ssSNPTarget

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




Supp. Table S1. Public resources for annotation in ssSNPTarget.

Category

Used Public Resources

Gene Mapping

- NCBI gene databases (downloaded on 2008-06)
- HUGO Gene Nomenclature Database (HGNC) (Eyre, et al., 2006)
- Mouse Gene Information (MGI) (Shaw, 2004)

Protein Domain

a representative sequence-based domain database
- Pfam (Bateman, et al., 2004)
- HMMER program

Disease Information

- Online Mendelian Inheritance in Man (OMIM) (Hamosh, et al., 2005)
- Gene Association Database (GAD, download on 2008-06) (Becker, et al., 2004)

Multiple Genome Alignments

- UCSC Table Track
-- 28 vertebrate genomes for human, hg18
-- 30 vertebrate genomes for mouse, mm9



Supp. Table S2. Nomenclature and schematic representation of ssSNP effects trigger mRNA truncation. To get affected transcripts by ssSNP, we checked chromosomal positions of splice sites at loci of the dotted lines against the transcripts’ positions.


Supp. Figure S1. Alternation strength of splice site including ssSNP. "splice.site.strength" means the strength scores of exon junction sites in reference genome (reference SNP alleles). The scores of changed strength by ssSNPs are presented as "altered.splice.site.strength" (alternate SNP alleles). Alternate SNP alleles have revealed much lower strength scores than reference SNP alleles.



♠ An example with exon extention events.



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