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Table 1 Candidate genes for Cairn terrier ocular melanosis with markers, chromosomal positions, and PCR primers

From: Exclusion of eleven candidate genes for ocular melanosis in cairn terriers

Gene, Protein, Positiona Markerb[Restriction enzyme] Marker Positionc Distance (kb)d P valuese
LYST Lysosomal Trafficking Regulator chr4:7,128,220-7,294,031 Microsat 1 (TTTTC)18(TTTTC)11 1§ 345 1.00 × 10-5
Microsat 2 (GAAA)5 (GAAA)13 2§ 368
MC1R Melanocortin 1 receptor chr5:66,692,398-66,693,344 SNP 1 (BICF2P987741) 2 560 1.34 × 10-5
SNP 2 (BICF2S23213233) [SsiI] 1 24
SILV Silverchr10:3,273,996-3,279,352 Microsat 1 (GAAA)7(GAAA)17 2§ 60 1.00 × 10-5
Microsat 2 (TTTC)15(TTCC)13 1§ 226
TYRP1 Tyrosinase related protein 1 chr11:36,344,712-36,361,793 SNP 1 (BICF2S23051528) [BC1I] 1 224 2.15 × 10-5
In/Del 2 96
GPNMB Glycoprotein NMB chr14:39,877,810-39,905,589 SNP 1 (BICF2P753624) [HpyCH4V] M1° 26 1.59 × 10-4
SNP 2 (BICF2P134952) 2 1200
MITF Microphthalmia transcription factor chr20:24,853,657-24,884,775 SNP 1 (BICF2G630233682) [BspHI] 2 73 3.80 × 10-5
SNP 2 (BICF2S23248988) 1 521
TYR Tyrosinasechr21:13,797,070-13,891,317 Microsat 1 (GAAA)17(GGAA)20(GAAA)10 2§ 428 1.00 × 10-9
Microsat 2 (TTTC)10(TTTC)4(TTTC)13 1§ 70
TYRP2 (DCT) Tyrosinase related protein 2 chr22:48,219,817-48,254,000 SNP 1 (BICF2S23137809) [sequenced] M2° 33 8.47 × 10-4
SNP 2 (BICF2P452919) [RsaI] M1° 8
ASIP Agouti signaling protein chr24:26,327,360-26,366,307 SNP 1 (BICF2P1186810) [MesI] 1 340 3.57 × 10-5
In/Del 2 105
COMT Catechol-O-Methyltransferase chr26:32,426,959-32,432,523 SNP 1 (BICF2S22923369) [ApaLI] 2 82 8.20 × 10-5
Microsat 1 (TTTA)15 1§ 676
GSK3B Glycogen Synthase Kinase 3-Beta chr33:26,516,949-26,699,712 Microsat 1 (CTATT)14 M2* 146 1.00 × 10-5
Microsat 2 (TTTA)13 M2* 143
  1. Key:
  2. a. Genes are listed in chromosomal order as obtained from the May 2005 build of the canine reference genome (UCSC Genome Browser:http://genome.ucsc.edu/), with the encoded proteins provided under the gene names.
  3. b. Microsatellite-based markers are shown with the repeat type and number of perfect repeats present in the canine reference genome. Repeat blocks are separated by one to several nucleotides that do not match the perfect repeat. SNPs are listed with Broad Institute CanFam 2.0 SNP designation (http://www.broadinstitute.org/mammals/dog). One marker for ASIP is an in/del of an undefined but variable nature. The restriction enzyme used for PCR-restriction enzyme method of genotyping SNPs is shown in square brackets. Note some were genotyped by sequencing.
  4. c. The location of each marker is given with respect to coding region of each gene as seen in the 2005 canine reference genome on UCSC Genome Browser. Designations are upstream (1) or downstream (2) of the gene start site, or within the gene upstream of the exact midpoint (M1) or to the downstream of the midpoint (M2).
  5. d. Distances are given from each marker to furthest end of the gene from that marker.
  6. e. Each P value is the probability (combined probability of the two markers) of falsely excluding the true causative gene (see Additional file2: Supplementary Methods for an example of how this was calculated). The method used for each marker is indicated in the column showing marker position: § used microsatellite mutation rate, ∆ used rate of recombination between marker and coding region, o used rate of recombination from marker to nearest end of the coding region (probability of the recombination WITHIN the gene), * Clark’s method for haplotype analysis[10].