ssSNPTarget: Genome-Wide Splice-Site Single Nucleotide Polymorphism Database

About this database


How does Single Nucleotide Polymorphism (SNP) in splice sites effect splicing process?

In humans, more than 90% of genes undergo an alternative splicing to generate different mRNAs and proteins mediated by alternative splicing sites. Recent deep sequencing study with human transcripts shows that most human genes (up to 94%) undergo alternative splicing (Wang, et al., 2008). The choice of splice sites at the exon/intron boundaries is controlled by splicing factors and regulatory sequences in transcripts (Black 2003; Black, D. L. 2003). Single Nucleotide Polymorphisms (SNPs) in splice sites can influence the splicing process. Therefore, SNPs in splice sites (ssSNPs) can be directly related to exon configuration. They can also produce or allow new splice sites, cryptic splice sites, that resemble authentic splice sites but cause incorrect sequences to be included in or excluded from mature mRNAs. Thus, SNPs involved in alternative splicing can change proteins more dramatically than non-synonymous SNPs, as they can alter protein domain or translation efficiency of the mRNA. Since ssSNPs can lead to important changes in phenotypes and disease susceptibility, it was necessary to develop a search engine that identifies ssSNPs on eukaryotic genomes and compile the results into a comprehensive database, and to systematically examine their effects related to splicing variation through alternative spliced transcripts.

We have developed a web-based database, ssSNPTarget, which enables the user to search ssSNPs and analyze their effects on transcripts and proteins. ssSNPTarget includes: 1) the number of ssSNPs that are distributed in human and mouse genes; 2) known effects of SNPs located in splice sites: junction strength change, amino acids change, and alternative splicing events such as exon skipping, 5’- or 3’-exon extension; 3) splice site conservation in eukaryotes from multiple genome alignments; and 4) related diseases information derived from OMIM, GAD, and HGMD (HGMD license; no providing this-related data). The ssSNPTarget contains 1,576 ssSNPs associated with 56,155 Ensembl transcripts and 56,722 UCSC knownGene transcripts in human and 549 ssSNPs in mouse (43,973 Ensembl transcripts and 49,410 UCSC knownGene transcripts). The user can query with several types of search terms (gene symbol, SNP rs number, transcript ID, or genomic position) and the information can be accessed through or

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