Table 1.
Gene Exon/Intron Characteristics
| Exon: | Intron: | ||||||
| Gene | Length (bp) | cDNA position (bp) | Detected by GRAIL? | Detected by GenScan | Length (bp) | Splice acceptor | Splice donor |
| Nmu | |||||||
| exon a | 54 | 541–594 | No | No | 1575 | gtcatccttatttcttccagGCAGAATAC | TTATTCAGGgtacgtaca |
| exon b | 40 | 595–634 | No | No | 2145 | tctaatttattatttcgcagCCACGCAAC | TTTAAAATGgtatgtgct |
| exon c | 182 | 635–816 | No | No | N.A. | tttttttttcttttttgcagGATGTGAAA | 3′UTR after stop |
| Pdcl2 | |||||||
| exon a | 121 | (1–121) | No | Yes | 596 | tttttgggggatgggggtagGATCCAAAC | AGGCCATGGgtagtgcg |
| exon b | 91 | (122–212) | − both ends | Yes | 5024 | acctaagatttctgttttagTTAAACCAT | AATATATAGgtacagcac |
| exon c | 144 | (213–356) | Yes | Yes | 1117 | aatatttttgttttacttagAGAAAAGCG | TAGATCAAGgtaattatc |
| exon d | 209 | (357–565) | Yes | Yes | 5201 | actgtgtattctctctttagTGTCCCAAT | AGCTAGAAGgtaatggtg |
| exon e | 473 | (566–1038) | No | Yes | N.A. | taggtttttatctattgtagAACTTGAAT | 3′UTR after stop |
| Clock | |||||||
| exon 1a | (70) | (1–70) | No | No | (1152) | 5′UTR | GCGCTCCCGgtgagtgcg |
| exon 1b | 181 | 1–181 | No | No | 865 | 5′UTR | TCAGGCACGgtgaggacg |
| exon 2 | 79 | 182–260 | No | No | 29386 | tctggtgttttctattgcagTGAAAGAAA | ACCAGCAAGgtaatttcc |
| exon 3 | 85 | 261–435 | −3′ end | No | 7069 | cttttgtttttttaaaacagAGTTCTGAT | GTGAAAGAGgtaaaggcg |
| exon 4 | 90 | 436–495 | Yes | −5′ end | 383 | atgttttcttttctcacaagGAGAAGTAC | TGTTGACAGgtatgtttt |
| exon 5 | 60 | 436–495 | +5′ end | Yes | 417 | ctctgtcttttctcttgtagAGATGACAG | AGCAAAAAGgtagttagc |
| exon 6 | 149 | 496–644 | +3′ end | Yes | 3025 | taatttctttttcttcatagAGTATCTAG | AACATAAAGgtaaagtgc |
| exon 7 | 92 | 645–736 | Yes | Yes | 8211 | acgtgtcaatctgtttacagAGACCACTG | ATGTTAGAGgtatgttca |
| exon 8 | 90 | 737–826 | No | No | 5903 | accattatgtttaatttcagGCTCTTGAT | CATTTACCAgtaagtatg |
| exon 9 | 121 | 827–947 | Yes | No | 2820 | tttttttttttatttttcagTCTGATCTT | ACTTAAAATgtaagtagg |
| exon 10 | 114 | 948–1061 | No | No | 107 | ctttttatcacttattccagCAAAAAATC | TAACCAGTGgtaagttaa |
| exon 11 | 119 | 1062–1180 | No | Yes | 2034 | atgtctccttgctgttttagTATCAACTT | TTCATCAAGgtatgcttc |
| exon 12 | 83 | 1181–1263 | No | Yes | 190 | acttgttaatttgtttgtagGAAATGTGT | AGATCACAGgtaacatta |
| exon 13 | 107 | 1264–1370 | Yes | Yes | 764 | attattactgtataatttagGGCACCACC | ACGAGCACTgtaagtagc |
| exon 14 | 148 | 1371–1518 | No | Yes | 923 | ttttatttttttatttttagTAATGCAAT | TGTAGTAAGgtaataact |
| exon 15 | 76 | 1519–1594 | Yes | Yes | 3709 | ttggttctttccatttgtagTTATTGCAG | GCTGACAAAgtatgtttc |
