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Get SNP and or Design primers for PCR-RFLP of Cow SNP

This site was designed to be used in two related ways:

  1. Obtain annotated SNP for any region of the cow genome
  2. Design primers for any SNP with the option of selecting SNP cut by a given restriction exnzyme
The expected method of use is to test different parameters until you have a suitable number of SNP. Then there will be the option to download them and design primers for them

All publically available bovine SNP were downloaded from Ensembl using their Perl API

If the number of SNP returned is less than 10000 then you will be able to design primers against each of them

Select TB type
Gene NameEnsembl Gene IDGene description
eg: ARBK2_BOVINENSBTAG00000000005Beta-adrenergic receptor
Exon ID
Use % sign as wildcard eg 'ENSBTAG%' will find all SNP within gene regions and 'ENSBTAE%' will find all SNP with Exons
Co-ordinates of region of interest in Bta4.0
Chromosome (integer)StartEnd
Eg; 180000000100000000
Positions cut by restriction enzyme(s)
SNP with these consequences
Minimum interval between adjacent SNP

Values in the form are sticky click to clear them and start again

SNP for public SNP from Ensembl;
Count 0

SNP were selected for: public SNP from Ensembl; Enzyme restriction site: ;

If the Number of loci looks about right then get the sequences for primer design

Health Warning

All SNP are relative to Hereford reference genome. Most SNP were descovered by low coverage Sanger sequencing and have not been validated. All data is provisional and subject to change.