Table 1.

Primers for STSs Used in This Work

Locus name Gene location F-primer[i] R-primer[i] Size (bp)[iii] Reference
Naip-RS Naip exon 3AGCTCATGGATACCACAGGAGATGATATCCCTTGGACATAAAATGGC263(Scharf et al. 1996)
Ocln Unmapped exonATTATGCACCAAGCAATGACAATGCACATCACAATAATGAGCA169(Growney  et al. 2000)
Smn Smn exon 4intron 4TGGAAAGTTGGTGACAAGTGCGTCTGTGGAAACTTGACTTC435This work
D13Die3 Naip1 intron 7ACGACAGCGTCTTCGCTAATGGGCAGCATTGCAGACAT209(Scharf et al. 1996)
D13Die6 Smnupstream  regionCACAGTGCACAAAACCATCCAACTTCAACAAGGCCACACC126(Scharf et al. 1996)
D13Die7 Naip-ΔNaip  intergenic  regionAATTTCTGTGTGGTTGTGTGATAAACCATCCCTAGTTGCCTG125–136(Scharf et al;  1996)
D13Die24 Naip2 intron 4CGGTGAGAGGCTCAGAGTTCTGGTGTAGCCCTTTTCTGCT154(Endrizzi et al. 1999)
D13Die25 Naip5, 7, 4, 6  intron 8TGCAGAGGACTTCAAGGTTTCAACACTGACAGAATCACTGGA216–250(Endrizzi et al. 1999)
D13Die26 Naip2 intron 12TGGAGAACAATTCTGAAACACAAACAGATTTCCCCCAAAGCT164(Endrizzi et al. 1999)
D13Die27 Naip2–Naip5  intergenic  regionTGGGGTTCTCTAAGGTAACAGAGGCCTTTGTGAGAAGGAACA151(Endrizzi et al. 1999)
D13Die30 Naip exon 16ΔNaip exon  8 junctionAGACACCCCCAGTCCAAACCTTGTTGTGCTCTTGTATTGGG1479(Growney  et al. 2000)
D13Die30.2 Naip6-ΔNaip  junctionCTGTAGAGCTGAACAGAGACTGAGACTTCTTGGTGTCTGCTTCC2904This work
D13Die31 Naip intron 13  type 1ATGCTTTGAAGCCATGACCT[ii] AAAACAAAATTTGGCAAAATGTA = 385 B = 366 C = 353 D = 337This work
D13Die32 Naip intron 13  type IIATGCTTTGAAGCCATGACCT[ii] GGCCCATTAGACTTGCAAAC410This work
D13Die33 Naip intron 13  type IITGACAGCTTCTGGGACAGGGAAGATGAAGGCCCAAAACA272This work
D13Die34 Naip exon 11GAAGCTGGCAGTGGAAAGACGTATAGGCGGATGTCTCTGACC366(Growney  et al. 2000)
D13Die35 Naip5/Naip 6  intron 11AAGGACATGAGAGAAAGAAGCCACTTGCTAGTGAGAGGGAGAGC172–270This work
D13Die36 Naip3/ΔNaip  intron 14AGGACAACTGTACACAGCTTGCTCTCCTCCCATTGATGACCT215–230This work
D13Die37 Naip2 intron 8GAGAGATCACTCATGCTCATGACAAGGATGGTGATTTCCCC357This work
D13Die38180a3 SP6GTGCACAAGTACACACATGGGGAGGATTTGCTCGAATATTTGG272This work
D13Die39182m7 T7TAGCCATGTAACGGGCTACCTGTGGGGCCTTAGGTTAGTG193This work
D13Die40220n14 SP6AAGAAGAGTCGGCTCCACAATGTCTTAACGTCCGTTTGCA322This work
D13Die41434i9 T7  64m10 T7CCCTGTAAACCCAGCACCTACAAGCTTGGTGTGTTAGTGCA205This work
D13Die42404e1 T7CTTTTTTAGTTCGGGAGGGGTGTTATATACCAGAAACCCCGG202This work
D13Die4320l12 SP6TCAGAGCAGGGACATGAGCAAAGGCACCTTACATCTGAAGG291This work
D13Die44480i6 T7 477p2 SP6 201g3 SP6ACAGCATAAGGACCTTCACTCCAGGCAGAGTCTCCCACTGAA278This work
D13Die45180a11 T7AGACTACCCACACAGGGGCCCCCTGACCCAGTTGCTATA148This work
D13Die46179b7 SP6TCCTGGCATCTGCCTCTCCCCTCCCCAGCTAAGAGAAC192This work

[i] Novel STS were developed using Primer 0.5 (http://www.genome.wi.mit.edu/). Primers for all STS except D13Die30.2 were chosen to be 18–22 bp in length, with an optimal melting temperature of 60°C (range 57°C–63°C). Primers for STS D13Die30.2 were developed for long PCR. Primers were chosen to be 20–23 bp in length, with an optimal melting temperature of 64°C (range 60°C–68°C).

[ii] D13Die31 and D13Die32 share a common forward primer mapping to Naip exon 13.

[iii] PCR product sizes predicted from 129 genomic sequence.