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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:	36.3	March, 2008
RefSeq Transcripts:	Release 32	November, 2008
GenBank Transcripts:	Release 168	October, 2008
Total Genes:	20,093
Unique Splice Variants:	75,839
Mouse
Genome Build:	37.1	July, 2007
RefSeq Transcripts:	Release 32	November, 2008
GenBank Transcripts:	Release 168	October, 2008
Total Genes:	19,689
Unique Splice Variants:	39,417
Rat
Genome Build:	4.1	July, 2006
RefSeq Transcripts:	Release 32	November, 2008
GenBank Transcripts:	Release 168	October, 2008
Total Genes:	14,668
Unique Splice Variants:	18,901
Arabidopsis
Genome Build:		November, 2005
RefSeq Transcripts:	Release 32	November, 2008
GenBank Transcripts:	Release 168	October, 2008
Total Genes:	27,081
Unique Splice Variants:	35,712
C elegans
Genome Build:		February, 2006
RefSeq Transcripts:	Release 32	November, 2008
GenBank Transcripts:	Release 168	October, 2008
Total Genes:	20,120
Unique Splice Variants:	24,281
Cow
Genome Build:	4.1	August, 2008
RefSeq Transcripts:	Release 32	November, 2008
GenBank Transcripts:	Release 168	October, 2008
Total Genes:	9,178
Unique Splice Variants:	11,165
Fly
Genome Build:		November, 2005
RefSeq Transcripts:	Release 32	November, 2008
GenBank Transcripts:	Release 168	October, 2008
Total Genes:	13,758
Unique Splice Variants:	23,482
Zebrafish
Genome Build:	3.1	June, 2008
RefSeq Transcripts:	Release 32	November, 2008
GenBank Transcripts:	Release 168	October, 2008
Total Genes:	10,304
Unique Splice Variants:	13,773
Rice
Genome Build:		October, 2007
RefSeq Transcripts:	Release 32	November, 2008
GenBank Transcripts:	Release 168	October, 2008
Total Genes:	26,775
Unique Splice Variants:	26,947

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