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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Nucleic Acid Database Resource Report Resource Website 10+ mentions |
Nucleic Acid Database (RRID:SCR_003255) | NDB | data or information resource, database | A database of three-dimensional structural information about nucleic acids and their complexes. In addition to primary data, it contains derived geometric data, classifications of structures and motifs, standards for describing nucleic acid features, as well as tools and software for the analysis of nucleic acids. A variety of search capabilities are available, as are many different types of reports. NDB maintains the macromolecular Crystallographic Information File (mmCIF). | nucleic acid, dna, nucleopeptide, nucleoprotein, nucleotide, rna, transfection, sequence, structure, function, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: MINAS - Metal Ions in Nucleic AcidS is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: Jenalib: Jena Library of Biological Macromolecules has parent organization: Rutgers University; New Jersey; USA |
NSF ; DOE ; NIH |
PMID:24185695 PMID:1384741 |
Free, Available for download, Freely available | nif-0000-03184, biotools:ndb, r3d100010415 | https://bio.tools/ndb, https://doi.org/10.17616/R3531R | SCR_003255 | 2026-08-29 11:29:27 | 37 | |||||
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NCBI Taxonomy Resource Report Resource Website 100+ mentions |
NCBI Taxonomy (RRID:SCR_003256) | NCBI Taxonomy | data or information resource, database | Database for a curated classification and nomenclature that contains the names of all organisms that are represented in the public sequence databases with at least one nucleotide or protein sequence. Data provided encompasses archaea, bacteria, eukaryota, viroids and viruses. The NCBI taxonomy database is not a primary source for taxonomic or phylogenetic information. Furthermore, the database does not follow a single taxonomic treatise but rather attempts to incorporate phylogenetic and taxonomic knowledge from a variety of sources, including the published literature, web-based databases, and the advice of sequence submitters and outside taxonomy experts. Consequently, the NCBI taxonomy database is not a phylogenetic or taxonomic authority and should not be cited as such. | viroid, virus, nucleotide, protein, sequence, phylogeny, taxonomic, taxonomy, nomenclature, cladistics, classification, animal, genetic code, gold standard |
is used by: NIF Data Federation is used by: Vertebrate Taxonomy Ontology is listed by: re3data.org is related to: Taxonomy is related to: NEWT is related to: Phenoscape Knowledgebase is related to: EBIMed is related to: GOTaxExplorer is related to: Whatizit is related to: Integrated Manually Extracted Annotation has parent organization: NCBI is parent organization of: NCBITaxon |
PMID:18940862 PMID:18940867 |
Free, Freely available | nif-0000-03179, r3d100010776 | http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html, https://doi.org/10.17616/R3X039 | SCR_003256 | NCBI Taxonomy Browser, Taxonomy Browser, Entrez Taxonomy Browser, NCBI Taxonomy Database | 2026-08-29 11:29:21 | 296 | |||||
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mtDB - Human Mitochondrial Genome Database Resource Report Resource Website 50+ mentions |
mtDB - Human Mitochondrial Genome Database (RRID:SCR_002945) | mtDB | data or information resource, database | A database of human mitochondrial genomes containing mtDNA sequences, polymorphic sites, and the ability to search for specific variants. It contains 1865 complete sequences and 839 coding region sequences. | human genome, mitochondrial dna, sequence, variant, population genetics, coding region, polymorphic site, population, mitochondrial sequence, mitochondrial polymorphism, FASEB list |
is listed by: OMICtools has parent organization: Uppsala University; Uppsala; Sweden |
Swedish Research Council | PMID:16381973 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02994, OMICS_01642 | SCR_002945 | Human Mitochondrial Genome Database | 2026-08-29 11:29:17 | 59 | |||||
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ASAP: the Alternative Splicing Annotation Project Resource Report Resource Website 10+ mentions |
ASAP: the Alternative Splicing Annotation Project (RRID:SCR_003415) | ASAP | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on 8/12/13. Database to access and mine alternative splicing information coming from genomics and proteomics based on genome-wide analyses of alternative splicing in human (30 793 alternative splice relationships found) from detailed alignment of expressed sequences onto the genomic sequence. ASAP provides precise gene exon-intron structure, alternative splicing, tissue specificity of alternative splice forms, and protein isoform sequences resulting from alternative splicing. They developed an automated method for discovering human tissue-specific regulation of alternative splicing through a genome-wide analysis of expressed sequence