ASHESdb - Alternatively Spliced Human genes by Exon Skipping - A Database

 

 

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Useful Links to Alternative Splicing Resources

  1. Infogene database : includes all predicted genes and proteins for the Human genome draft. Contains information about the splice site pairs of a particular gene extracted automatically.

  2. GOLD[TM]: Genomes OnLine Database HomePage : World Wide Web resource for comprehensive access to information regarding complete and ongoing genome projects around the world.

  3. Mammalian Gene Collection: a complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for human and mouse

  4. SpliceDB: canonical and non-canonical splice site sequences in mammalian genes

  5. Database of Alternative Spliced forms (4560) and 3011 human mRNAs that have direct role in disease progression. Brett uses EST data to find splice forms. Data download is available.

  6. Alternative Splicing Database: ASDB published database of alternatively spliced forms derived using keyword search to extract AS forms published in Genbank or SwissProt. Drayluk, 1999. Contains information on alternatively spliced genes, their products, and their expression patterns. More details.

  7. Putative ALternative Splicing Database (PALS db) : putative alternative splicing (AS) sites to all known human genes. We used the unique sequences of UniGene clusters as reference sequences to construct PALS db.

  8. HASDB : data set for understanding the role of alternative splicing in the human genome providing detailed alignment of the EST, mRNAs, genomic DNA and protein sequences.

  9. AsMamDB : database to facilitate the systematic study of alternatively spliced genes of mammal. Alternative splicing patterns are represented by multiple alignments of gene's various transcripts and graphs of their topological structures. Gene structures are illustrated by showing distributions of exons, introns and various regulatory elements. There are 4,204 DNAs, 3,977 mRNAs, 8,989 CDSs, 126,931 ESTs in the present database.

  10. Intronerator : a collection of tools for exploring the molecular biology and genomics of C. elegans with a special emphasis on alternative splicing. Includes display of cDNA alignments with genomic sequence, catalog of alternatively spliced genes and database of introns.

  11. ISIS (Intron Sequence and Information Database) : multiple organism nuclear intron database.

  12. AltExtron Database : A High Quality Data Set of Human Transcript-confirmed Constitutive & Alternative Exons and Introns. EST-confirmed human splice sites

  13. Yeast Intron Database : contains information about the spliceosomal introns of the yeast Saccharomyces cerevisiae.

  14. Yeast Intron DataBase (YIDB) contains currently available information about all introns encoded in the nuclear and mitochondrial genomes of the yeast Saccharomyces cerevisiae.

  15. AEDB : alternative exons from the literature using "alt splicing" as keyword search via MEDLINE and these data are analyzed statistically. Collected features on species, their splicing mechanisms, tissue specificity, developmental regulation, regulatory features, sequences of the alternatively spliced exons and flanking constitutive exons.

  16. Minigene : A minigene contains a genomic fragment including the alternative exon(s) and the surrounding introns as well as the flanking constitutively spliced cloned in a eukaryotic expression vector. Thus, the transfected minigenes should contain all RNA-elements necessary to show the same alternative splicing pattern as the corresponding endogenous alternatively spliced gene when compared in a specific cellular environment.

  17. The contribution of exon-skipping events on Chromosome 22 to Protein Coding Diversity.
    Winston A. Hide, Vladimir N. Babenko, Peter A. van Heusden, Cathal Seoighe, and Janet F. Kelso.
    Genome Research. 2001 11 : 1848-1853. Exon skipping data

  18. Prosplicer - A Putative Alternative Splicing Database Based on Proteins, mRNAs and EST Clusters

  19. ASAP - Alternative Splicing Annotation Project

    Algorithms available

  1. Tap (Transcript Assembly Program) : EST-based gene finder that infers the predominant and alternative gene structures in anonymous genomic sequences. The entire prediction process consists of 3 steps.
    (1) The genomic sequence is searched against dbEST using WU2BLASTN (Gish, 1996-2001).
    (2) High-scoring EST hits are aligned to the genomic sequence using sim4 (Florea et al. 1998).
    (3) Based on genomic EST alignments, TAP predicts the predominant gene structure on both strands of the genomic sequence, identifies the poly-A sites and gene boundaries, and infer alternatively spliced gene structures. The program was developed mainly for predicting human genes

  2. Stack (Sequence Tag Alignment and Consensus Knowledgebase) : Sequence Tag Alignment and Consensus Knowledgebase, is generated by processing EST and mRNA sequences obtained from Genbank through a pipeline consisting of masking, clustering, alignment and variation analysis steps.

  3. Gene2EST BLAST Server

  4. Gene Resource Loader : map millions of ESTs to the human genome for the study of the exon-intron structures of genes, the alternative splicing of pre-mRNAs, the promoter regions of full-length-enriched cDNA sequences, and the gene-expression patterns associated with ESTs.

  5. PROCRUSTES: Gene Recognition via Spliced Alignment. It explores all possible exon assemblies and finds the multi-exon structure with the best fit to a related protein using EST data. It has found alternative spliced genes occurring in the 5' UTR regions when applied to the TIGR EST assemblies. Majority of the alternative splicing events occur at coding regions producing additional protein domains rather than alternating domains. Mironov, 1999.

  6. Asalign : a multiple alignment program for revealing alternative splicing patterns from a group of nucleotide sequences related to a gene. Ji, 2000.

  7. Repeat Masker : screens DNA sequences in fasta format against a library of repetitive elements and returns a masked query sequence ready for database searches as well as a table annotating the masked regions. More details.

  8. Splice Site Score calculator : It calculates the scores of donor, acceptor and branch sites in human genomic DNA.

  9. Splice Site Finder : It finds the potential splice sites in human genomic DNA.

  10. Gibbs algorithm : algorithm to find common locally conserved regions that represent motifs.

  11. Stamm's program to search, align into sub groups and analyze, calculate splice site strengths, splice site composition and scores

  12. WABA : Wobble Aware Bulk Aligner - program to recognize homologous regions of DN despite rapid divergence in wobble position of most codons

  13. XenoAli : program to restrict the returned sequences to introns or exons only.