TABLE 4

Primers used to amplify protein-coding loci

LocusReference/GenBank accessionPrimersProduct size (bp)Detection method
Proopiomelanocortin (POMC)D. Parichy (unpublished data)F-CCGAAGGAACAGCACGGGGGCCAGT156NP
R-TCTTGCCTTTCCATGGCGTCTCCCTCCT
Topoisomerase 1 (TOP1)S. Voss (unpublished data)F-CTTGCTYTGAGAGCWGGCAATGAAAAGG183NP
R-TTCTCMACAGGSACYTTGTTRTAG
Distaless-homeobox3 (DLX3)U59480F-GGCGAGGCGCACCTCTCCAACTGGTGA184RD DpnII
R-AGGCTCCCACCTTCTGAGTTGGGAAGG
Collagen 1a (COL1A1)S. Voss (unpublished data)F-CACCGAAGCCTCCCAAAACATCAC1150RD EaeI
R-GAGCCCTTCCATCTTAGTCGT
Red cone visual pigment (RCP)AF038947F-TCCCATACGCAGAAAACCA327SSCP
R-TACCGCAAGGAAATGGGAAGCAGT
Ultraviolet cone visual pigment (UVCP)AF050653F-GAAGCGAGGTCTGCAAGGAGGATG301RD RsaI
R-TACCGCAAGGAAATGGGAAGCAGT
Rod-specific transducin (GNAT1)AF050653F-CCCATGCTGCGGAAGAGA486RD DraI
R-TTAGAGGGCGAAAAAGTGTCATC
Cone-specific transducin (GNAT2)AF050654F-ATGCACAACCCCGATACTACCAAC432ASA
R-AGTCGGGCCCTTTAAATGAATACG
Fork head protein g1b (FOXG1B)U43547F-GATGGACTGCTAATCTTTTGAGACCC269RD MnlI
R-AACAAGTGGGGCAAACAACCAACCAGC
Chondroitin sulfate proteoglycan 2 (CSPG2)Parichy et al. (1999)F-GACAGCAGTGGAGACAGATGAAGAAC708RD RsaI
R-TCTACAGCGACGGGAGATGACG
Homeo box a4 (HOXA4)D. Gardiner (unpublished data)F-CTGCAGCACTGGCAGGTCCTGCTG1190LV
R-TGGCGAGCGCATCTTGGTGTTGG
Homeo box a9 (HOXA9)U20941F-AGGCACTACGGCATCAAGCC430SSCP
R-ACTCCTTAGGCCGGTCCTTGT
Homeo box b13 (HOXB13)AF298184F-GTCTCCTTTTGCTTGATTTCCG376RD NsiI
R-TCACCAAAATCACAGAACACCTGC
Homeo box c10 (HOXC10)AF298185F-TGCCCATACAGCGAGCTTACAGACAT413RD PstI
R-GCACACGAGACCCACAACAACAAAA
Homeo box d8 (HOXD8)AF031246F-CGGACTGTAAATCGTCCAGTGGTCAC738RD HpaII
R-GCTGGGAACTTGTCTTTGTTGTTCTC
Homeo box d11 (HOXD11)AF031481F-ACATCATCTTCGGGACTGTAACAAGG699RD Sau96I
R-AACCAGGTCCCCTTAGTTCTATTCAGG
Glyceraldehyde-3-phosphate dehydrogenase (GAPD)J-X. Ma (unpublished data)F-AACGCCTCCTGCACCACCAACT336RD DpnII
R-CTCTGCCATCGCGCCACATTT
Kit ligand (KITLG)AF119044F-ACCTCCCAAGTGACTACAGTATATC263SSCP
R-ACCTCCCACTCAAACAGCTTC
Platelet-derived growth factor receptor a (PDGFRA)D. M. Parichy (unpublished data)F-CGGGTCATTGAGTCCATCAGCC1000RD/SSCP RsaI
R-CAGTGGGTTTTAACATTTTCACAG
Rhodopsin (RHO)U36574F-CCAAGAGTTCTGCCATCTACAATCCAG1200ASA
R-CGCAGGAGAAACCTGGCTGGAAGACAC
Wingless-type MMTV integration site family, member 1 (WNT1)AF001958F-CAGCGCCAAATCACACCTCA400HincII
R-TCCATAAACGCTGCCAAAATAAAG
Sodium bicarbonate cotransporter (SLC4A4)AF001958F-TCCGCTTGCAGCAGTCTCCTTGCTCTC223SSCP
R-TAACGGCCTGATTGATGACCAGCGAAG
Thyroid hormone receptor α (THRA)Voss et al. (2000)F-TCCTGACAGTGAGACGCTG150SSCP
R-TAGGGCCACTTCGGTGTCATC
Thyroid hormone receptor β (THRB)Voss et al. (2000)F-CCCGGAAAGCAAAACCTT136RD XcmI
R-TATCATCCAGGTTAAATGAC
Aldehyde oxidase (AOX1)K. Mason (unpublished data)F-TACAAGGACACGAATAGCGAGACA205RD DdeI
R-CCACTGAGAACTTTAGGGGTATGA
v-kit (KIT)K. Mason (unpublished data)F-TCCGTGTGGGAATCCAGTCACT950LV
R-AGATGGCATATCTGGGACATATTC
  • Polymorphisms were revealed by restriction digestion (RD), length variation (LV), single-strand conformation polymorphism (SSCP), or allele-specific amplification (ASA). No polymorphism (NP) was detected for two loci.