Aberrant Splicing Database

This database was constructed by Kenta Nakai. Please cite the following reference when you published the result of using this database:

Kenta Nakai and Hiroshi Sakamoto
Construction of a novel database containing aberrant splicing mutations of mammalian genes.
Gene 141: 171-7 (1994)

Compilation of aberrant splicing phenomena.

# of EX represents the total number of exons in each gene. SS indicates the 5' or 3' splice site affected by mutations. IVS represents the position number of mutated introns. When mutations were observed within exon sequences, the nearest introns are noted. Change indicates description of each mutation, for example, G1T indicates that the original nucleotide G at position +1 was changed for A; ins[+2T] indicates that the nucleotide T was inserted at position +2; del[-29:+1] indicates that nucleotides at positions from -29 to +1 were deleted; TTT-17:-15AAA indicates that the sequence TTT at positions from -17 to -15 was changed for the sequence AAA. Result(major) and Result(minor) indicate the resultant aberrant splicing pattern, for example, ES[8] indicates that the eighth exon was skipped; IR[7] indicates that the seventh intron was retained; C5[+88] indicates that a cryptic 5' splice site was activated at position +88; N3[-17] indicates that a new 3' splice site was activated at position -17. In some cases, comments are added, for example, EXP indicates that the result was not derived from direct analysis of the cDNA sequence. A typical case is that a portion of the mutated gene was analyzed using transfection into cultured cells. Similarly, induced indicates that an aberrant splicing was induced by artificial mutagenesis. Ref. indicates the reference number.
Gene # of EX SS IVS Change Result (major) Result (minor); Comments Ref.
mitochondrial acetoacetyl-coenzyme A thiolase (T2) 12 5 8 G1T ES[8] 1
3 10 A-2C ES[11] 1
medium-chain acyl-CoA dehydrogenase (MCAD) 12 ? ? ? (nothing?) ES[complex] 2
adenine phosphoribosyl-transferase (APRT) 5 5 4 ins[+2 (or3) T ] ES[4] 3
adenosine deaminase (ADA) 12 ? ? ? ES[4] half 4
? ? ? IR[7] or ES[7] 4
serum albumin 15 3 6 A-2G ?(no mRNA?) 5
5 14 del[-29:+1] & ins[-4 AAAA T] ES[14] 6
serum albumin (rat) 15 5 HI del[+5:+11] ES[H] ES[G&H or H&I] 7 8
fructose 1-phosphate aldolase (aldolase B) 9 3 8 del[-1:+6] & ins[+2G] ? 9
androgen receptor 8 5 4 G1T C5[-123] 10
apolipoprotein A-II (apo A-II) 4 5 3 G1A ? 11
apolipoprotein C-II 4 5 2 G1C ? 12
apolipoprotein E 4 3 3 A-2G C3[-53] or IR[3] 13
(argininosuccinate lyase) 16 ? ? (nothing?) (ES[7]) 5-10% usually 14
argininosuccinate synthetase 16 3 15 G-1C C3[+7] C3[+395] or IR[15] 15 16
? ? ? ES[7] 15
? ? ? ES[13] 15
placental aromatase (P-450AROM) 10 5 6 T2C C5[+88] 17, 18
branched chain alpha-keto acid dehydrogenase (E1alpha) 9? ? ? ? ES[6] 19
