Functional analysis of expressed sequence tags from the liver and brain of Korean Jindo dogs
2011
Kim, J.Y., National Institute of Animal Science, RDA, Suwon, Republic of Korea | Park, H.S., National Institute of Animal Science, RDA, Suwon, Republic of Korea | Lim, D.J., National Institute of Animal Science, RDA, Suwon, Republic of Korea | Jang, H.C., National Institute of Animal Science, RDA, Suwon, Republic of Korea | Park, H.S., National Institute of Animal Science, RDA, Suwon, Republic of Korea | Lee, K.T., National Institute of Animal Science, RDA, Suwon, Republic of Korea | Kim, J.S., Korean Jindo and Domestic Animals Center, Jindo, Republic of Korea | Oh, S.I., Korean Jindo and Domestic Animals Center, Jindo, Republic of Korea | Kweon, M.S., Sungkyunkwan University, Suwon, Republic of Korea | Kim, T.H., National Institute of Animal Science, RDA, Suwon, Republic of Korea | Choi, B.H., National Institute of Animal Science, RDA, Suwon, Republic of Korea
We generated 16,993 expressed sequence tags (ESTs) from two libraries containing full-length cDNAs from the brain and liver of the Korean undo 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 undo 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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