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 a54541–594NoNo1575gtcatccttatttcttccagGCAGAATACTTATTCAGGgtacgtaca
exon b40595–634NoNo2145tctaatttattatttcgcagCCACGCAACTTTAAAATGgtatgtgct
exon c182635–816NoNoN.A.tttttttttcttttttgcagGATGTGAAA3′UTR after stop
Pdcl2
exon a121(1–121)NoYes596tttttgggggatgggggtagGATCCAAACAGGCCATGGgtagtgcg
exon b91(122–212)− both endsYes5024acctaagatttctgttttagTTAAACCATAATATATAGgtacagcac
exon c144(213–356)YesYes1117aatatttttgttttacttagAGAAAAGCGTAGATCAAGgtaattatc
exon d209(357–565)YesYes5201actgtgtattctctctttagTGTCCCAATAGCTAGAAGgtaatggtg
exon e473(566–1038)NoYesN.A.taggtttttatctattgtagAACTTGAAT3′UTR after stop
Clock
exon 1a(70)(1–70)NoNo(1152)5′UTRGCGCTCCCGgtgagtgcg
exon 1b1811–181NoNo8655′UTRTCAGGCACGgtgaggacg
exon 279182–260NoNo29386tctggtgttttctattgcagTGAAAGAAAACCAGCAAGgtaatttcc
exon 385261–435−3′ endNo7069cttttgtttttttaaaacagAGTTCTGATGTGAAAGAGgtaaaggcg
exon 490436–495Yes−5′ end383atgttttcttttctcacaagGAGAAGTACTGTTGACAGgtatgtttt
exon 560436–495+5′ endYes417ctctgtcttttctcttgtagAGATGACAGAGCAAAAAGgtagttagc
exon 6149496–644+3′ endYes3025taatttctttttcttcatagAGTATCTAGAACATAAAGgtaaagtgc
exon 792645–736YesYes8211acgtgtcaatctgtttacagAGACCACTGATGTTAGAGgtatgttca
exon 890737–826NoNo5903accattatgtttaatttcagGCTCTTGATCATTTACCAgtaagtatg
exon 9121827–947YesNo2820tttttttttttatttttcagTCTGATCTTACTTAAAATgtaagtagg
exon 10114948–1061NoNo107ctttttatcacttattccagCAAAAAATCTAACCAGTGgtaagttaa
exon 111191062–1180NoYes2034atgtctccttgctgttttagTATCAACTTTTCATCAAGgtatgcttc
exon 12831181–1263NoYes190acttgttaatttgtttgtagGAAATGTGTAGATCACAGgtaacatta
exon 131071264–1370YesYes764attattactgtataatttagGGCACCACCACGAGCACTgtaagtagc
exon 141481371–1518NoYes923ttttatttttttatttttagTAATGCAATTGTAGTAAGgtaataact
exon 15761519–1594YesYes3709ttggttctttccatttgtagTTATTGCAGGCTGACAAAgtatgtttc
exon 161421595–1736YesYes638tgttcctcttatctccttagAGCCAAGATACCCTTCCTgtgagtgcc
exon 171011737–1837NoYes426tctctgttgactgtctttagCCACACCGAAGCAGTCAGgtacgcctt
exon 18901838–1927NoYes4217atcttttattttgcttctagTCCATAAACATGTCACAGgtatttttg
exon 191531928–2080−5′ endYes1045ctttccatgtgctgcttcagTTTCAGTTTGGGCTACAGgtaacttat
exon 202062081–2481−3′ endYes601tgtgatctttgttttcaaagATGTTTTTGTCAACTCAGgtaattgac
exon 212062276–2481−5′ endYes2105ttccatacgatcttttctagCAGAGTCAAACAGATAAGgtagttgtc
exon 222952483–2776+3′ endYes9847tattttgttttctctcacagATTTTCTCATTCTTACAGgtaaccccc
exon 2347022777–7478NoYesN.A.atcatcctttttgttttagACATCTAGG3′UTR after stop
Tpardl
exon 14022–405−5′ endYes149885′UTRCGGGCCGAGgtgagagcc
exon 2226406–631YesYes4536atttggtttttgattttcagAAAGGATTGGCTTGTCGGgtaagggca
exon 3176632–807YesYes453tgttggcatttccttacagtTTTTGTTTGGATGAAGAAgtaagttgt
exon 4180808–987NoYes2989gtatttttcatttgtttcagTTCCAACGAGCTAGAGAGgtgagtgta
exon 5106988–1093NoYes606caagctacatctgcttccagGACCCTTATTCCGAACTGgtaaggtct
exon 67351094–1828No−3′ endN.A.cttctctctctcttttccagTGACAATCA3′ UTR after stop
Srd5a2l
exon a(278)(1–278)−5′ end−5′ end7139N.D.CCCCAAGAGgtaacgtcg
exon b143(279–421)YesYes1363aactcttcctccttctgcagGTACTTTTCAGTTCCAAGgtaatttgg
exon c36(422–457)YesYes519cttgcttttcctttggcagCCCTGGAGAGGATGCCAGgtaagtgct
exon d198(458–655)−5′ endYes3578ccttctctcctgcattgcagCGGCTGAGCACAAGAATGgtaagtggc
exon e135(656–710)NoYes858cagaactcctattcccgtagTGTATGTTCACAAAAAAGgtgaggtga
exon f936(791–1726)Yes−3′ endN.A.cgatcgcccttccgtttcagGTGTGGTCA3′ UTR after stop

[i] 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.