tags (ESTs), which involves classifying human EST libraries according to tissue categories and Bayesian statistical analysis. They use the UniGene clusters of human Expressed Sequence Tags (ESTs) to identify splices. The UniGene EST's are clustered so that a single cluster roughly corresponds to a gene (or at least a part of a gene). A single EST represents a portion of a processed (already spliced) mRNA. A given cluster contains many ESTs, each representing an outcome of a series of splicing events. The ESTs in UniGene contain the different mRNA isoforms transcribed from an alternatively spliced gene. They are not predicting alternative splicing, but locating it based on EST analysis. The discovered splices are further analyzed to determine alternative splicing events. They have identified 6201 alternative splice relationships in human genes, through a genome-wide analysis of expressed sequence tags (ESTs). Starting with 2.1 million human mRNA and EST sequences, they mapped expressed sequences onto the draft human genome sequence and only accepted splices that obeyed the standard splice site consensus. After constructing a tissue list of 46 human tissues with 2 million human ESTs, they generated a database of novel human alternative splices that is four times larger than our previous report, and used Bayesian statistics to compare the relative abundance of every pair of alternative splices in these tissues. Using several statistical criteria for tissue specificity, they have identified 667 tissue-specific alternative splicing relationships and analyzed their distribution in human tissues. They have validated our results by comparison with independent studies. This genome-wide analysis of tissue specificity of alternative splicing will provide a useful resource to study the tissue-specific functions of transcripts and the association of tissue-specific variants with human diseases. | gene, genome, human, isoform, mechanism, metazoa, molecular, mrna, nucleus, process, protein, sequence, splice, tissue specificity, transcription, transcript, alternate splicing, microarray, alternative splicing, biological process, alternatively spliced isoform, contig, cancer, image |
is listed by: Biositemaps is related to: Alternative Splicing Annotation Project II Database has parent organization: University of California at Los Angeles; California; USA |
NSF 0082964; NSF DGE-9987641; DOE DEFG0387ER60615 |
PMID:12519958 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33105 | SCR_003415 | Alternative Splicing, Alternative Splicing Annotation Project, Alternative Splicing Annotation Project database | 2026-08-29 11:29:22 | 33 | |||||
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MITOMAP - A human mitochondrial genome database Resource Report Resource Website 100+ mentions |
MITOMAP - A human mitochondrial genome database (RRID:SCR_002996) | MITOMAP | data or information resource, database | Database of polymorphisms and mutations of the human mitochondrial DNA. It reports published and unpublished data on human mitochondrial DNA variation. All data is curated by hand. If you would like to submit published articles to be included in mitomap, please send them the citation and a pdf. | gene, genome, diabetes, disease, disease-association, high resolution screening, human, inversion, metabolism, mitochondrial dna, mutation, phenotype, polymorphism, polypeptide assignment, pseudogene, restriction site, rna, sequence, trna, unpublished, variation, mitochondria, dna, insertion, deletion, FASEB list |
is used by: HmtVar is listed by: OMICtools is related to: Hereditary Hearing Loss Homepage has parent organization: Childrens Hospital of Philadelphia - Research Institute; Pennsylvania; USA has parent organization: Emory University School of Medicine; Atlanta; Georgia; USA |
NIH ; Muscular Dystrophy Foundation ; Ellison Foundation ; Diputacion General de Aragon Grupos consolidados B33 ; NIGMS GM46915; NINDS NS21328; NHLBI HL30164; NIA AG10130; NIA AG13154; NINDS NS213L8; NHLBI HL64017; NIH Biomedical Informatics Training Grant T15 LM007443; NSF EIA-0321390; Spanish Fondo de Investigacion Sanitaria PI050647; Ciber Enfermedades raras CB06/07/0043 |
PMID:17178747 PMID:15608272 PMID:9399813 PMID:9016535 PMID:8594574 |
Except where otherwise noted, Creative Commons Attribution License, The community can contribute to this resource | nif-0000-00511, OMICS_01641 | SCR_002996 | 2026-08-29 11:29:18 | 405 | ||||||
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Marvel Resource Report Resource Website 1+ mentions |
Marvel (RRID:SCR_017621) | alignment software, data processing software, image analysis software, software application, software resource, software toolkit | Software set of tools that facilitate overlapping, patching, correction and assembly of noisy long reads. | Overlapping, patching, correction, assembly, noisy, long, read, sequence, align | Free, Available for download, Freely available | SCR_017621 | 2026-08-29 11:28:11 | 2 | |||||||||||
