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H-DBAS / Human-transcriptome DataBase for Alternative Splicing
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.
EID / Exon-Intron Database
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.
TassDB / TAndem Splice Site DataBase
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.
ASG / Alternative Splicing Gallery
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.
Spliceosome Database
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.
Database for Bacterial Group II Introns
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.
This database was built upon genomic annotation of splicing patterns of known genes derived from spliced alignment of complementary DNAs (cDNAs) and expressed sequence tags. Hollywood was implemented as a relational database and currently contains comprehensive information for human and mouse. It is accompanied by a web query tool that allows searches for sets of exons with specific splicing characteristics or splicing regulatory element composition, or gives a graphical or sequence-level summary of splicing patterns for a specific gene.
TCGA SpliceSeq / The Cancer Genome Atlas SpliceSeq
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A web-based resource that provides a quick, user-friendly, highly visual interface for exploring the alternative splicing patterns of TCGA tumors. Percent Spliced In (PSI) values for splice events on samples from 33 different tumor types, including available adjacent normal samples, have been loaded into TCGA SpliceSeq. Investigators can interrogate genes of interest, search for the genes that show the strongest variation between or among selected tumor types, or explore splicing pattern changes between tumor and adjacent normal samples. The interface presents intuitive graphical representations of splicing patterns, read counts and various statistical summaries, including percent spliced in. Splicing data can also be downloaded for inclusion in integrative analyses.
Provides occurrences of alternative-splicing (AS) modes in human genome, including exon skipping, 5’-alternative splicing, 3’-alternative splicing and intron retention. SpliceInfo uses comparison between a pair of nucleotide sequences (DNA with mRNA) and DNA sequence with protein sequence for evidence of alternative splicing in a given gene. It provides features that allow the selection of a range of functions to retrieve the database contents in an efficient manner and the selection of a variety of graphical interfaces to effectively represent the analyzed results.
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).
AtRTD-QUASI / Arabidopsis Thaliana Reference Transcript Dataset - Quantification of Alternatively Spliced Isoforms
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 tool for assigning function to the human protein-coding splice variants (PCSVs). Most of previous studies have been focused only on the gene-centric functional annotation but now evidence is accumulating that different splice variants from a single Human gene can function differently. Therefore, there is a need to do the functional annotation at transcript-level and assign function to the human protein-coding splice variants. IsoFunc is a freely available tool for the global scientific community.
BBBomics / Blood Brain Barrier omics
A comprehensive portal for blood-brain barrier transcriptomics data, obtained by sequencing mRNA (mRNA-seq) and microRNA (miRNA-seq) of polarized hCMEC/D3 cell monolayers. This data encompasses coding (gene expression, alternate splice forms, expressed single nucleotide variants -eSNVs) and non-coding (microRNA, LincRNA, circular RNA) counts that are easily accessible through BBBomics hub database. We also superimposed the RNA-seq coding data on 285 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, which include canonical, non-canonical, and/or atypical pathways retrievable using BBBomics hub.
Provides a description of molecular interactions associated with human alternative splicing (AS) events. MiasDB covers 938 interactions between human splicing factors, RNA elements, transcription factors, kinases and modified histones for 173 human AS events. Every entry includes the interaction partners, interaction type, experimental methods, AS type, tissue specificity or disease-relevant information, a simple description of the functionally tested interaction in the AS event and references.
KIR / Kiwifruit Information Resource
Hosts a wide range of kiwifruit genomics and genetics datasets based on the latest and most accurate genome annotation. KIR aims to be a comprehensive online platform for users to search, visualize, download, retrieve literature and perform cross-species queries with unrestricted public access. It integrated all publicly available high-throughput sequences, experimental datasets, links to other useful databases and related analysis tools. To provide up to date gene/protein annotations, we will continue to collect and incorporate literature-based curation data.
