MSU Rice Genome Annotation Project Release 7 (October 31, 2011)

The all.chr directory contains the sequence and other information files for each of the 12 pseudomolecules.  The
following file types are available:

all.locus_brief_info.7.0: This file lists the information about the chromosome, locus, model,
                 start, stop, orientation, model_locus, if the gene model protein related to transposon or
                 retro-transposon elements, if the model has expression support, is the model is the representative model, and the functional annotation.

                
all.cdna file:     nucleotide sequences of the gene model containing the untranslated region but no intron sequences for each of the 12 pseudomolecules, the Syngenta pseudomolecule and the unanchored BAC pseudomolecule.

all.cds file:      nucleotide sequence of the gene models for each of the 12 pseudomolecules (coding sequence only: i.e. intron-less and no untranslated region), the Syngenta pseudomolecule and the unanchored BAC pseudomolecule.

all.chrs.con file:     complete genome sequence for each of the 12 pseudomolecules
                 Please note that 1000 Ns have been inserted for each physical gap. Also, note that the sequence of
                 some BAC/PAC clones is unfinished and may contain other gaps denoted by a string of Ns.

all.con:  complete genome sequence for each of the 12 pseudomolecules, the Syngenta pseudomolecule and the unanchored BAC pseudomolecule.

all.pep file:      Amino acid sequences corresponding to gene models for each of the 12 pseudomolecules, the Syngenta pseudomolecule and the unanchored BAC pseudomolecule.

all.seq file:      Gene sequences, including exons, introns and upstream/downstream untranslated regions for each of the 12 pseudomolecules, the Syngenta pseudomolecule and the unanchored BAC pseudomolecule.


all.gff3 file:    Generic Feature Format version 3 (GFF3) for the MSU rice genome annotation. This file also includes the annotation for the Syngenta and unanchored BAC pseudomolecules.

all.pfam:          This file lists the Pfam domain matches for each of the 12 pseudomolecules, the Syngenta pseudomolecule and the unanchored BAC pseudomolecule.

all.interpro:      This file lists Interpro database matches for each of the 12 pseudomolecule, the Syngenta pseudomolecule and the unanchored BAC pseudomolecule.

all.GOSlim_assignment: Plant GOSlim associations for each gene model.

rice_r7_all_tiling_path.gff3: GFF3 of the BAC tiling path including the physical gaps.

Similar files are provided for each chromosome in the individual directories.


For the detailed gene nomenclature at MSU Rice Genome Annotation Project, please visit: http://rice.plantbiology.msu.edu/gene_nomenclature.shtml

For more details about the MSU Rice Genome Annotation Project pseudomolecules, please visit our web site at:
    http://rice.plantbiology.msu.edu/pseudomolecules/info.shtml

The main page for the MSU Rice Genome Annotation Project is :
    http://rice.plantbiology.msu.edu/

For questions about MSU rice genome related issues, please send e-mail to:
    rice@plantbiology.msu.edu

Researchers who wish to cite the MSU Rice Genome Annotation Project website are encouraged to refer to our recent publications:

    * Ouyang, S., Zhu, W., Hamilton, J., Lin H., Campbell, M., Childs, K., Thibaud-Nissen, F., Malek, R.L., Lee, Y., Zheng, L, Orvis, J., Haas, B., Wortman, J. and Buell, C.R. 2007. The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Research 35:D883-D887

    * Yuan, Q., Ouyang, S., Wang, A., Zhu, W., Maiti, R., Lin, H., Hamilton, J., Haas, B., Sultana, R., Cheung, F., Wortman, J., and Buell, C.R. 2005. The Institute for Genomic Research Osa1 Rice Genome Annotation Database. Plant Physiology 138: 18-26

Thank you for your interest in the MSU Rice Genome Annotation Project Resources.