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Bhak, Jong
KOrean GenomIcs Center(KOGIC)
Research Interests
  • Geromics, genomics, bioinformatics, protein Engineering, OMICS

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ssSNPTarget: Genome-wide Splice-site Single Nucleotide Polymorphism Database

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Title
ssSNPTarget: Genome-wide Splice-site Single Nucleotide Polymorphism Database
Other Titles
ssSNPTarget: Genome-Wide Splice-Site Single Nucleotide Polymorphism Database
Author
Yang, Jin OkKim, Woo-YeonBhak, Jong Hwa
Keywords
Disease; SNP; Splice site; ssSNPTarget; Variation
Issue Date
2009-12
Publisher
WILEY-BLACKWELL
Citation
HUMAN MUTATION, v.30, no.12, pp.E1010 - E1020
Abstract
Deep sequencing has shown that over 90% of human genes undergo alternative splicing. The splicing process requires exon-intron boundary recognition. SNPs located in the boundaries (splice sites) influence exon configuration. Also, splice site SNPs (ssSNPs) alter translation efficiency of the mRNA and lead to important changes in disease susceptibility. We developed the ssSNPTarget database to provide ssSNPs on human and mouse genes. It includes: 1) ssSNP distribution information in human and mouse genes; 2) effects of SNPs in splice sites: junction strength change, protein domain change, and alternative splicing events (exon skipping, 5'- or 3'-exon extension); 3) splice site conservation in eukaryotes; and 4) associated disease information derived from OMIM, GAD, and HGMD. ssSNPTarget contains 1,576 human ssSNPs associated with 1,193 genes and 538 mouse ssSNPs associated with 281 genes. Users can query ssSNPTarget with several types of search terms (gene symbol, SNP rs number, transcript ID, or genomic position), and the information can be accessed at http://variome.kobic.re.kr/ssSNPTarget/ or http://ssSNPTarget.org. (C) 2009 Wiley-Liss, Inc
URI
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DOI
10.1002/humu.21128
ISSN
1059-7794
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BME_Journal Papers
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