UCSC Gene Predictions for mm9

Description

A set of genomic coordinate data for gene transcripts, and related annotations, for M. musculus. Coordinates are relative to the mm9 build. All coordinates are in nucleotides from the 5' end of the positive "+" strand. In the below, “gene” is synonymous with “spliced transcript”, so each row corresponds to a transcript variant with a particular TSS, TES, and exon configuration. A single coding start (cdsStart) and end (cdsEnd) are predicted for each gene/transcript.

Usage

data(geneMouse)

Format

A data frame with 49409 observations on the following 12 variables.

name

The name of the gene.

chrom

The name of the chromosome the gene is located on.

strand

The strand the gene is coded on, "+", or "-".

txStart

Transcription start site.

txEnd

Transcription stop site.

cdsStart

Start position of the coding sequence.

cdsEnd

End position of the coding sequence.

exonCount

The number of exons.

exonStarts

A comma separated list of the exon start positions.

exonEnds

A comma separated list of exon stop positions.

proteinID

An ID for the protein produced, missing values are coded as NA

.

alignID

Unique identifier of each gene and RNA alignment pair, apparently redundant with name.

Details

For genes coded on the negative strand the txStart is really the end, and similarly for the coding regions.

Source

This table was taken directly from the knownGene table in the UCSC database for mm9, see 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.

Examples

data(geneMouse)
str(geneMouse)