geneMouse          package:GenomicFeatures          R Documentation

_U_C_S_C _G_e_n_e _P_r_e_d_i_c_t_i_o_n_s _f_o_r _m_m_9

_D_e_s_c_r_i_p_t_i_o_n:

     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.

_U_s_a_g_e:

     data(geneMouse)

_F_o_r_m_a_t:

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

     '_n_a_m_e' The name of the gene.

     '_c_h_r_o_m' The name of the chromosome the gene is located on.

     '_s_t_r_a_n_d' The strand the gene is coded on, '"+"', or  '"-"'.

     '_t_x_S_t_a_r_t' Transcription start site.

     '_t_x_E_n_d' Transcription stop site.

     '_c_d_s_S_t_a_r_t' Start position of the coding sequence.

     '_c_d_s_E_n_d' End position of the coding sequence.

     '_e_x_o_n_C_o_u_n_t' The number of exons.

     '_e_x_o_n_S_t_a_r_t_s' A comma separated list of the exon start positions.

     '_e_x_o_n_E_n_d_s' A comma separated list of exon stop positions.

     '_p_r_o_t_e_i_n_I_D' An ID for the protein produced, missing values are
          coded as NA.

     '_a_l_i_g_n_I_D' Unique identifier of each gene and RNA alignment pair,
          apparently redundant with 'name'.

_D_e_t_a_i_l_s:

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

_S_o_u_r_c_e:

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

_E_x_a_m_p_l_e_s:

     data(geneMouse)
     str(geneMouse)

