ABSTRACT
The Mouse Genome Database (MGD) forms the core of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a model organism database resource for the laboratory mouse. MGD provides essential integration of experimental knowledge for the mouse system with information annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genotype (sequence) through phenotype information, including highly detailed reports about genes and gene products. Primary foci of integration are through representations of relationships among genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent improvements in MGD discussed here include the enhancement of phenotype resources, the re-development of the International Mouse Strain Resource, IMSR, the update of mammalian orthology datasets and the electronic publication of classic books in mouse genetics.
Subject(s)
Databases, Genetic , Genomics , Mice/genetics , Animals , Genes , Genome , Genotype , Internet , Mice, Mutant Strains , Phenotype , Systems Integration , User-Computer InterfaceABSTRACT
Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.
Subject(s)
DNA, Complementary/genetics , Genomics , Mice/genetics , Transcription, Genetic/genetics , Alternative Splicing/genetics , Amino Acid Motifs , Animals , Chromosomes, Mammalian/genetics , Cloning, Molecular , Databases, Genetic , Expressed Sequence Tags , Genes/genetics , Genomics/methods , Humans , Membrane Proteins/genetics , Physical Chromosome Mapping , Protein Structure, Tertiary , Proteome/chemistry , Proteome/genetics , RNA, Antisense/genetics , RNA, Messenger/analysis , RNA, Messenger/genetics , RNA, Untranslated/analysis , RNA, Untranslated/genetics , Transcription Initiation SiteABSTRACT
SUMMARY: A single gene can generate multiple transcribed gene products. An extensive list of alternatively transcribed mouse genes has been generated, and is publicly available from http://www.informatics.jax.org/report.html. CONTACT: mgi-help@informatics.jax.org
