MGI Releases Version 3.51

JAX® NOTES Issue 504, Winter 2005

Mouse Genome Informatics (MGI) is pleased to announce its release of version 3.51. This new version has the following features:

  • Genome coordinates updated to NCBI Mouse Build 36 and dbSNP Build 126, dbSNP is the official source of SNP based mouse genomic variation in MGI and serves as a cen tral repository for single nucleotide polymorphisms (SNPs), multiple nucleo tide polymorphisms (MNPs), and short insertion/deletion polymorphisms (IN-DELs);
  • Computational genome annotations from Ensembl and NCBI;
  • Manually curated gene models from the Vertebrate Genome Annotation (VEGA) group at the Sanger Institute;
  • MGI's Mouse GBrowse updated to Build 36;
  • Mouse genome annotations from VEGA, NCBI, and Ensembl integrated into a unified catalog of mousegenome features;
  • 6,496 additional genes (a 5% increase) and 4,615 additional pseudogenes (a 400% increase);
  • Genome coordinate data for microRNAs (from mirBASE);
  • Genome coordinates for many mouse QTL regions;
  • SNPs that map to the Y chromosome; and
  • More refSNPs (from 1.8 to 6.5 million).

For example, to sample the new VEGA data for the Opa interacting protein 5 (Oip5) gene, see the MGI gene detail page. In the Sequence Map section, click the link to the VEGA ContigView. In the Sequences section, click the VEGA Gene Model link to a VEGA Mouse GeneView curated locus report. To find this (or similar) information yourself, enter a gene name on the MGI Genes and Markers Query Form. You can also enter a gene's VEGA accession ID (for Oip5, it is OTTMUSG00000015949) or a gene's name in the Search box on the MGI home page (click Accession IDs for the former or Gene symbols/names for the latter search).

To see a summary of all microRNA data in MGI, set the Type field on the Genes and Markers Query Form. To find details, click any of the symbols on the microRNA Summary page that appears. The following Web site is an example of an MGI detail page with microRNA coordinates.

Please send questions and comments to User Support, mgi-help@informatics.jax.org.