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General ReleaseNotes Database Array-Check siRNA-Check Primer-Check Peptide-Check Batch Array-Check Batch siRNA-Check Batch Primer-Check Batch Peptide-Check Expression-Check

When was the database built?

The most recent build was completed in June of 2010. Check your organism of interest in the summary statisic below to see which build genome from NCBI was used. If you would prefer to work with the previous build (approximately two years older), it is available here.

How is the database of alternative spliceforms constructed?

A batch process retrieves all of the complete coding mRNA records from RefSeq and GenBank. NCBI Gene data files are used to associate transcript records to genes. The transcripts are aligned to chromosomal sequence to determine the exon structure of the transcript. Quality assurance is done to eliminate poor quality transcript sequences and transcripts with duplicate exon structure are eliminated. The chromosomal coordinates of each exon of the remaining transcripts are stored in a relational database.

A detailed description of the build process can be found in this document: SpliceCenter_DataBuild.doc

Are summary statistics available for the splice variant database?

Here is some high-level information about the contents of the database:
Human
Genome Build:37.1 August, 2009
RefSeq Transcripts:Release 41 May, 2010
GenBank Transcripts:Release 178 June, 2010
Total Genes:20,066
Unique Splice Variants:81,142
Mouse
Genome Build:37.1 July, 2007
RefSeq Transcripts:Release 41 May, 2010
GenBank Transcripts:Release 178 June, 2010
Total Genes:20,311
Unique Splice Variants:42,830
Rat
Genome Build:4.1 July, 2006
RefSeq Transcripts:Release 41 May, 2010
GenBank Transcripts:Release 178 June, 2010
Total Genes:15,443
Unique Splice Variants:19,973
Arabidopsis
Genome Build:September, 2009
RefSeq Transcripts:Release 41 May, 2010
GenBank Transcripts:Release 178 June, 2010
Total Genes:27,217
Unique Splice Variants:36,713
C elegans
Genome Build: February, 2006
RefSeq Transcripts:Release 41 May, 2010
GenBank Transcripts:Release 178 June, 2010
Total Genes:20,173
Unique Splice Variants:24,321
Cow
Genome Build:4.1 August, 2008
RefSeq Transcripts:Release 41 May, 2010
GenBank Transcripts:Release 178 June, 2010
Total Genes:9,556
Unique Splice Variants:11,729
Fly
Genome Build: December, 2009
RefSeq Transcripts:Release 41 May, 2010
GenBank Transcripts:Release 178 June, 2010
Total Genes:13,687
Unique Splice Variants:24,287
Zebrafish
Genome Build:3.1 June, 2008
RefSeq Transcripts:Release 41 May, 2010
GenBank Transcripts:Release 178 June, 2010
Total Genes:11,041
Unique Splice Variants:14,938
Rice
Genome Build: October, 2007
RefSeq Transcripts:Release 41 May, 2010
GenBank Transcripts:Release 178 June, 2010
Total Genes:25,303
Unique Splice Variants:25,305

Which microarray platforms are available in SpliceCenter?

We have pre-computed probe target location for 48 microarrays from Affymetrix, Agilent, Illumina, and ExonHit. Our Microarray database contains the target location of more than 14 million probes.
Tiger Team Bioinformatics Group