic receptors | Â | Â | Â | Â | Â |
   P2RX1 | NM_002558 | BM469621 | NE: 57% ↑ variant/total ratio | INTRON 3 | <0.001 |
|  | NM_002558 | BP372168 | ASD: 17% ↑ reference/total ratio | EXON 1 | 0.002 |
   P2RXL1 | NM_005446 | BC064805 | ASD: 24% ↑ variant/reference ratio | EXON 1 | 0.013 |
Cyclic nucleotide gated channels | Â | Â | Â | Â | Â |
   CNGA1 | NM_000087 | CN366905 | NEs: 20% ↓ variant/total ratio | 5' upstream | 0.011 |
   CNGB3 | NM_019098 | AI150392 | ES: 19% ↓ variant/total ratio | EXON 18 | 0.016 |
Amiloride-sensitive cation channel | Â | Â | Â | Â | Â |
   ACCN2 | NM_020039 | BC028722 | NE: 19% ↓ variant/reference | INTRON 3 | 0.017 |
|  | NM_020039 | AX683970 | NE: 23% ↓ variant/reference | INTRON 3 | 0.019 |
Two pore segment channels | Â | Â | Â | Â | Â |
   TPCN1 | NM_017901 | CQ729206 | ASA: 27% ↑ variant/reference ratio | EXON 10 | <0.001 |
   TPCN2 | NM_139075 | AW178475 | NE: 87% ↑ variant/total ratio | INTRON 9 | <0.001 |
Mucolipin | Â | Â | Â | Â | Â |
   MCOLN1 | NM_020533 | BQ723075 | ASD: 17% ↓ variant/reference ratio | EXON 2 | <0.001 |
|  | NM_020533 | CA489568 | ASD: 69% ↑ variant/reference ratio | EXON 7 | 0.011 |
Ryanodine receptors | Â | Â | Â | Â | Â |
   RYR3 | NM_001036 | CQ730808 | ES: 28% ↑ variant/total ratio | EXON 84 | 0.017 |
Miscellaneous other ion channels/interacting proteins | Â | Â | Â | Â | Â |
   C6orf69 | NM_173562 | BC023525 | EsS: 33% ↑ reference/total ratio | EXONS 3-5 | 0.003 |
   KCNIP2 (potassium channel interacting protein) | NM_014591 | NM_173191 | ASA: 37% ↑ variant/reference ratio | EXON 3 | 0.004 |
|  | NM_014591 | NM_173193 | EsS: 19% ↑ variant/reference ratio | EXONS 2-3 | 0.018 |
|  | NM_014591 | NM_173197 | ES: 9% ↓ reference/total ratio | EXON 7 | 0.015 |
   MLC1 (megalencephalic leuko-encephalopathy with subcortical cysts) | NM_015166 | BX451200 | ASD: 31% ↓ variant/reference ratio | EXON 8 | 0.009 |
   PKD1L2 (polycystic kidney disease 1-like) | NM_052892 | CQ741519 | ES: 82% ↑ variant/reference ratio | EXON 7 | 0.006 |
   PKD2L2 (polycystic kidney disease 2like) | NM_014386 | AF182034 | NEs: 38% ↑ variant/total ratio | INTRON 13/3' downstream | 0.005 |
   SH3KBP1 (SH3KBP1 binding protein) | NM_138392 | BX366064 | ASD: 26% ↓ variant/reference ratio | EXON 10 | 0.002 |
|  | NM_138392 | AL523485 | ASD: 26% ↑ reference/total ratio | EXON 13 | 0.005 |
   VGCNL1 (voltage-gated channel) | NM_052867 | BM556576 | NE: 31% ↓ variant/total ratio | INTRON 7 | <0.001 |
|  | NM_052867 | AK094669 | EsS: 28% ↓ reference/total ratio | INTRON 12 | 0.019 |