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SpliceCenter is a suite of user-friendly tools that evaluate the impact of gene splicing variation
on specific molecular biology techniques. Each of the utilities has a Help panel and a link to
populate a sample query. Select a SpliceCenter tool from the list below.
Note: New SpliceCenter release on 10/26/09. Details here.
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Interactive Graphical Tools
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Batch Tools
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Array-Check
displays a gene's splice variants and identifies the target location of probes from common
expression microarrays. This visualization identifies the variants target by each
probe and allows cross-platform comparison variant coverage.
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Batch Array-Check
accepts a file of gene symbols and returns a tabular version of the information available
in Array-Check. The ouput indicates the splice variants that are targeted by each microarray probe.
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siRNA-Check
presents a graphical display of siRNA/shRNA target locations within the known splice variants of a gene.
Effective use of RNAi to silence gene expression requires an understanding of the specific splice variants
that will be targeted by a given siRNA/shRNA.
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Batch siRNA-Check
is a high-throughput process that evaluates large numbers of siRNAs/shRNAs. Tabular position
reports provide RNAi target location details and a Hit/Miss report lists targeted/non-targeted splice variants.
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Primer-Check displays the target location
of RT-PCR primers and microarray probes on known splice variants of a gene. When RT-PCR
is used to confirm microarray results, it is important that the PCR primers and microarray
probes are measuring the same splice variants.
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Batch Primer-Check performs high-throughput
identification of the target location of PCR primers/probes. A file of primer sequences is submitted
and the tabular results identify targeted/non-targeted splice variants.
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Peptide-Check displays the location
of the coding sequence for a protein fragment within the known splice variants of a gene.
This capability is
useful in identifying gene isoforms that do / do not contain the peptide sequence in
question.
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Batch Peptide-Check performs high-throughput
identification of peptide sequences within splice variants of genes. Result files indicate the
gene that contains the peptide, its position within the gene and the variants
that do / do not include it.
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Expression-Check displays microarray
expression data for a single gene in a graphic that includes the gene's splice variants.
Expression values are displayed based on the target position of the microarray probes.
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