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OrthoFinder Resource Report Resource Website 1000+ mentions |
OrthoFinder (RRID:SCR_017118) | data analysis software, data processing software, software application, software resource | Software Python application for comparative genomics analysis. Finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of gene duplcation events in those gene trees, infers rooted species tree for species being analysed and maps gene duplication events from gene trees to branches in species tree, improves orthogroup inference accuracy. Runs set of protein sequence files, one per species, in FASTA format. | comparative, genomic, analysis, find, orthogroup, ortholog, infer, gene, tree, duplicate, accuracy, protein, sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Bill and Melinda Gates Foundation ; UKAID |
PMID:26243257 DOI:10.1101/466201 |
Free, Available for download, Freely available | biotools:OrthoFinder, OMICS_09733, BioTools:OrthoFinder | https://bio.tools/OrthoFinder, https://bio.tools/OrthoFinder, https://bio.tools/OrthoFinder | SCR_017118 | OrthoFinder2, OrthoFinder | 2026-08-29 11:28:10 | 3413 | |||||
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PASC Resource Report Resource Website 1+ mentions |
PASC (RRID:SCR_016642) | PASC | analysis service resource, data access protocol, data or information resource, database, production service resource, service resource, software resource, web service | Web tool for analysis of pairwise identity distribution within viral families. Used for virus sequence-based classification. Data in the system are updated every day to reflect changes in virus taxonomy and additions of new virus sequences to the public database. | analysis, pairwise, identity, distribution, viral, family, sequence, classification, data, taxonomy | has parent organization: NCBI | National Library of Medicine | PMID:25119676 | Free, Public | SCR_016642 | PAirwise Sequence Comparison | 2026-08-29 11:27:42 | 6 | ||||||
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IMGT HighV-QUEST Resource Report Resource Website 10+ mentions |
IMGT HighV-QUEST (RRID:SCR_018196) | alignment software, analysis service resource, data or information resource, data processing software, image analysis software, portal, production service resource, service resource, software application, software resource | Next generation B and T cell sequence alignment and characterization online surface by IMGT. Web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing. | Next generation sequencing, B cell, T cell, sequence alignment, immunoglobulin, antibody, T cell receptor, analysis, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian |
CNRS ; GENCI ; MESR ; NHMRC ; Université Montpellier 2 ; France |
PMID:22647994 PMID:23995877 PMID:22665256 |
Restricted | biotools:IMGt_HighV-QUESt | https://bio.tools/IMGT_HighV-QUEST | SCR_018196 | IMGT/HighV QUEST, IMGT/HighV-QUEST, IMGT web portal | 2026-08-29 11:27:46 | 15 | |||||
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SignalP Resource Report Resource Website 10000+ mentions |
SignalP (RRID:SCR_015644) | software resource, web application | Web application for prediction of the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks. | prediction, signal peptide, cleavage site, amino acid, sequence, artificial neural network |
is listed by: SoftCite has parent organization: DTU Center for Biological Sequence Analysis |
PMID:28451972 | Freely available, Acknowledgment requested, Free, Available for download, Runs on Windows, Runs on Mac OS | SCR_015644 | 2026-08-29 11:28:14 | 10033 | |||||||||
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DynaMine Resource Report Resource Website 10+ mentions |
DynaMine (RRID:SCR_014559) | software resource, web application | An NMR based method for protein folding prediction. Users can enter a UniProt identifier, FASTA sequences, or upload a file containing FASTA sequences and results are returned., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | nmr, protein folding, prediction, fasta, sequence, dynamics | PMID:24225580 | THIS RESOURCE IS NO LONGER IN SERVICE | http://dynamine.ibsquare.be | SCR_014559 | 2026-08-29 11:28:22 | 44 | |||||||||
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Topology Data Bank of Transmembrane Proteins Resource Report Resource Website 1+ mentions |
Topology Data Bank of Transmembrane Proteins (RRID:SCR_007964) | TOPDB | data or information resource, database | Collection of transmembrane protein datasets containing experimentally derived topology information from the literature and from public databases. Web interface of TOPDB includes tools for searching, relational querying and data browsing, visualisation tools for topology data. | collection, transmembrane, protein, dataset, topology, public, data, sequence, database |
has parent organization: Hungarian Academy of Sciences; Budapest; Hungary works with: CCTOP |
Bolyai János Scholarship ; Hungarian research and development funds ; OTKA ; Öveges fellowship |