branched chain alpha-keto acid dehydrogenase dihydrolipoyl transacylase (E2) >11 3 4 TTT-17:-15 AAA N3[-17] 20
5 8 G-1A(1002) ES[8] ES[8:10] 21
5 8 del[-1 (or1) G] ES[8]! 22
? ? ? ES[multiple]? 23
CAD (CHO cell) ~37 3 4 G-1A IR[4], ES[5] 24
carbonic anhydrase II >7 3 5 G-1C ? (half activity?) 25
(alpha(s1)-casein (goat)) ? 3 9 (ins[-8 AAT] etc.) (ES[9&10&11]) 26
(beta-casein) ? 3 2 (int. polyY?) (ES[3]) comparison 27
catalase 13 5 4 G5A (& 6 changes) ES[4] suggestion from exp 28
CD18 (beta2 integrins) 16 3 6 C-14A N3[-12] 29
5 9 G3C ES[9]! 30
5 7 G1A IR[7] C5[+298], C5[+64] 31
cholesteryl ester transfer protein (CETP) >16 5 14 G1A ? (abolish) 32
choroideremia (CHM) gene >5 5 C ins[+3 T] C5[+35] or ES[C] 33
c-kit (mouse) ? 5 b G1A ES[B](?) ES[B&C] tissue-spc. 34
c-myb (mouse) ? 3 proviral integration new start & new EX far downstrm! 35
c-myb c-ets-1 (chicken) ? ? ? ? (fusion: exon E6 and a) 36
type I collagen pro-alpha1(I) (COL1A1)>50 5 6 G-1A ES[6] more than normal; nearly half 37 38
5 14 G5A ES[14] partial 39
type I collagen pro-alpha2(I) (COL1A2) >50 3 5 G-1C C3[+15] 40
5 6 G-1A ES[6] 41
5 6 G1A (&Tc7.3C) ES[6] ; half 42 43
5 6 T2C ES[6] 44
5 9 del[+3:+13] ES[9] 38
3 10 del[-5:+14 CTA..] ES[11] half; no cryptic 45
3 27 A-2G ES[28] major of half 46
5 33 G5A (&T661G) ES[33] 47
type III collagen (COL3A1) >43 5 16 G1A ES[16] 71% 48
5 20 G1A C5[+24] (60/156) IR[20] or ES[20] 48 49
5 25 G5T ES[25] 50
5 41 G1A ES[41] 69% 51
5 42 G1A C5[+30] 100% 48
complement C2 (C2D) 18 5 6 del[-9:19] ES[6] complete 52
complement C3 30 5 18 G1A C5[-61] 53
(complement C4 (mouse)) ? 13 (B2 insert) N3[], C5[] 54
cystic fibrosis transmembrane conductance regulator (CFTR) 27 5 4 G1T(621) ? 55
5 5 G1T(711) ? 55
3 10 G-1A ? 56
cytochrome P450(C21)B (steroid 21-hydroxylase B) 10 3 2 C-13G(656) C3[-19] 57
(cytochrome P450(C21)B (steroid 21-hydroxylase B) (bovine)) ? ? ? ? (C5[+20]) (normal??) 58
cytochrome P450IID6 (CYP2D6) (CYP2D7) 9 3 3 G-1A(1934) N3[+1]? probable (similar size of mRNA) 59
3 3 G-1A (no protein ??) 60
dihydrofolate reductase (CHO cell) 6 5 2 GG-1:1AA ES[2] 61
3 4 G-1A ES[5] 62
5 4 && G1A REVERTANT: partial C5[+4] && C3[+4] etc 62
3 4 G1T ES[5] 62
3 4 (G1A) REVERTANT 25% normal 62
5 5 G1C ES[5] 62
dystrophin >79 3 18 del[+31(~34):+82(~86)] ES[19] 63
factor VIII 26 5 4 G?A (TCGAAGTGAGT) N5[+?]? probable 64
factor XI (plasma thromboplastin) 15 5 N 14 G1A ? 65
ferrochelatase 11 3 1 C-23T ES[2] near BP 66
fibrillin ? 3 ? T26G & -64 polym.(G/A) ES[(B)] nonsense mut. 67
alpha2-globin 3 5 1 del[+2:+6 TGAGG] C5[-49] EXP 68 69
beta-globin 3 5 1 A-34G N5[-38] 25%; likely; normal:60% 70 71
5 1 T-18A N5[-16] 75% 72
5 1 G-1C ? C5[-38, -16, +13] ? total abolish 73 74
5 1 G1A C5[-38, -16, +13] 75
5 1 G1T C5[-38, -16, +13] ? 76
5 1 T2C C5[-38, +13] (not -16!) 77 78 79
5 1 T2G (prevents normal) 80
5 1 G5A ?; C5[-16] only; EXP 81 82
