\name{geneMouse}
\Rdversion{1.1}
\alias{geneMouse}
\title{UCSC Gene Predictions for mm9}
\description{

Gene coordinates and annotations for M. musculus from UCSC. Coordinates are
relative to the mm9 build and are in nucleotides from the 5' end of the
positive (\code{"+"}) strand. They are always *one-based*, that is, the
coordinate of the first (or leftmost) nucleotide in the strand is 1.
Each \dQuote{gene}, or row in the dataset, corresponds to a unique combination
of transcript (TSS, TES and exons) and coding sequence (start and end).

}

\usage{geneMouse()}

\value{
  A data frame with 49409 observations on the following 12
  variables.
  \enumerate{
    \item \code{name}: The name of the gene.
    \item \code{chrom}: The name of the chromosome the gene is located on.
    \item \code{strand}: The strand the gene is coded on, \code{"+"}, or
      \code{"-"}.
    \item \code{txStart}: Transcription start site.
    \item \code{txEnd}: Transcription stop site.
    \item \code{cdsStart}: Start position of the coding sequence.
    \item \code{cdsEnd}: End position of the coding sequence.
    \item \code{exonCount}: The number of exons.
    \item \code{exonStarts}: A comma separated list of the exon start positions.
    \item \code{exonEnds}: A comma separated list of exon stop positions.
    \item \code{proteinID}: An ID for the protein produced, missing values
      are coded as NA.
    \item \code{alignID}: Unique identifier of each gene and RNA
      alignment pair, apparently redundant with \code{name}.
  }
}
\note{
For genes coded on the negative strand the \code{txStart} is really the end,
and similarly for the coding regions.
}

\source{
This table was obtained by downloading the following database file
from UCSC (on Sep 28, 2009):
  \url{http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/knownGene.txt.gz}
and by translating the start coordinates found in the file from
zero-based to one-based.

The knownGene.txt.gz file is a database dump containing the
UCSC track called "UCSC Genes" and described here:
  \url{http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=knownGene}

See \url{http://genome.ucsc.edu/cgi-bin/hgTables} and
Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D. The UCSC
Known Genes. Bioinformatics. 2006 May 1;22(9):1036-46.

All the annotations in this package are freely available for public use,
except for the Swiss-Prot/UniProt data in the knownGene table, which has
the following terms of use:
\preformatted{
UniProt copyright (c) 2002 - 2004 UniProt consortium

For non-commercial use all databases and documents in the UniProt FTP
directory may be copied and redistributed freely, without advance
permission, provided that this copyright statement is reproduced with
each copy.

For commercial use all databases and documents in the UniProt FTP
directory, except the files

ftp://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz

and

ftp://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/uniprot_sprot.xml.gz

may be copied and redistributed freely, without advance permission,
provided that this copyright statement is reproduced with each copy.

More information for commercial users can be found in:
http://www.expasy.org/announce/sp_98.html

From January 1, 2005, all databases and documents in the UniProt FTP
directory may be copied and redistributed freely by all entities,
without advance permission, provided that this copyright statement is
reproduced with each copy.
}
}
\examples{
genes <- geneMouse()
str(genes)
transcripts(genes)
}