F344/Stm, LE/Stm BAC Browser

Outline

F344/Stm and LE/Stm BAC (Bacterial Artificial Chromosome) end sequence was obtained by the genome information upgrading program of NBRP.
BAC clones can be ordered from RIKEN BRC.

As part of our rat genome analysis project we constructed a BAC library of F344/Stm and LE/Stm strains in FY2005, and in FY2006, we completed BAC end sequencing of F344/Stm. We completed BAC end sequencing of LE/Stm in FY2008. Kyoto University was collaborating with the National Institute of Genetics in this project.

To F344 & LE Rat BAC browser

Rat strains

Search for rat strainsF344/Stm
One parental strain of the LEXF/FXLE rat recombinant inbred strains. Shisa et al. developed the F344/Stm strain from the F344/DuCrj (Charles River Japan, Inc.) at the Saitama Cancer Center Research Institute in Japan. Docile, good breeding performance, medium size. Albino (c) The polymorphic rate between BN/SsNHsd is 83%, LE/Stm is 73% (using 357 SSLP markers).
Rat Phenome database LE/Stm
One parental strain of the LEXF/FXLE rat recombinant inbred strains. Shisa et al. developed the LE/Stm from a closed colony of Long-Evans rats (University of Chicago) at the Saitama Cancer Center Research Institute in Japan. Small size, bleeding tendency. Fawn-hooded, ruby eye （a,B,C,h,r）. The polymorphic rate between BN/SsNHsd is 85%, F344/Stm is 73% (using 357 SSLP markers).

Contents

   Number
F344/Stm  BAC-End  174,739
 Clones  105,962
LE/Stm  BAC-End  240,942
 Clones  150,968

  • Gene structure
  • Gene structure on the genome sequence provided by NCBI Map Viewer
  • Gene structure on the genome sequence provided by Ensembl
  • End sequence mapping results
  • F344/Stm and LE/Stm BAC library mapping to the rat genome sequence
  • SNP rates derived from the end sequence
  • SNP rates calculated from F344/Stm and LE/Stm BAC library mapping
  • Repeat sequence
  • Repeat sequence information provided by UCSC Genome Browser
  • G+C content and CpG islands
  • G+C content and CpG islands of the rat genome sequence

    • Usage of BAC Browser
      Usage of the F344 & LE Rat BAC browser (pdf file)

    Place to obtain
      The DNA Bank, RIKEN BioResource Research Center,
      3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
      Fax: (+81)-29-836-9120
      e-mail: dnabank@brc.riken.jp

    About Genome analysis
    Address information:
     Institute of Laboratory Animals, Graduate School of Medicine,
     Kyoto University
     Yoshidakonoe-cho Sakyo-ku, Kyoto 606-8501, Japan
     Tel : (075)753-9318, Fax : (075)753-4409
     E-mail : nbrprat@anim.med.kyoto-u.ac.jp