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ssSNPTarget: genome-wide splice-site single nucleotide polymorphism database†

  1. Jin Ok Yang,
  2. Woo-Yeon Kim,
  3. Jong Bhak*

Article first published online: 16 SEP 2009

DOI: 10.1002/humu.21128

Issue

Human Mutation

Human Mutation

Volume 30, Issue 12, pages E1010–E1020, December 2009

Additional Information

How to Cite

Ok Yang, J., Kim, W.-Y. and Bhak, J. (2009), ssSNPTarget: genome-wide splice-site single nucleotide polymorphism database. Hum. Mutat., 30: E1010–E1020. doi: 10.1002/humu.21128

Author Information

  1. Korean BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong-gu, Daejeon 305-806, Korea

*111 Gwahangno, Yuseong-gu, Daejeon 305-806, Korea

  1. †

    Communicated by Alastair F. Brown.

Publication History

  1. Issue published online: 22 NOV 2009
  2. Article first published online: 16 SEP 2009
  3. Manuscript Accepted: 26 AUG 2009
  4. Manuscript Received: 23 MAR 2009

Funded by

  • Korean Ministry of Education, Science & Technology (MEST). Grant Number: No.BDC0900812

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Keywords:

  • SNP;
  • splice site;
  • ssSNPTarget;
  • variation;
  • disease

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. © 2009 Wiley-Liss, Inc.

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