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. 2012 Jan;40(Database issue):D1055-9.
doi: 10.1093/nar/gkr1171. Epub 2011 Dec 1.

SpliceDisease Database: Linking RNA Splicing and Disease

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Free PMC article

SpliceDisease Database: Linking RNA Splicing and Disease

Juan Wang et al. Nucleic Acids Res. .
Free PMC article

Abstract

RNA splicing is an important aspect of gene regulation in many organisms. Splicing of RNA is regulated by complicated mechanisms involving numerous RNA-binding proteins and the intricate network of interactions among them. Mutations in cis-acting splicing elements or its regulatory proteins have been shown to be involved in human diseases. Defects in pre-mRNA splicing process have emerged as a common disease-causing mechanism. Therefore, a database integrating RNA splicing and disease associations would be helpful for understanding not only the RNA splicing but also its contribution to disease. In SpliceDisease database, we manually curated 2337 splicing mutation disease entries involving 303 genes and 370 diseases, which have been supported experimentally in 898 publications. The SpliceDisease database provides information including the change of the nucleotide in the sequence, the location of the mutation on the gene, the reference Pubmed ID and detailed description for the relationship among gene mutations, splicing defects and diseases. We standardized the names of the diseases and genes and provided links for these genes to NCBI and UCSC genome browser for further annotation and genomic sequences. For the location of the mutation, we give direct links of the entry to the respective position/region in the genome browser. The users can freely browse, search and download the data in SpliceDisease at http://cmbi.bjmu.edu.cn/sdisease.

Figures

Figure 1.
Figure 1.
Distribution of mutation type and distribution of point mutation type in the SpliceDisease database. (A) Splicing mutation type: point, point mutation; ins, insertion mutation; del, deletion mutation; other, other types. (B) Axes of the histogram represent the proportions of different nucleotide substitutions in whole point mutations.
Figure 2.
Figure 2.
SpliceDisease results page. (A) Once a user runs a search, there comes the result summary page that includes nine items. (B) The direct link for entry to the respective position of mutation. The sequence of exon shows in upper case and intron shows in lower case. And one FASTA record per region (exon, intron) is used in the sequence file. The inton/exon of the location of mutation is highlighted in yellow color and specific nucleotide is marked in red color.

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