5 1 G5C C5[-38, -16, +13] partial; EXP 75
5 1 G5T C5[-38, -16] (partial) C5[+13] 83
5 1 T6C C5[-38, -16, +13] partial; EXP 75
3 1 G-21A(110) N3[-19] 90%; 80% abnormal 84 85 86
3 1 T-15G(116) N3[-14] >99% abnormal 86
3 1 T-3G ? 87
3 1 G-1C(130) ? 88
3 1 (G1C) ? (no effect?) (73)
3 1 (G1T) ? (no effect?) (73)
3 1 del[-22(-23):+3(2)] IR[1] 89
5 2 G1A (& G74T) C5[+47] or ES[2] EXP 90
5 2 C654T(-197) N5[+653] -> C3[+579] new exon (73nt) 91 92
5 2 T705G(-146) (& 5 changes) N5[+706] -> C3[+579!] new exon 93
5 2 T705G(-146) & A580G (-271) REVERTANT normal IVS2 EXP 94
5 2 C745G (-106) N5[+745] -> C3[+579] new exon EXP 75
3 2 T-8G ? 95
3 2 C-3A C3[-272] 87 96
3 2 A-2G C3[-272] no normal 97 98
3 2 A-2C(849) ? (normal size mRNA?) 99
delta-globin 3 5 1 G-11T(c27.1) N5[-16]? presumably; partial 100
5 1 T2C! ? 100
glucocorticoid receptor (mouse) 9? ? ? ? ES[2] rearrange?; cell 101
(glycophorin B) 5 5 (3) (G1T) (ES[3]) comparison with GPA 102
3 5 (A1T & T-10G) (C3[-10]) comparison with GPA 102
glycoprotein (GP) IIb platelet fibrinogen receptor 30 3 3 del[-3:+10] C3[+18] 103
glycosylasparaginase 9 5 8 G1T ES[8] 104
G(s alpha) protein ? ? ? ? large del.? (non GT-AG; cell) 105
(growth hormone hGH-N) 5 3 2 (A24G & CA17:18TG) (disable alt C5[+45]) compared with hGH-V BPmut? 106
(growth hormone hCS-L) 5 5 2 (G1A) (C5[+19]) compared with hGH-N 107
3 2 (T-28G & C2G) (N3[-28]) compared with hGH-N 107
growth hormone (rat) 5 3 3 G-1A N3[+1] 108
beta-N-acetylhexosaminidase A alpha chain (beta-hexosaminidase) 14 5 2 G1A ES[2] low amount 109
5 4 G5A ES[4] 3% 109
5 5 G-1A ES[5] ES[5&4] 110
5 7 (G-1A) nothing (aa change only) ? 111
5 9 del[-12:-8 TCTCC] ? unpublished (Triggs-Raine & Gravel) 112
5 12 G1C equal IR[12] or ES[12] && ES[downstrm] 113 114
beta-N-acetylhexosaminidase A beta chain (beta-hexosaminidase) 14 3 10 C8T! C3[+112] (2/14) or ES[11] (1/14) 115
3 12 G-26A N3[-24] no normal 116
3 13 dup[-16:+2] N3[-18] most 117
hypoxanthine phosphoribosyl-transferase (HPRT) 9 5 1 G5A C5[+50!] induced 118 119
5 1 G5T C5[+50!] induced 118 119
5 1 del[-2:+34] C5[+50] 119
3 1 A-2G ES[2] ES[2&3], C3[+5] 119
3 1 A-2T C3[?] ES[2] 120
3 2 C17T ES[2&3] 50% normal 50%? 119
3 2 A29T normal 90% ES[2&3] 10%? 119
3 2 G75T normal 60-70% C3[-111] 20-40%? (& ES[2&3]) 119
3 3 A-2T ES[4] 119
3 3 G-1A ES[4] 119
5 4 G1A ES[4] 119
5 5 T2G C5[+68!] 121
5 5 T2C C5[+68] 119
5 5 AA3:4GT C5[+68!] induced 118 119
5 5 G5A C5[+68!] induced 118 119
3 5 G-1A C3[+1] 119
3 5 GG-1:1AA ES[6] 119
5 6 G-1A ES[6] 119
5 6 G1A(35020) ES[6] 122 119
3 6 A-2T ES[7] 119
5 7 G1A ES[7] 119
5 7 G5A ES[7] 120
3 7 T-3A ES[8] induced 123
3 7 G-1A C3[+21],ES[8] either or both 119
3 7 G12A(544) normal 95% ES[8] 5%? induced 118 119
3 7 C19T(551) normal 70% ES[8] 30%? 119
5 8 C-13T ES[8] 90% normal 10%? 119
5 8 G5A ES[8] 120
5 8 del[-11:+3] ES[8] 119
