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August 17, 2017 , 17h21.

THE CANINE RH10K MAP

The RH10K map present 1299* Microsatellites [ Simple Tandem Repeat : di-, tri-, tetra- and pentanucleotides ]
included within 1054 gene-marker sequences that have been identified by screening the 10,000 marker
sequences using the sputnik program [ reference ] .

A subset of 511 microsatellites selected for their high potential of polymorphism based on their highly repeated motif number is available
and can be retrieved by using the select marker informativity query form option below.

Comparisons of the 511 microsatellite-containing marker sequences between the 1.5x genomic sequence
from TIGR (Poodle) and the 7x sequence assembly from the BROAD institute (Boxer) revealed 125 (25%) size
polymorphisms that differ by the number of tandem repeat copy number.

 


 
  • SEARCH the RH map for microsatellite-containing gene(s) :  

     

    Request : Browser response :
  • chr25
  • Displays microsatellites for all of chromosome 25
    [chr01; chr02 ; ... chr09 term MUST be used when searching for chr1 to 9]
  • PNLIP
  • Displays all of PNLIP gene marker
  • BAC
  • Displays data for all microsatellites-containing BAC clone markers present in the RH map
  • tetranucleotide
  • Displays data for all tetranucleoitde-containing gene markers
  • polymorphism
  • Displays data for all markers presenting a STR size polymorphism between Boxer seq. and Poodle seq.
  • chr
  • Displays data for all markers (1299 answers returned)
  •  

  • Or get all microsatellites data for all chromosomes as compressed raw text file with tabulation field separator: [- Get tar file -]
  •  

      ALL Microsatellites-containing markers on the RH map are characterized with :

      1- A dual location on the RH map and on the canine sequence (release 1.0)
      2- Forward and Reverse primers already designed
      3- Amplification on genomic DNA and have been successfully tested
      4- Microsatellites are located within canine gene sequences
      5- Polymorphism content estimated


    * : the 1299 set of microsatellites correspond to 1054 unique markers ( some markers having multiple repeat)
    ** : the subset of 557 microsatellites correspond to 511 unique markers