cSNP mining from full-length enriched cDNA libraries of the Korean native pig

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Title
cSNP mining from full-length enriched cDNA libraries of the Korean native pig
Author(s)
V R Dirisala; J Kim; K Park; N Kim; K T Lee; S J Oh; J H Oh; Nam-Soon Kim; S J Um; H T Lee; K I Kim; C Park
Bibliographic Citation
Genes & Genomics, vol. 27, no. 4, pp. 329-335
Publication Year
2005
Abstract
Full-length enriched cDNA libraries from spleen and brainstem tissues of a Korean native pig were constructed in an effort to characterize its genome. The frequency of translation initiation site containing clones for spleen and brainstem libraries was 60% and 80% respectively. Unreported 5′ untranslated regions (UTRs) were identified from some of the selected clones, showing these libraries have full-length enriched characteristics. Chromatograms of 40,000 pig expressed sequence tags (ESTs) were retrieved from the GenBank trace file archive and combined with 1,205 EST sequences generated in this study. Sequences with Phred quality value higher than 30 were chosen and assembled using the CAP3 sequence assembly program. A total of 417 contigs were assembled. Among them, 65 contigs consisted of more than two Korean native pig sequences and more than two public EST sequences were selected and further analysis was performed to find single nucleotide polymorphisms (SNPs). From the contigs, SNPs between Korean native pigs and other breeds were identified. Among them, 17 putative SNPs from 10 loci were presented. The highest variations were found from the mitochondrial solute carrier family 25 member 6 gene showing 5 SNPs. Our full-length enriched Korean native pig cDNA libraries will serve as a useful resource for functional analysis of pig genome including mining of SNPs and identification of promoter regions.
Keyword
ESTsfull-length cDNA librariesKorean native pigSNPs
ISSN
1976-9571
Publisher
Springer
Type
Article
Appears in Collections:
Division of Biomedical Research > Rare Disease Research Center > 1. Journal Articles
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