5 8? ? (no change?) C5[+14] 121
3 8 G-16A C3[-14] 119
3 8 A-2G C3[+17] 123 124
3 8 A-2T C3[+17?] 120
? ? ? not(I1A I2D I2A I3D I3A I4D) ES[2(&3)] 119
? ? ? not(I3A I4D) ES[4] 121 119
? ? ? ES[5] 121
? ? ? ES[7] 123
? ? ? not I7A ES[8] 119
? ? ? not I8A C3[+17] 119
hypoxanthine phosphoribosyl-transferase (HPRT) (mouse) 9 ? ? ? ES[2] ES[2&3] 125
immunoglobulin kappa L chain (2) ? ? V J (many changes) ES[VJ] 126
5? 2 (no J) ? C5[+62] 127
immunoglobulin mu H chain (6?) 5 2 large ins/del at VDJ ES[VDJ] 128
immunoglobulin alpha H chain ? ? ? (complex) (complex) 129
immunoglobulin gamma2b H chain (mouse) ? 5 ch1 del[99nt] ES[CH1] 130
isovaleryl-CoA dehydrogenase (IVD) ? ? ? ? ES[2] 131
lipoprotein lipase (LPL) 10 5 2 G1A C5[-18] 1/12 C5[+43,+146, +250,+387] 132, 133
(MHC classII DC-3beta) >5 3 4? (G-1A) (ES[?]) compared with Ab 134
MHC Ia E(w17)(beta) (mouse) ? 5 1 ins[+3T] no mRNA? 135
ornithine (delta-) aminotransferase (OAT) 11 5 3 C292?G N5[?] -> C3[0.15kb] new exon (142nt) antisense Alu 136
3 4 del[-5:+4] ES[5] 137
3 5 G13A ES[6] nonsense mut. 67
3 7 G53A ES[8] nonsense mut. 67
ornithine transcarbamylase (OTC) 10 3 4 A-2T C3[+12] 138
5 7 T2C ES[7] 138
5 7 A3G! ES[7] 138
ornithine transcarbamylase (OTC) (mouse) 10 5 4 G-1A C5[+49!] partial 139
p53 11 3 3 G-1C C3[+19] or ES[4] 140
5 4 G-1A IR[4] 141
5 5 G5C C5[-46] 142
5 7 G1T IR[7] 140
(pancreatic polypeptide) 4 5 3 (A-2T & A4G) (C5[+42]) compared with rat 143
parathyroid hormone (PTH) 3 5 2 G1C ES[2] 144
peroxisomal membrane protein 70K (PMP70) ? 5 ? G1A C5[+23] 145
phenylalanine hydroxylase (PAH) >13 3 10 G-11A(546) N3[-9] 146 147
5 7 G1A ? 148
5 12 G1A ES[12] 149
muscle phosphofructokinase 24 5 13 G1T (& silent T(516)C) C5[-75] 150
porphobilinogen (PBG) deaminase 15 5 1 G-1T ? 151
5 1 G1A ? (tissue-spc.) 152
5 10 G-1T C5[-9] 153
5 12 G-1A ES[12] 154
myelin proteolipid protein (PLP) (mouse) 7 3 4 A-2G ES[5] (74 nt) 155 156
(myelin proteolipid protein (PLP) (frog)) ? 5 3 (?) (C5) (comparison; no isoform) 157
purine nucleotide phosphorylase (PNP) 6 5 2 G-1T ES[2] 158
retinoblastoma (Rb) antioncogene ? 3 20 A-2G ES[21] (35aa) 159
beta-spectrin ? 5 X A4G ES[X] 160
5 Y G3T ES[Y] 161
steel factor (mouse) ? 3 7 T-11A ES[8] 162
(sulfatide activator protein (SAP-1)) ? - - - (6 or 9 bp exons) alternative 163
thyroglobulin >14 3 3 C-3G ES[4] 164
(thyroglobulin (Africander cattle)) ? 5 9 ? (ES[9 ] (1500nt!) alternative?) 165
thyroid peroxidase (TPO; thyroperoxidase) >17 ? ? ? ES[16] ? (alternative?) 166
thyroid peroxidase (TPO; thyroperoxidase) (rat cell) ? 5 7 G1A C5[+54] 167
uroporphyrinogen decarboxylase (URO-D) 10 5 6 G1C ES[6] 168
Wilms' tumor gene (WT1) 10 5 9 G5A ? (not ES) 169
group A xeroderma pigmentosum complementing gene (XPAC) 6 3 3 G-1C C3[+2] && ES[3] 170

References


Any comments or questions should be addressed to:
nakai@imcb.osaka-u.ac.jp