Table 1 Candidate genes for which CHORI-231 was screened and subsequently 454 sequenced
Candidate gene probe | Probe sequence source | No. of positive signals as evaluated by no. of T7 BACs hits | Phenotype(s)/condition potentially involving the candidate genes | Acc. no. | Coverage of the gene 454 sequenced | Content of the clone(s) being sequenced | SSRs in the clone(s) contig | No. of contigs per gene | No. of overlaping clones included for 454 sequencing | Size of genomic information generated (in Kb) |
|---|---|---|---|---|---|---|---|---|---|---|
KIT ligand ( KITL ) | Dog and human | 4 | Roan, Spotted, and White phenotypes (excluding Albino but including Hedlund white, associated with deafness) | JF288175 | Complete | KITL | 13 | 83 | 2 | 226 |
Microphthalmia-associated transcription factor ( MITF ) | Dog | 12 | Â | JF288172 | Complete | MITF | 23 | 46 | 2 | 205 |
KIT ( CD117 or C-KIT ) | Mink & dog | 4 | Â | JF288168 | Clone missing exon 1 | KIT | 26 | Â | 2 | 160 |
Melanophilin ( MLPH ) | Dog | 11 | Silver | JF288169 | Complete | +COL4A1 | 18 | 38 | 2 | 267 |
Lysosomal trafficking regulator ( LYST) | Dog | 4 | Alutian color (associated with Chediak-Higashi syndrome) | JF288176 | Complete | LYST | 11 | 42 | 2 | 274 |
Silver ( SILV or PMEL ) | Dog | 1 | Blue/silver phenotypes | JF288177 | Complete | Gene rich | 27 | 1 | 2 | 183 |
Tyrosinase ( TYR ) | Mink | 12 | Albino and Himalayan type | JF288171 | Complete | + GRM5, NOX4 &RPL23A | 38 | 32 | 2 | 320 |
Protein atonal homolog 1 ( Atoh-1 ) | Dog | 10 | Hedlund white, associated with deafness | JF288173 | Complete | Atoh-1 | 23 | 30 | 3 | 195 |
Melanocortin 2/3 Receptor ( MC2R&MC3R ) | Dog | 6 | Involved in a wide range of physiological functions, including pigmentation | JF288181 | Complete | + MLC5R, KPNA2 &RNMT | 5 | 13 | 3 | 97 |
Fibroblast growth factor 5(FGF5 ) | Dog | 5 | Hair length | JF288167 | Complete | + LDHR &PRDM8 | 22 | 33 | 2 | 177 |
R-spondin-2(RSPO2 ) | Dog | 7 | Hair growth and coarseness | JF288170 | Clone missing exon 5 | RSPO-2 | 30 | 24 | 1 | 153 |
Melanocyte stimulating hormone ( POMC ) | Dog & human | 7 | Various types of pigmentation | JF288182 | Missing 15 nt in exon 2 at 5' | + EFR3 & DNMT3A | 17 | 79 | 2 | 223 |
Melanocortin 1 Receptor ( MC1R ) | Mink & dog | 1 | Palomino, Pastel, Pearl & Reddish phenotypes | JF288183 | Complete | Gene rich | 2 | 96 | 1 | 124 |
Solute carrier family 24, member ( SLC24A5 ) | Dog | 5 | Differences in skin pigmentation | JF310744 | Missing 9 nt in exon 1 at 5' | CTXN2 &MYEX2 | 17 | 37 | 2 | 218 |
Agouti related protein ( AGRP ) | Dog | 5 | Agouti and Pearl phenotypes loci were found to be closely linked | JF288166 | Missing 106 nt in exon 2 at 5' | Gene rich | 10 | 20 | 1 | 193 |
Integrin-B ( ITGB1 ) | Dog | 6 | Aleutian Disease Virus (ADV) and Influenza susceptibility/resistance | JF288179 | Missing over 500 nt in several exons | ITGB1 | 15 | 70 | 1 | 105 |
Major Histocompatibility Complex, class II, DR beta 1 ( HLA-DRB1) | Dog | 3 | Â | JF288174 | Missing 160nt in one exon | RPL7A | 19 | 33 | 1 | 139 |
B-defensine ( DEFB1 ) | Dog | 4 | Â | JF288178 | Inconsistent cds | Â | 5 | 51 | 2 | 186 |
Keratin71 ( KRT71 ) | Dog | 15 | Coarseness | JF288180 | 9 exons covered | 10 members of the KRT family | 3 | 101 | 2 | 56 |
Transmembrane inner ear ( TMIE ) | Dog | None | Hedlund white associated with deafness | - | - | - | - | - | - | - |
Tyrosinase-related protein 1 ( TYRP1 ) | Dog | None | Associated with pigmentation genetics | - | - | - | - | - | - | - |