Alternative splicing databases | RNA modification data analysis
Alternative splicing (AS) is a post-transcriptional regulatory mechanism for gene expression regulation. Splicing decisions are affected by the combinatorial behavior of different splicing factors that bind to multiple binding sites in exons and introns.
Gathers information about the spliceosomal introns of the yeast Saccharomyces cerevisiae. Yeast Intron Database make an inventory of known spliceosomal introns in the yeast genome and documented used splice sites. Besides, the database aims to identify and analyze splice site context in terms of the nature and activities of the trans-acting factors that mediate splice site recognition.
Supplies data about human alternative splicing (AS) variants from the viewpoints of protein functions affected by AS. H-DBAS is based on cDNA information from the H-Invitational cDNA Annotation Project that were manually inspected and annotated. It offers the possibility for users to discover the world of human AS. This database stores AS events according to whether they are transcribed from conserved genomic regions or whether the corresponding transcripts that are also identified in mice.
Captures gene expression in the developing cortex. Cortecon uses RNA-seq technology to provide a repository that groups transcriptome changes during human in vitro corticogenesis and offers a standard for dataset comparison. The database can also be used for a better grasp of developmental pathways by using network analysis strategies. Searches can be made by gene, disease, KEGG pathway or by gene ontology (GO) ontology.
Allows users to find different types of gene expression. Brain RNA-seq is an online database that utilizes a sensitive algorithm to detect alternative splicing events in each cell type. This online resource hosts different information presented through several graphs. These graphs contain information on mouse brain and human brain (astrocytes, neurons).
Offers a comprehensive and convenient dataset of sequences for computational biologists who study exon-intron gene structures and pre-mRNA splicing. The collection of exons and introns has been extended beyond coding regions and current versions of EID contain data on untranslated regions of gene sequences as well. Intron-less genes are included as a special part of EID. For species with entirely sequenced genomes, species-specific databases have been generated. A novel Mammalian Orthologous Intron Database (MOID) has been introduced which includes the full set of introns that come from orthologous genes that have the same positions relative to the reading frames.
Offers the access of over 2000 human samples. IRBase offers an online database of intron retention (IR). This resource permits to assess a specified intron retention event within a tissue/cell type with a gene symbol and a tissue/cell type, or assess genome-wide intron retention within an RNA-seq dataset with an RNA-seq dataset. IRBase is a part of the toolbox developed by the CNRS to study the impact of IRintron retention on gene regulation.
Stores extensive data about alternative splice events at donors and acceptors, both confirmed and unconfirmed cases. TassDB offers a user-friendly interface to search for specific genes or for genes containing tandem splice sites with specific features as well as the possibility to download result datasets. TassDB provides comprehensive resources for researchers interested in both targeted experimental studies and large-scale bioinformatics analyses of short distance tandem splice sites.
Gathers data about regulation and functional associations of Alternative Splicing (AS) events. VastDB provides information from about 1,470 independent RNA-seq datasets including 108 human, 139 mouse, and 61 chicken. The database allows to view information by gene or by event and searches can be made by gene or by coordinates. Moreover, it contains multiple additional datasets which can be downloaded.
Contains the U12-type introns of completely sequenced eukaryotic genomes. U12DB uses queries constructed of a combination of text fields, drop-down lists, radio buttons and check boxes. It was created to catalog the U12-type introns in a framework that groups orthologous introns with each other. The database can help users to study the evolution and mechanism of U12-dependent splicing.
Integrates transcripts derived from a gene into a single splicing graph. ASG permits users to explore and visualize gene structure and alternative splicing. It includes transcript information from Ensembl, RefSeq, STACK, TIGR and UniGene to compile an exhaustive transcript catalog. This database allows the systematic investigation of gene structure and the transcriptome. It provides a sequence builder that permits users to interactively assemble exons, and to retrieve upstream and downstream regions.
A database of spliceosome-associated proteins and snRNAs. SpliceosomeDB provides tools to search for spliceosome genes/proteins based on several characteristics including name(s), complex designation, identification in particular mass spectrometry experiments, source organism and conserved motif/domain signatures. Each gene/protein is linked to additional sources of information and to orthologous genes in several model systems. Tools are also available for comparing the composition of different intermediate splicing complexes and for directly examining the lists of proteins identified in mass spectrometry experiments analyzing purified spliceosome complexes.
A database of new exon boundaries induced by pathogenic mutations in human disease genes. This resource will be useful for fine-tuning splice-site prediction algorithms, better definition of auxiliary splicing signals and design of new reporter assays.
Provides a unified resource to analyze the effects of alternative splicing events on the structure of the resulting protein isoforms. ProSAS comprehensively annotates protein structures for several Ensembl genomes and alternative transcripts can be analyzed on the protein structure and protein function level using the intuitive user interface of the database which provides several features and tools.
Stores non-canonical splice site sequences extracted from mammalian annotated genes. SpliceDB is a database that includes (i) the GenBank accession number, (ii) intron number, (iii) positions of donor and acceptor splice junctions in the InfoGene sequence, (iv) sequence around splice sites, and (v) type of splice site in the classification as well as the information about expressed sequence tag (EST) used to support the splice pair.
Permits to quantify transcripts. AtRTD-QUASI was created to use in Quantification of Alternatively Spliced Isoforms with Salmon or Kallisto and demonstrate that it outperforms other available transcriptomes for RNA-seq analysis. It is able to generate accurate quantification of alternative splicing isoforms for the major part of genes. The dataset can be used to investigate alternative splice junctions in the padded regions in the 3' and 5' untranslated regions.
A free database that provides a list of human internal exons and reports all their known splice events based on EST information from the UCSC Genome Browser . This list can be restricted by the user to either only a specific region in the genome (by specifying the chromosome, the strand and the start and end position), to a whole chromosome or to a group of genes. Furthermore, exons can be filtered according to their splicing type (constitutive exons, cassette exons and exons with one or more alternative 3' and/or 5' splice sites).
Harbors a set of human transcript-confirmed constitutively and alternatively spliced introns and exons, for conservation in mouse. AltExtron was constructed by analysing mouse transcript sequences for the presence of transcripts that match a human sequence tag comprising the flanking exons of a human splice junction. It also contains hypotheses concerning alternative splicing and genome organization.
Offers an alternative splicing (AS) annotation system integrating heterogeneous genomic information. ASpedia is a comprehensive human database that encompasses genomic features and isoform-level functions. It supports a retrieval system that identifies unique AS IDs and a browser to visualize each AS event. This resource was established from the integration of AS events inferring from gene models and associated annotation dataset.
Provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank. The Database for Bacterial Group II Introns website is divided into three sections. The first section provides general information on group II intron properties, structures and classification. The second and main section lists information for individual introns, including insertion sites, DNA sequences, intron-encoded protein sequences and RNA secondary structure models. The final section provides tools for identification and analysis of intron sequences. These include a step-by-step guide to identify introns in genomic sequences, a local BLAST tool to identify closest intron relatives to a query sequence, and a boundary-finding tool that predicts 5′ and 3′ intron-exon junctions in an input DNA sequence. Finally, selected intron data can be downloaded in FASTA format.