SpliceInfo

An information repository for mRNA alternative splicing in human genome

SpliceInfo : Several modes of mRNA alternative splicing, such as exon skipping, alternative 5'-splicing sites, alternative 3'-splicing sites and mutually exclusive exons are computationally derived and extracted. Finally, for each type of alternative splicing, the flanking intronic sequences are collected and then exploited by motif discovery tools. The tissue-specific information and gene functionalities that correspond to the selected regions are also considered. The database provides a means of investigating alternative splicing and can be used for identifying alternative splicing - related motifs, such as the exonic splicing enhancer (ESE), the exonic splicing silencer (ESS) and other intronic splicing motifs.

Query By Gene
Query Fields (Gene Name, e.g., BRC) (Ensembl Gene ID, e.g., ENSG00000141837) (Swiss-Prot Protein Accession Number, e.g., O43497) (NCBI RefSeq Protein ID, e.g., NP_005239.1) (NCBI UniGene ID, e.g., Hs.122359)

Query By Filtering Constraints
Gene Lists	Ensembl_Gene_ID Lists
	Gene_Name Lists	BRCA1 BRCA2
	Splicing Type
	Containing Spliced-Out Protein Domain
Filtering Constraints	Alternative Splicing Modes
	Containing Repeat Feature (e.g., SINE, LINE,...)
	GC Ratio of Exons	>=
	Minimum Exon/Intron Length	>=
	Tissue Specificity [EST evidences]	Choose a Tissue
	Tissue Specificity [Protein evidences]	Choose a Tissue
	Containing Protein Domains
	Gene Ontology Aspect
	Gene Ontology Term

Demo 1 : Name group of genes which has annotations of Exonic Splicing Enhancers (ESEs). Demo 2 : Name group of genes which has annotations of Exonic Splicing Silencers (ESSs). Demo 3 : Name group of genes which has annotations of Intronic Splicing Enhancers (ISEs) or Silencers (ISSs). Demo 4 : Filtering constraints of BRCA exon skipping. Case Study 1 : An alternative spliced gene (BRCA1) Case Study 2 : A variety of genes which has ESEs Case Study 3 : Conserved exon skipping between human and mouse GoTo SpliceMotif

Department of Computer Science and Information Engineering, National Central University, Taiwan

Department of Biological Science and Technology, Institute of Bioinformatics
National Chiao Tung University,Hsinchu, Taiwan

Contact with: bryan@mail.NCTU.edu.tw

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