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Korean Society for Biochemistry and Molecular Biology (생화학분자생물학회)
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Functional analysis of expressed sequence tags from the liver and brain of Korean Jindo dogs

  • Kim, Jae-Young (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration) ;
  • Park, Hye-Sun (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration) ;
  • Lim, Da-Jeong (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration) ;
  • Jang, Hong-Chul (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration) ;
  • Park, Hae-Suk (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration) ;
  • Lee, Kyung-Tai (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration) ;
  • Kim, Jong-Seok (Korean Jindo and Domestic Animals Center) ;
  • Oh, Seok-Il (Korean Jindo and Domestic Animals Center) ;
  • Kweon, Mu-Sik (Department of Genetic Engineering, Sungkyunkwan University) ;
  • Kim, Tae-Hun (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration) ;
  • Choi, Bong-Hwan (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration)
  • Received : 2010.06.23
  • Accepted : 2011.01.18
  • Published : 2011.04.30
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Abstract

We generated 16,993 expressed sequence tags (ESTs) from two libraries containing full-length cDNAs from the brain and liver of the Korean Jindo dog. An additional 365,909 ESTs from other dog breeds were identified from the NCBI dbEST database, and all ESTs were clustered into 28,514 consensus sequences using StackPack. We selected the 7,305 consensus sequences that could be assembled from at least five ESTs and estimated that 12,533 high-quality single nucleotide polymorphisms (SNPs) were present in 97,835 putative SNPs from the 7,305 consensus sequences. We identified 58 Jindo dog-specific SNPs in comparison to other breeds and predicted seven synonymous SNPs and ten non-synonymous SNPs. Using PolyPhen, a program that predicts changes in protein structure and potential effects on protein function caused by amino acid substitutions, three of the non-synonymous SNPs were predicted to result in changes in protein function for proteins expressed by three different genes (TUSC3, ITIH2, and NAT2).

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