PMID:17921502 | Free, Available for download, Freely available for non commercial users | nif-0000-03568 | SCR_007964 | Topology Data Bank of Transmembrane Proteins, TOPDB | 2026-08-29 11:30:16 | 6 | |||||
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SIMAP Resource Report Resource Website 10+ mentions |
SIMAP (RRID:SCR_007927) | SIMAP | data or information resource, database | It provides a database based on a pre-computed similarity matrix covering the similarity space formed by >4 million amino acid sequences from public databases and completely sequenced genomes. The database is capable of handling very large datasets and is updated incrementally. For sequence similarity searches and pairwise alignments, we implemented a grid-enabled software system, which is based on FASTA heuristics and the Smith Waterman algorithm. SimpleSIMAP and AdvancedSIMAP retrieve homologs for given protein sequences that need to be contained in the SIMAP database. While SimpleSIMAP provides only selected parameters and preconfigured search spaces, the AdvancedSIMAP allows the user to specify search space, filtering and sorting parameters in a flexible manner. Both types of queries result in lists of homologs that are linked in turn to their homologs. So the web interfaces allow users to explore quickly and interactively the protein world by homology. Sponsors: SIMAP is supported by the Department of Genome Oriented Bioinformatics of the Technische Universitt Mnchen and the Institute for Bioinformatics of the GSF-National Research Center for Environment and Health. | genome, alignment, amino acid, homolog, matrix, protein, protein domain and protein classification databases, sequence | SCR_007927 | The Similarity Matrix of Proteins, Similarity Matrix of Proteins | 2026-08-29 11:30:16 | 14 | ||||||||||
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Signaling Pathway Database Resource Report Resource Website 50+ mentions |
Signaling Pathway Database (RRID:SCR_008243) | SPAD | data or information resource, database | It is divided to four categories based on extracellular signal molecules (Growth factor, Cytokine, and Hormone) and stress, that initiate the intracellular signaling pathway. SPAD is compiled in order to describe information on interaction between protein and protein, protein and DNA as well as information on sequences of DNA and proteins. There are multiple signal transduction pathways: cascade of information from plasma membrane to nucleus in response to an extracellular stimulus in living organisms. Extracellular signal molecule binds specific intracellular receptor, and initiates the signaling pathway. Now, there is a large amount of information about the signaling pathway which controls the gene expression and cellular proliferation. We have developed an integrated database SPAD to understand the overview of signaling transduction. | expression, extracellular, gene, cellular, cytokine, dna, growth factor, hormone, intermolecular interactions and signaling pathways databases, intracellular, molecule, organism, pathway, plasma membrane, proliferation, protein, receptor, response, sequence, signal, stimulus, stress, transduction, FASEB list | has parent organization: Kyushu University; Fukuoka; Japan | nif-0000-21376 | SCR_008243 | Signaling Pathway Database | 2026-08-29 11:30:21 | 51 | ||||||||
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Intergrated Transcription Factor Platform Resource Report Resource Website 10+ mentions |
Intergrated Transcription Factor Platform (RRID:SCR_008119) | data or information resource, database | ITFP is an integrated transcription factor (TF) platform, which included abundant TFs and targets message of mammalian. Support vector machine (SVM) algorithm combined with error-correcting output coding (ECOC) algorithm was utilized to identify and classify transcription factor from protein sequence of Human, Mouse and Rat. For transcription factor targets, a reverse engineering method named ARACNE was used to derive potential interaction pairs between transcription factor and downstream regulated gene from Human, Mouse and Rat gene expression profile data. Detailed information of gene expression profile data can be found in help page. Moreover, all data provided by the platform is free for non-commercial users and can be downloaded through links on help page. | expression, gene, human, message, mouse, protein, rat, sequence, target, transcription factor | has parent organization: Fudan University; Shanghai; China | nif-0000-20862 | SCR_008119 | ITFP | 2026-08-29 11:30:17 | 25 | |||||||||
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PrimerStudio Resource Report Resource Website 1+ mentions |
