RGD is happy to announce its 3rd major release of 2007. This release includes the addition of Celera genome positions for genes, major developments in ortholog data and comparative map information, improved protein information and links; and gene families and disease gene data.
•Celera Genome Positionsnew–RGD now provides genomic positions for genes on the Celera Assembly as well as a Celera Assembly option on the GBrowse to provide users with a view of data elements within the context of the Celera Assembly.-view example , Go to GBrowser
•New Protein Linksnew–Weekly updates of data from the International Protein Index now provide users with the most up to date links to essential protein and family information and identifiers including IPI, UNIPARC, Ensembl Protein, InterPro, Pfam, PRINTS, PROSITE, PANTHER, RZPD, SMART, ProDom, Superfamily-SCOP, TIGRFAM, and Gene3D-Cath. -view example
•Human and Mouse Genesnew –Weekly downloads from EntrezGene now provide RGD users with up-to-date, complete data on human and mouse genes including:
- Genomic and cytogenetic map positions
- Summary description paragraphs for human genes and some mouse genes -view example
- Links to GDB, MGD, KEGG, Uniprot, PubMed, HGNC, NPRD, EntrezGene, UniGene, OMIM
- Links to human and mouse genes in UCSC Browser and NCBI MapView
- Links to nucleotide and protein sequences
- Links to GEO for expression data
- Links to PubMed references
- Gene searches for any or all species are available through the general search or gene query form
•Orthology Datanew –Ortholog relationships among rat, mouse and human are now updated weekly. Comparative map data for all three species are provided on each gene report as well as a link to the comparative map at NCBI Map Viewer.
•Disease Genesnew –The Rat orthologs of 1547 genes listed at OMIM have been fully curated using all rat papers published on each gene.
•Gene Families and Nomenclaturenew –The nomenclature for two major gene families, alpha tubulin and prolactin related genes has been completed. Identification and nomenclature assignment was coordinated with Dr. Michael Soares and the Mouse Genome Database. Details were published in Soares et al, Mammalian Genome 2007, Mar 18(3):154-6. A publication on the nomenclature resolution of the alpha tubulin family will appear in Genomics soon.
•Ontology Annotation Filesnew –Annotations files for pathway, phenotype and disease information for rat, mouse, and human genes and QTLs as well as rat strains are now available on the FTP site in a folder entitled “annotated_rgd_objects_by_ontology”. Files containing GO annotations for rat genes are in the gene_association files on the FTP site. All files are updated weekly.
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