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URL: http://www.bioinf.mdc-berlin.de/splice/db/

Proper Citation: Extended Alternatively Spliced EST Database (RRID:SCR_008186)

Description: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. An online available compendium of alternative splice forms for several organisms (Arabidopsis thaliana, Bos taurus, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Homo sapiens, Mus musculus, Rattus norvegicus, Xenopus laevis). Alternative splice forms are defined by comparing high-scoring ESTs to mRNA sequences (both from GenBank) with known exon-intron information (from ENSEMBL database) using BLAST. Repetitive sequences of all mRNAs have beforehand been masked by MaskerAid. Filtering programs with defined parameters compare the ends of each aligned sequence pair for deletions or insertions in the EST sequence, which suggest the existence of alternative splice forms. The database is accessible by typing in accession numbers (ACC) or keywords like description, gene names, organism or other keywords. (If more than one hit was found a list of all results is given.) And the result page is divided into 4 major parts. The first part (General Information About The Entry) summarizes the most important information as database ids, organism, and description. The so called alternative splice profile (ASP) of each human sequence is shown in the second part (Alternative Splice Frequency). The ASP indicates the number of alternatively spliced ESTs (NAE), the number of constitutively spliced ESTs (NCE) as well as the number of alternative splice sites (NSS) per mRNA. NAE and NCE corresponds to the EST coverage and can be used as a quality value for the predicted alternative splice variants. The NSS value specifies the splice propensity of a gene. Moreover the number of ESTs from cancerous tissues is shown. The histological source and the developmental stages are illustrated with several colors to enables the user to get an overview of the origins of the matching ESTs. Also, the Splice Site View shows graphically all alternative splice sites for the whole transcript.

Abbreviations: EASED

Synonyms: Extended Alternatively Spliced EST Database

Resource Type: data or information resource, database

Keywords: drosophila melanogaster, est, exon, filtering, form, gene structure, aligned, alternative, arabidopsis thaliana, bos taurus, caenorhabditis elegans, cancerous, color, danio rerio, deletion, developmental, histological, homo sapien, insertion, intron, mrna, mus musculus, nucleotide sequence, organism, pair, rattus norvegicus, sequence, splice, splice sites databases, stage, tissue, xenopus laevis