PrimerStudio (RRID:SCR_008232) | data or information resource, database | PrimerParadise is an online PCR primer database for genomics studies. The database contains predesigned PCR primers for amplification of exons, genes and SNPs of almost all sequenced genomes. Primers can be used for genome-wide projects (resequencing, mutation analysis, SNP detection etc). The primers for eukaryotic genomes have been tested with e-PCR to make sure that no alternative products will be generated. Also, all eukaryotic primers have been filtered to exclude primers that bind excessively throughout the genome. Genes are amplified as amplicons. Amplicons are defined as only one genes exons containing maximaly 3000 bp long dna segments. If gene is longer than 3000 bp then it is split into the segments at length 3000 bp. So for example gene at length 5000 bp is split into two segment and for both segments there were designed a separate primerpair. If genes exons length is over 3000 bp then it is split into amplicons as well. Every SNP has one primerpair. In addition of considering repetitive sequences and mono-dinucleotide repeats, we avoid designing primers to genome regions which contain other SNPs. -There are two ways to search for primers: you can use features IDs ( for SNP primers Reference ID, for gene/exon primers different IDs (Ensembl gene IDs, HUGO IDs for human genes, LocusLink IDs, RefSeq IDs, MIM IDs, NCBI gene names, SWISSPROT IDs for bacterial genes, VEGA gene IDs for human and mouse, Sanger S.pombe systematic gene names and common gene names, S.cerevisiae GeneBanks Locus, AccNo, GI IDs and common gene names) -you can use genome regions (chromosome coordinates, chromosome bands if exists) -Currently we provide 3 primers collections: proPCR for prokaryotic organisms genes primers -euPCR for eukaryotic organisms genes/exons primers -snpPCR for eukaryotic organisms SNP primers Sponsors: PrimerStudio is funded by the University of Tartu. | eukaryotic, exon, gene, amplicon, amplifcation, analysis, dinucleotide, dna, genome, genomic, molecular probe and primer databases, mononucleotide, mutation, organism, pcr, primer, prokaryotic, region, repetitive, segment, sequence, snp, snp detection | nif-0000-21334 | SCR_008232 | PrimerStudio | 2026-08-29 11:30:00 | 1 | ||||||||||
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ChickBase Resource Report Resource Website 1+ mentions |
ChickBase (RRID:SCR_008147) | data or information resource, database | This website contains the mapping sequence of poultry. The ArkDB database system aims to provide a comprehensive public repository for genome mapping data from farmed and other animal species. In doing so, it aims to provide a route in to genomic and other sequence from the initial viewpoint of linkage mapping, RH mapping, physical mapping or - possibly more importantly - QTL mapping data. It's supported, in part, by the USDA-CSREES National Animal Genome Research Program in order to serve the poultry genome mapping community. This system represents a complete rewrite of the original version with the code migrated to java and the underlying database targeted at postgres (although any standards-compliant database engine should suffice). The initial release records details of maps and the markers that they contain. There are alternative entry points that target either a chromosome or a specific mapping analysis as the starting point. Limited relationships between markers are recorded and displayed. As with the previous version, all maps are drawn using data extracted from the database on the fly. | animal, chicken, genome, linkage, map, mapping, marker, meeting, physical, poultry, qtl, rh, sequence, specie | has parent organization: Iowa State University; Iowa; USA | nif-0000-20970 | http://birdbase.arizona.edu/birdbase/ | http://www.genome.iastate.edu/chickmap/ | SCR_008147 | Chick Base | 2026-08-29 11:30:18 | 8 | |||||||
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Migratory Locust EST Database Resource Report Resource Website 1+ mentions |
Migratory Locust EST Database (RRID:SCR_008201) | data or information resource, database | The migratory locust (Locusta migratoria) is an orthopteran pest and a representative member of hemimetabolous insects. Its transcriptomic data provide invaluable information for molecular entomology study of the insect and pave a way for comparative studies of other medically, agronomically, and ecologically relevant insects. This first transcriptomic database of the locust (LocustDB) has been developed, building necessary infrastructures to integrate, organize, and retrieve data that are either currently available or to be acquired in the future. It currently hosts 45,474 high quality EST sequences from the locust, which were assembled into 12,161 unigenes. This database contains original sequence data, including homologous/orthologous sequences, functional annotations, pathway analysis, and codon usage, based on conserved orthologous groups (COG), gene ontology (GO), protein domain (InterPro), and functional pathways (KEGG). It also provides information from comparative analysis based on data from the migratory locust and five other invertebrate species, such as the silkworm, the honeybee, the fruitfly, the mosquito and the nematode. LocustDB also provides information from comparative analysis based on data from the migratory locust and five other invertebrate species, such as the silkworm, the