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The vertebrate genome annotation (Vega) database.

Nucleic acids research | Jan 15, 2008

The Vertebrate Genome Annotation (Vega) database (http://vega.sanger.ac.uk) was first made public in 2004 and has been designed to view manual annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute. Since its initial release, the number of human annotated loci has more than doubled to close to 33 000 and now contains comprehensive annotation on 20 of the 24 human chromosomes, four whole mouse chromosomes and around 40% of the zebrafish Danio rerio genome. In addition, we offer manual annotation of a number of haplotype regions in mouse and human and regions of comparative interest in pig and dog that are unique to Vega.

Pubmed ID: 18003653 RIS Download

Mesh terms: Alternative Splicing | Animals | Databases, Nucleic Acid | Genome, Human | Genomics | Humans | Internet | Major Histocompatibility Complex | Mice | Mice, Inbred NOD | Mice, Knockout | User-Computer Interface | Zebrafish

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This is a list of tools and resources that we have found mentioned in this publication.


NIH Knockout Mouse Project (KOMP)

A trans-NIH initiative to generate a comprehensive and public resource comprised of mouse embryonic stem (ES) cells containing a null mutation in every gene in the mouse genome. By capitalizing on efficiencies of scale and a centralized production effort, the project intends to make this catalog of mutants available in mouse strain C57BL/6 for two reasons: it is the most widely used strain and it is the strain for which complete genome sequence has been made available. The NIH KOMP initiative aims to: 1) use gene targeting to make the resource of null alleles, marked with a high utility reporter, preferably in C57BL/6; 2) support a repository to house the products of this resource as well as an additional "repatriation" effort to bring into repositories 1000 of the existing high priority mouse knockouts not already stored in a public repository; 3) develop improved C57BL/6 ES cells that show robust germline transmission, so that they may be used in a high throughput pipeline in generating this resource; and 4) implement a data coordination center which will make the status and relevant data of the production effort available to the research community. Towards those ends, NIH awarded five-year cooperative agreements totaling up to $47.2 million to two groups for the creation of the knockout mice lines. Recipients of those awards are Regeneron Pharmaceuticals, Inc., in Tarrytown, N.Y., and a collaborative team from Children's Hospital Oakland Research Institute (CHORI) in Oakland, Calif., the School of Veterinary Medicine, University of California, Davis (UC Davis); and the Wellcome Trust Sanger Institute in Hinxton, England. Under its cooperative agreement, the team plans to systematically create mouse ES cell lines in which 5,000 genes have been knocked out by gene targeting. The VelociGene division of Regeneron, will take aim at a different set of 3,500 genes. Both groups will utilize information from the finished mouse genome sequence to design targeting vectors, which will be built by large-scale, automated technologies. The combined collection of mouse ES cells with knockouts in 8,500 genes will be useful for producing knockout mice. In addition, The Jackson Laboratory will set up a Data Coordination Center that will allow the research community to track the scheduling and progress of knockout production. The center will also serve as a central information resource for all publicly available knockout mutants and will integrate with other databases that contain mouse DNA sequence, additional information on mouse genetics and information on the physical and biochemical characteristics of the knockout mice. The NIH has also provided $4.8 million to establish and support a repository for the Knockout Mouse Project. Finally, NIH awarded cooperative agreements to improve the efficiency of methods for creating knockout lines. They will focus on developing methods to create ES cell lines suitable for high-throughput gene targeting or trapping in C57BL/6.

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SNP2NMD

A database for human SNPs (single nucleotide polymorphisms) that result in PTCs (premature termination codons) and trigger nonsense-mediated mRNA decay (NMD). The SNP2NMD interfaces provide extensive genetic information on and graphical views of the queried SNP, gene, and disease terms.

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