Table 1. Brain-specific alternative exons analyzed in this study.
| Gene name |
Ref. |
Source |
Exon size (nt) |
5′ splice
site/score |
3′ splice
site/score |
No. of ugcaug 0–100 |
| Ankyrin B, large insert | (46) | AC073240.2 | 6255 | AGgtattt = 74.3 | cattcacatcaaagA = 74.6 | 0 |
| FHL1B | (47) | AL078638.9 | 200 | CGgtaagt = 91.8 | tttgccatcctcagG = 93.0 | 0 |
| PMCA4 calcium pump | (48) | AL356980.4 | 178 | CAgtgagt = 76.1 | ctgattctttgcagA = 91.8 | 1 |
| SCN8 sodium channel | (49) | AF050730 | 123 | GGgtaaaa = 72.1 | ctgtttctgtgtagG = 87.3 | 1 |
| Amphiphysin II (region I) | (50) | AC012508 | 93 | AGgtgaca = 76.8 | cctccccaccccagC = 83.9 | 0 |
| N-type Ca channel | (51) | AC020707.4 | 63 | CCgtgagt = 75.0 | ttttgcatgtgcagT = 85.2 | 0 |
| NMDA-R1 exon 5 | (33,52) | Z32773 | 63 | AGgtatat = 74.3 | acattattcatcagA = 80.4 | 1 |
| CLCB | (53) | AC010297.3 | 54 | GTgtacgt = 67.9 | acctttccctcaagG = 83.5 | 0 |
| Myelin-associated glycoprotein, exon 12 | (54) | AC002132.1 | 45 | AGgtaggt = 89.2 | tccttctccaatagT = 78.6 | 1 |
| 4.1R exon 15 | (55) | AL357500.6 | 42 | AGgttagc = 84.1 | ttatggcaaaacagA = 71.8 | 0 |
| B-KSR1 | (56) | AC015688.3 | 42 | AGgtgagt = 96.7 | tcttctgtttaaagC = 80.5 | 1 |
| 4.1N | (57) | AL121895.21 | 36 | AGgtactg = 69.5 | ccacatcccactagC = 70.1 | 1 |
| 4.1B exon 15 | (58) | AC007445 | 36 | AGgtagaa = 69.2 | cttgatgctggcagT = 78.3 | 0 |
| HDlg | (59) | AC011322.3 | 36 | AGgtccat = 64.1 | gtctaatatgaaagT = 62.8 | 0 |
| KOR-3aa | (60) | U32929.1 | 34 | AGgtgagg = 92.2 | ctgtttttttccagC = 92.4 | 0 |
| Agrin exon 33a | (61) | M92657.1 | 33 | AGgtaagc = 94.2 | ctctcgtctcaaagC = 76.0 | 1 |
| MHC-B | (26) | AC011061.4 | 30 | AGgcaagt = 81.8 | tttgtaatgaacagC = 75.0 | 0 |
| NF1 exon 9a | (62) | AC004526.1 | 30 | CTgtaagt = 79.0 | aactgactacatagA = 66.1 | 1 |
| LAR tyrosine phosphatase | (63) | AL158083.3 | 27 | ATgtaagt = 87.2 | tctcccgcggtcagT = 79.1 | 0 |
| agrin exon 32a | (61) | M92657.1 | 24 | GCgtaagt = 78.7 | tctttgtttacaagC = 80.0 | 0 |
| Type II activin receptor | (64) | AC009480 | 24 | AGgtaaga = 94.4 | tttttcttcacaagC = 80.5 | 0 |
| GABAγ2 | (33,65) | AF165124.1 | 24 | AGgtataa = 68.6 | ctacaaacccaaagC = 63.2 | 1 |
| c-src, exon N | (66) | AL133293 | 18 | AGgtgtgt = 85.4 | tcgctggcccttagG = 78.2 | 1 |
| agrin exon 28 | (67) | AL390719.3 | 12 | AGgtactg = 69.5 | tcttcggaggccagA = 75.7 | 0 |
| FE65 | (68) | AF029234 | 6 | AGgtacta = 68.4 | gctgctggacccagA = 74.1 | 0 |
Except where noted, splicing studies and genomic sequences were derived from the human genes. Data for UGCAUG elements is derived from the analysis presented in Table 4 and Figure 1. The algorithm to calculate the scores of donor and acceptor sequences is based on Shapiro and Senapathy (35) and is available at http://www.genet.sickkids.on.ca/~ali/splicesitescore.html.
aSplicing studies performed with the mouse gene; gene sequences also from the mouse genomic clone due to unavailability of the human sequence.
bSplicing studies performed with the rat gene; gene sequences derived from the orthologous human genomic clone.