Provides metadata of RNA-Seq datasets related with splicing factors with either loss- or gain-of-function experiments. SFMetaDB presents the Accession ID, description, the number of samples, associated curated splicing factors, perturbation and PubMed references of each RNA-Seq dataset. The database permits users to perform potential target identification for a specific splicing factor. It offers a view on how a splicing event is regulated across different biological contexts.
An integrated data portal for isoform-level expression, function and network analysis in the mouse. First, MIsoMine allows retrieval of top co-expressed isoforms in diverse tissues and experimental conditions based on the RNA-seq data collected from the Sequence Read Archive (SRA) database. Upon a gene/isoform query, the server will retrieve the top-correlated isoforms across different experiments as a heat map. Second, this data portal allows users to explore the function predictions and the functional network of alternatively splice isoforms.
A list of exon-exon junctions. We aligned 21,504 publicly available Illumina-sequenced human RNA-seq samples from the Sequence Read Archive (SRA) to the human genome and compared detected exon-exon junctions with junctions in several recent gene annotations. 56,865 junctions (18.6%) found in at least 1,000 samples were not annotated, and their expression associated with tissue type. Newer samples contributed few novel well-supported junctions, with 96.1% of junctions detected in at least 20 reads across samples present in samples before 2013.
Collects into a unique resource several heterogeneous information about splicing regulatory proteins, their binding sites and context-specific activity. Information of binding sites includes the corresponding genes, their genomic coordinates, the splicing effect, the experimental procedures used to assess binding and the related references. All these data have been manually extracted and collected by extensive database and literature screenings, yielding information on 71 splicing proteins, all those investigated so far to our knowledge for which some information is available on their RNA targets.
A database containing genes with frameshifts (fs-genes) predicted by GeneTack. The database includes 206 991 fs-genes from 1106 complete prokaryotic genomes and 45 295 frameshifts predicted in mRNA sequences from 100 eukaryotic genomes. The whole set of fs-genes was grouped into clusters based on sequence similarity between fs-proteins (conceptually translated fs-genes), conservation of the frameshift position and frameshift direction (−1, +1). The fs-genes can be retrieved by similarity search to a given query sequence via a web interface, by fs-gene cluster browsing, etc. Clusters of fs-genes are characterized with respect to their likely origin, such as pseudogenization, phase variation, etc. The largest clusters contain fs-genes with programed frameshifts (related to recoding events).
ASTRA / Alternative Splicing and TRanscription Archives
Stores the patterns (e.g. cassette type) of alternative splicing and transcriptional initiation (ASTI). ASTRA detects these patterns with an algorithm that converts alignments between human genomic DNA sequence and a set of cDNA/ expressed sequence tag (EST) sequences to binary arrays. The patterns stored in the database were detected by mapping full-length cDNA sequences onto genomic sequences and converting the derived exon-intron structures. It can graphically display and organize splicing patterns on demand.
DBATE / DataBase of Alternative Transcripts Expression
A web-based repository storing expression values and functional annotation of alternative splicing variants. The possibility to perform complex queries by cross-referencing different functional annotations permits the retrieval of desired subsets of splicing variant expression values that can be visualized in several ways, from simple to more informative. DBATE is intended as a tool to help appreciate how, and possibly why, the transcriptome expression is shaped.
ASAP / Alternative Splicing Annotation Project
Provides genome-wide alternative splicing analyses for insect, 15 vertebrate, and other animal species. ASAP supplies comparative genomics information in order to compare alternative splicing and splice site conservation through 17 aligned genomes. This database represents a resource for studies of gene structure evolution. The web interface shows detailed exploration of the data, and integrating comparative genomics information accompanied of alternative splicing data.
PALS db / Putative Alternative Splicing database
Provides a collection of Putative Alternative Splicing (PALS). PALS db is an online resource that furnishes several keyword search methods, such as identification numbers. It offers average 20.000 human UniGene clusters and more than 16.000 mouse UniGene clusters. A friendly interface was designed to present both the Alternative splicing (AS) site view and the supporting sequences view. The users can then set threshold criteria interactively to mark high-quality predictions.
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