| exon 16 | 142 | 1595–1736 | Yes | Yes | 638 | tgttcctcttatctccttagAGCCAAGAT | ACCCTTCCTgtgagtgcc |
| exon 17 | 101 | 1737–1837 | No | Yes | 426 | tctctgttgactgtctttagCCACACCGA | AGCAGTCAGgtacgcctt |
| exon 18 | 90 | 1838–1927 | No | Yes | 4217 | atcttttattttgcttctagTCCATAAAC | ATGTCACAGgtatttttg |
| exon 19 | 153 | 1928–2080 | −5′ end | Yes | 1045 | ctttccatgtgctgcttcagTTTCAGTTT | GGGCTACAGgtaacttat |
| exon 20 | 206 | 2081–2481 | −3′ end | Yes | 601 | tgtgatctttgttttcaaagATGTTTTTG | TCAACTCAGgtaattgac |
| exon 21 | 206 | 2276–2481 | −5′ end | Yes | 2105 | ttccatacgatcttttctagCAGAGTCAA | ACAGATAAGgtagttgtc |
| exon 22 | 295 | 2483–2776 | +3′ end | Yes | 9847 | tattttgttttctctcacagATTTTCTCA | TTCTTACAGgtaaccccc |
| exon 23 | 4702 | 2777–7478 | No | Yes | N.A. | atcatcctttttgttttagACATCTAGG | 3′UTR after stop |
| Tpardl | |||||||
| exon 1 | 402 | 2–405 | −5′ end | Yes | 14988 | 5′UTR | CGGGCCGAGgtgagagcc |
| exon 2 | 226 | 406–631 | Yes | Yes | 4536 | atttggtttttgattttcagAAAGGATTG | GCTTGTCGGgtaagggca |
| exon 3 | 176 | 632–807 | Yes | Yes | 453 | tgttggcatttccttacagtTTTTGTTTG | GATGAAGAAgtaagttgt |
| exon 4 | 180 | 808–987 | No | Yes | 2989 | gtatttttcatttgtttcagTTCCAACGA | GCTAGAGAGgtgagtgta |
| exon 5 | 106 | 988–1093 | No | Yes | 606 | caagctacatctgcttccagGACCCTTAT | TCCGAACTGgtaaggtct |
| exon 6 | 735 | 1094–1828 | No | −3′ end | N.A. | cttctctctctcttttccagTGACAATCA | 3′ UTR after stop |
| Srd5a2l | |||||||
| exon a | (278) | (1–278) | −5′ end | −5′ end | 7139 | N.D. | CCCCAAGAGgtaacgtcg |
| exon b | 143 | (279–421) | Yes | Yes | 1363 | aactcttcctccttctgcagGTACTTTTC | AGTTCCAAGgtaatttgg |
| exon c | 36 | (422–457) | Yes | Yes | 519 | cttgcttttcctttggcagCCCTGGAGA | GGATGCCAGgtaagtgct |
| exon d | 198 | (458–655) | −5′ end | Yes | 3578 | ccttctctcctgcattgcagCGGCTGAGC | ACAAGAATGgtaagtggc |
| exon e | 135 | (656–710) | No | Yes | 858 | cagaactcctattcccgtagTGTATGTTC | ACAAAAAAGgtgaggtga |
| exon f | 936 | (791–1726) | Yes | −3′ end | N.A. | cgatcgcccttccgtttcagGTGTGGTCA | 3′ UTR after stop |
-
Clock exon 1a does not appear in the Genbank cDNA entry (accession no. AF000998), hence the parentheses around its values.Nmu, Pdcl2 and Srd5a2l exons are assigned by letters rather than numbers, as the 5′ ends of these genes have not been experimentally mapped; exon position values are in parentheses for the same reason. Intron sequence is noted in lowercase, exon sequence in uppercase. Under columns for Detected by GRAIL and Detected by GenScan, “−” and “+” denote that the predicted exon was underestimated or overestimated, respectively, at the specified end. N.A., not applicable. N.D., not determined.
