Table 1.
Primers for STSs Used in This Work
| Locus name | Gene location | F-primer | R-primer | Size (bp) | Reference |
| Naip-RS | Naip exon 3 | AGCTCATGGATACCACAGGAGATG | ATATCCCTTGGACATAAAATGGC | 263 | (Scharf et al. 1996) |
| Ocln | Unmapped exon | ATTATGCACCAAGCAATGACA | ATGCACATCACAATAATGAGCA | 169 | (Growney et al. 2000) |
| Smn | Smn exon 4intron 4 | TGGAAAGTTGGTGACAAGTG | CGTCTGTGGAAACTTGACTTC | 435 | This work |
| D13Die3 | Naip1 intron 7 | ACGACAGCGTCTTCGCTAAT | GGGCAGCATTGCAGACAT | 209 | (Scharf et al. 1996) |
| D13Die6 | Smnupstream region | CACAGTGCACAAAACCATCC | AACTTCAACAAGGCCACACC | 126 | (Scharf et al. 1996) |
| D13Die7 | Naip-ΔNaip intergenic region | AATTTCTGTGTGGTTGTGTG | ATAAACCATCCCTAGTTGCCTG | 125–136 | (Scharf et al; 1996) |
| D13Die24 | Naip2 intron 4 | CGGTGAGAGGCTCAGAGTTC | TGGTGTAGCCCTTTTCTGCT | 154 | (Endrizzi et al. 1999) |
| D13Die25 | Naip5, 7, 4, 6 intron 8 | TGCAGAGGACTTCAAGGTTT | CAACACTGACAGAATCACTGGA | 216–250 | (Endrizzi et al. 1999) |
| D13Die26 | Naip2 intron 12 | TGGAGAACAATTCTGAAACACA | AACAGATTTCCCCCAAAGCT | 164 | (Endrizzi et al. 1999) |
| D13Die27 | Naip2–Naip5 intergenic region | TGGGGTTCTCTAAGGTAACAGA | GGCCTTTGTGAGAAGGAACA | 151 | (Endrizzi et al. 1999) |
| D13Die30 | Naip exon 16ΔNaip exon 8 junction | AGACACCCCCAGTCCAAAC | CTTGTTGTGCTCTTGTATTGGG | 1479 | (Growney et al. 2000) |
| D13Die30.2 | Naip6-ΔNaip junction | CTGTAGAGCTGAACAGAGACTGA | GACTTCTTGGTGTCTGCTTCC | 2904 | This work |
| D13Die31 | Naip intron 13 type 1 | ATGCTTTGAAGCCATGACCT | AAAACAAAATTTGGCAAAATGT | A = 385 B = 366 C = 353 D = 337 | This work |
| D13Die32 | Naip intron 13 type II | ATGCTTTGAAGCCATGACCT | GGCCCATTAGACTTGCAAAC | 410 | This work |
| D13Die33 | Naip intron 13 type II | TGACAGCTTCTGGGACAGG | GAAGATGAAGGCCCAAAACA | 272 | This work |
| D13Die34 | Naip exon 11 | GAAGCTGGCAGTGGAAAGAC | GTATAGGCGGATGTCTCTGACC | 366 | (Growney et al. 2000) |
| D13Die35 | Naip5/Naip 6 intron 11 | AAGGACATGAGAGAAAGAAGCC | ACTTGCTAGTGAGAGGGAGAGC | 172–270 | This work |
| D13Die36 | Naip3/ΔNaip intron 14 | AGGACAACTGTACACAGCTTGC | TCTCCTCCCATTGATGACCT | 215–230 | This work |
| D13Die37 | Naip2 intron 8 | GAGAGATCACTCATGCTCATGA | CAAGGATGGTGATTTCCCC | 357 | This work |
| D13Die38 | 180a3 SP6 | GTGCACAAGTACACACATGGG | GAGGATTTGCTCGAATATTTGG | 272 | This work |
| D13Die39 | 182m7 T7 | TAGCCATGTAACGGGCTACC | TGTGGGGCCTTAGGTTAGTG | 193 | This work |
| D13Die40 | 220n14 SP6 | AAGAAGAGTCGGCTCCACAA | TGTCTTAACGTCCGTTTGCA | 322 | This work |
| D13Die41 | 434i9 T7 64m10 T7 | CCCTGTAAACCCAGCACCTA | CAAGCTTGGTGTGTTAGTGCA | 205 | This work |
| D13Die42 | 404e1 T7 | CTTTTTTAGTTCGGGAGGGG | TGTTATATACCAGAAACCCCGG | 202 | This work |
| D13Die43 | 20l12 SP6 | TCAGAGCAGGGACATGAGC | AAAGGCACCTTACATCTGAAGG | 291 | This work |
| D13Die44 | 480i6 T7 477p2 SP6 201g3 SP6 | ACAGCATAAGGACCTTCACTCC | AGGCAGAGTCTCCCACTGAA | 278 | This work |
| D13Die45 | 180a11 T7 | AGACTACCCACACAGGGGC | CCCCTGACCCAGTTGCTATA | 148 | This work |
| D13Die46 | 179b7 SP6 | TCCTGGCATCTGCCTCTC | CCCTCCCCAGCTAAGAGAAC | 192 | This work |
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↵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).
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↵D13Die31 and D13Die32 share a common forward primer mapping to Naip exon 13.
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↵PCR product sizes predicted from 129 genomic sequence.