honeybee, the fruitfly, the mosquito and the nematode. It starts with the first transcriptome information for an orthopteran and hemimetabolous insect and will be extended to provide a framework for incorporation of in-coming genomic data of relevant insect groups and a workbench for cross-species comparative studies. | ecologically, entomology, est, fruitfly, functional, gene, agronomically, analysis, annotation, codon, comparative, data, domain, genomic, hemimetabolous, homologous, honeybee, insect, invertebrate, invertebrate databases, locust, locusta migratoria, medically, migratory, molecular, mosquito, nematode, orthologous, orthopteran, pathway, pest, protein, sequence, silkworm, specie, transcriptome, transcriptomic, unigene, ontology | has parent organization: BGI; Shenzhen; China | nif-0000-21244 | SCR_008201 | LocustDB | 2026-08-29 11:30:18 | 7 | |||||||||
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Caenorhabditis Genome Sequencing Projects Resource Report Resource Website |
Caenorhabditis Genome Sequencing Projects (RRID:SCR_008155) | data or information resource, database | The Sanger Institute and the Genome Sequencing Center at the Washington University School of Medicine, St. Louis have collaborated to sequence the genomes of both C. elegans and C. briggsae. The completed C. elegans genome sequence is represented by over 3,000 individual clone sequences which can be accessed through this site (or through WormBase). These sequences are submitted to EMBL whenever the sequence or annotation changes (e.g. modification to gene structures) and these submissions are then mirrored to GenBank and DDBJ. These sequences (along with ESTs and proteins) can be searched on our C. elegans BLAST server. WormBase is the repository of mapping, sequencing and phenotypic information for C. elegans. The worm informatics group at the Sanger Institute play a key role in assembling the whole database. They also curate and develop some of the constituent databases that comprise WormBase. | elegans, briggsae, caenorhabditis, clone, genome, mapping, phenotypic, sequence | has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom | nif-0000-21001 | SCR_008155 | CGSP | 2026-08-29 11:30:18 | 0 | |||||||||
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Alternative Exon Database Resource Report Resource Website |
Alternative Exon Database (RRID:SCR_008157) | AEdb | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 27, 2013. A manual generated database for alternative exons and their properties from numerous species - the data is gathered from literature where these exons have been experimentally verified. Most alternative exons are cassette exons and are expressed in more than two tissues. Of all exons whose expression was reported to be specific for a certain tissue, the majority were expressed in the brain. At the moment, AEdb products that are available are sequence (a database of alternative exons), function (a database of functions attributed to constitutive and alternative exon), regulatory sequence (a database of transcript regulatory motifs), minigenes (a table of minigenes and their associations to splicing events), and diseases (a table of diseases associated with splicing and their associations to AltSplice). Alternative splicing is an important regulatory mechanism of mammalian gene expression. The alternative splicing database (ASD) consortium is systematically collecting and annotating data on alternative splicing. The continuation and upgrade of the ASD consists of computationally and manually generated data. Its largest parts are AltSplice, a value-added database of computationally delineated alternative splicing events. Its data include alternatively spliced introns/exons, events, isoform splicing patterns and isoform peptide sequences. AltSplice data are generated by examining gene-transcript alignments. The data are annotated for various biological features including splicing signals, expression states, (SNP)-mediated splicing and cross-species conservation. AEdb forms the manually curated component of ASD. It is a literature-based data set containing sequence and properties of alternatively spliced exons, functional enumeration of observed splicing events, characterization of observed splicing regulatory elements, and a collection of experimentally clarified minigene constructs. | element, exon, expression, gene, alignment, alternative, brain, conservation, cross-specie, disease, isoform, mechanism, minigene, pattern, peptide, regulatory, sequence, signal, splice, splicing, structure intron, tissue, transcript, nucleotide sequence, gene structure, intron, splice site, alternative splicing, sequence, alternative exon, function, constitutive exon, alternative exon, regulatory sequence, transcript regulatory motif, minigene, disease | has parent organization: European Bioinformatics Institute | PMID:16381912 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21009 | SCR_008157 | 2026-08-29 11:30:17 | 0 |
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