UC Davis School of Veterinary Medicine Veterinary Genetics Laboratory


Pre-designed primer sets for fine-resolution mapping and DNA sequence interrogation in the dog

Sequencing Primer Guide

Gene Features

Exon annotations are from the March 2008 Ensembl gene build (Release 49).

Promoter regions are definied as the 1500 bp interval upstream of the first annotated exon.

ECR positions were obtained from ECRbase (http://ecrbase.dcode.org/) and described in:

     G.G. Loots and I. Ovcharenko
     ECRbase: Database of Evolutionary Conserved Regions, Promoters, 
     and Transcription Factor Binding Sites in Vertebrate Genomes
     Bioinformatics, 23(1):122-4 (2007)

Ultra-ECRs were previously described in:

     Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D.
     Ultraconserved Elements in the Human Genome.
     Science, 304(5675), pp. 1321-1325 (2004).

Primer3 Parameters

Product Size:300-600 bp
Primer Size (min)19
Primer Size (opt)20
Primer Size (max)22
Tm (min)59
Tm (opt)62
Tm (max)64

T3/T7 Tails

The T3 tail sequence is appended to the 5' end of the forward primer and T7 sequence is appended to the 5' end of the reverse primer. This affords sequencing independent PCR products with conventional sequencing primers for high-throughput.

Veterinary Genetics Laboratory, One Shields Ave, Davis, CA 95616-8744, Tel 530-752-2211,Email VGL