Genome and annotation data


Genome sequences

Os-Nipponbare-Reference-IRGSP-1.0

Genome sequence of the aus rice cultivar 'Kasalath'. (Sakai et al., 2014)

  • Genome assemblies
    [DOWNLOAD] (gz file, 199MB)

Gene annotation:

version

Gene set (genes supported by FL-cDNAs, ESTs or proteins)

  • Gene structure and function information in GFF format.
    [DOWNLOAD] (gz file, 15MB)
  • Gene structure (only exon) information in GTF format.
    [DOWNLOAD] (gz file, 2.1MB)
  • Gene annotation information in tab-delimited text format.
    [DOWNLOAD] (gz file, 2.8MB)
  • Gene sequences (CDS + UTRs + introns) in FASTA format.
    [DOWNLOAD] (gz file, 39MB)
  • Transcript sequences (CDS + UTRs) in FASTA format.
    [DOWNLOAD] (gz file, 21MB)
  • CDS sequences in FASTA format.
    [DOWNLOAD] (gz file, 12MB)
  • Protein sequences (translated CDSs) in FASTA format.
    [DOWNLOAD] (gz file, 7.7MB)
  • 1 kb upstream sequences of genes in FASTA format.
    [DOWNLOAD] (gz file, 13MB)
  • 2 kb upstream sequences of genes in FASTA format.
    [DOWNLOAD] (gz file, 26MB)
  • 3 kb upstream sequences of genes in FASTA format.
    [DOWNLOAD] (gz file, 39MB)
  • 1 kb downstream sequences of genes in FASTA format.
    [DOWNLOAD] (gz file, 13MB)
  • 2 kb downstream sequences of genes in FASTA format.
    [DOWNLOAD] (gz file, 26MB)
  • 3 kb downstream sequences of genes in FASTA format.
    [DOWNLOAD] (gz file, 38MB)

Gene set (computationally predicted genes)

  • Gene structure information in GFF format.
    [DOWNLOAD] (gz file, 805KB)
  • Gene structure information (only exon) in GTF format.
    [DOWNLOAD] (gz file, 207KB)
  • Gene annotation information in tab-delimited text format.
    [DOWNLOAD] (gz file, 63KB)
  • CDS sequences in FASTA format.
    [DOWNLOAD] (fasta file, 4.4MB)
  • Protein sequences (translated CDSs) in FASTA format.
    [DOWNLOAD] (fasta file, 1.5MB)

ID converter

  • Table of RAP and MSU's LOC_Os IDs.
    [DOWNLOAD] (gz file, 315KB)

Misc

  • rRNA and tRNA genes predicted on the Os-Nipponbare-Reference-IRGSP-1.0 assembly.
    [DOWNLOAD] (gz file, 18KB)
  • Table of transcript-IDs and corresponding accession number and species name of transcript evidences as of Apr 11, 2012.
    [DOWNLOAD] (gz file, 332KB)
  • Vegetative and reproductive stage specific sRNAs detected by Meng et al. of Hangzhou Normal University.
    [DOWNLOAD] (zip file, 7.7MB)
  • Repeat information, in GFF format, detected by Censor with MIPS and MSU repeat data on the Os-Nipponbare-Reference-IRGSP-1.0 assembly.
    [DOWNLOAD] (gz file, 4.4MB)
  • Organelle gene structure and function information in GFF format.
    [DOWNLOAD] (gff file, 171KB)
  • Organelle genome sequences in FASTA format.
    [DOWNLOAD] (fasta file, 635KB)

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