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.
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.
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.
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.
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.
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.