Ultraconserved sequences (UCRs) are genomic sequences that were found identical comparing human, rat and mouse genomes. Because of their extreme conservation it has been postulated that these regions must have biological functions essential to mammal cells.
A web tool dedicated to the analysis of ultraconserved sequences (UCRs). UCRs are 481 sequences >200 bases sharing 100% identity among human, mouse and rat genomes. They are frequently located in genomic regions known to be involved in cancer or differentially expressed in human leukemias and carcinomas. UCbase is a platform-independent web resource that includes the updated version of the human genome annotation (hg19), information linking disorders to chromosomal coordinates based on the Systematized Nomenclature of Medicine classification, a query tool to search for single nucleotide polymorphisms (SNPs) and a new text box to directly interrogate the database using a MySQL interface. To facilitate the interactive visual interpretation of UCR chromosomal positioning, UCbase includes a graph visualization interface directly linked to UCSC genome browser.
Provides data and tools for exploring genomic organization of highly conserved noncoding elements (HCNEs) for multiple genomes. Ancora includes a genome browser that shows HCNE locations and features novel HCNE density plots as a powerful tool to discover developmental regulatory genes and distinguish their regulatory elements and domains.
Identifies uniquely conserved regions (UCRs) as candidate diagnostic targets for a selected group of organisms solely from their genomic sequences. Using a sequence-indexing algorithm to identify UCRs and a k-mer integer-mapping model for computational efficiency, this method has successfully identified UCRs within the bacteria domain for 15 test groups, including pathogenic, probiotic, commensal and extremophilic bacterial species or strains. The UCRs identified for the 15 bacterial species are freely available.
Provides the means to refine models of the regulatory circuitry. The catalogue of functional enhancers in human Embryonic Stem Cells (hESCs) is a database that encompasses a comprehensive collection of functional enhancer sequences in hESCs. This resource provides a valuable knowledge base for systematic analysis of the core transcriptional network circuitry underlying hESC maintenance and differentiation.
A database of candidate tissue-specific enhancers in human and mouse. The database of EI candidate tissue-specific enhancers provides further support for the notion that sequence-based features in vertebrate cis-regulatory elements are computationally recognizable, similar to previous successes in the inference of coding, intron–exon, core promoter, and repetitive DNA sequence signatures.
Collects human–mouse conserved elements associated to disease genes. DG-CST is an annotated collection of conserved sequences related to genes involved in genetic diseases. The database contains a large number of annotations and is designed to allow easy retrieval of conserved sequence tag (CST) information. It can be useful for investigators interested in studying the molecular mechanisms that underlie genetic diseases and may help in deciphering the spectrum of pathogenetic mutations that determine genetic diseases.
Provides users with detailed synteny structure interconnecting pair of genomes. ECRbase is a portal to pre-computed, post-processed whole-genome comparative data that allows the extraction of evolutionary conserved regions (ECRs). It promotes sequences as well as the transcription factor binding sites (TFBSs) associated with them, for all available vertebrate genomes. This resource allows for constant growth to accommodate the dynamic nature of genome research where newly emerging genomes.