- Presentation slides for the DB Workshop in the 63rd JSPP meeting are now available on the "Publications" page.
- We have updated CGSNL annotation and manual curation data (see update_2022-03-11.txt).
- We have started to provide the new user interface of locus/transcript annotation page (RAP-DB beta). Please click the banner at the top of the current annotation pages to see it (e.g. Os01g0911700, Os01t0911700-01).
- Transcriptome information previously provided from TENOR, RiceXPro and RiceFREND has been integrated into RAP-DB beta. In addition, publicly available RNA-Seq data of 565 experiments can be viewed. See the "Expression (TENOR) " section of transcript annotation page and the "Expression (RiceXpro)" and "CoExp Network" section of locus page in RAP-DB beta (e.g. Os06t0133000-01, Os06g0133000). RNA-Seq data is also available in JBrowse.
- Genome-wide variation data among 685 rice varieties is available in the latest version of TASUKE+ (Browser > TASUKE+ (685 varieties)).
- The list of "Agronomically important genes" has been updated (Documents > Agri. Genes). In addition, we have started to provide known functional alleles and mutations for the agronomically important genes (see the "Diversity" section of transcript annotation pages in RAP-DB beta, e.g., Os05t0158500-01).
- We have updated CGSNL annotation and manual curation data (see update_2021-11-11.txt).
- New track for IsoSeq was added to JBrowse and GBrowse.
- We have updated CGSNL annotation and manual curation data (see update_2021-05-10.txt).
- Gene expression profiles and co-expression networks in RiceXPro and RiceFREND can now be displayed in the “Expression” and “CoExp Network” tabs for each transcript (e.g. Os09t0565200-02).
- Gene annotations of the rice SDRLK gene subfamily have been updated based on the information reported in Naithani et al. 2021.
- We have updated CGSNL annotation and manual curation data (see update_2020-12-02.txt).
- “FAQ” is now available. (Documents > FAQ)
- We have updated CGSNL annotation and manual curation data (see update_2020-09-09.txt).
- "Experimentally confirmed subcellular location" was added to the “DB references” tab in annotation pages.
- A search by Transcript evidence, Literature PMID or Oryzabase ID was newly allowed in the "Advanced keyword search”.
- The list of "Agronomically important genes" has been published (Documents > Agri. Genes).
- Genome-wide variation data among >500 rice accessions is available in TASUKE+ (Browser > TASUKE).
- Gene annotation data has been updated (see update_2019-08-29.txt).
- Genotype data (SNPs/InDels called against the Nipponbare IRGSP-1.0 reference genome) for 333 rice varieties are available in the TASUKE multiple genome browser. User can access to the TASUKE from top navigation menu (Browser->TASUKE) and each transcript view page.
- We have updated CGSNL annotation and manual curation data (see update_2017-08-04.txt).
- miRNA data from miRBase and FST data of the Taiwan Rice Insertional Mutant (TRIM) have been updated.
- We are pleased to announce that RAP-DB has been reopened. We apologize for a long period of maintenance. Please note that RAP-DB legacy site (http://rapdblegacy.dna.affrc.go.jp) has been closed and integrated into the current version. Users may want to refer to the previous data on GBrowse by selecting from the 'Data Source' pull-down menu, or download the data listed at the bottom of the 'Download' page.
- We have updated CGSNL annotation and corrected the annotation of three genes (see update_2014-06-25.txt).
- Kasalath chromosome sequences in separate FASTA files have been added to the download data.
- RAP-DB has reopened with a new design!
- We have updated CGSNL annotation and manual curation data (see update_2014-03-05.txt).
- Chromosome sequences of the aus rice cultivar 'Kasalath' are available at Download site.
- Coordinates of miRNAs obtained from miRBase database are shown in the new track, "miRBase" in "RNAs" category.
- Alignments of the Illumina short-reads of Koshihikari genome are now available on Short-read Assembly Browser.
- We have updated CGSNL annotation and manual curation data (see update_2012-09-21.txt).
- New track for vegetative and reproductive stage specific sRNAs was added. The data was provided by Meng et al. of Hangzhou Normal University and is available on the download site.
- A new track for MSU gene annotation (MSU Osa1 Rice Gene Models) was added to GBrowse.
- We have updated the Minimum Tiling Path information in which a BAC clone (OSJNBb0018L01) was assigned a new accession number (AP011111.1).
- Unanchored sequences have been updated. The sequence errors were corrected by making use of next generation sequencing data. Through the correction procedure, three clones, AP008225.1 (OSJNOa109J19), AP008248.2 (B1326C05), and AP009051.1 (OSJNOa063K24), were discarded.
- New tool, "Build5 -> IRGSP-1.0 History (List)", is now available. Users can refer to the full list of change history showing whether exon/intron structure or sequences changed or not between Build5 and IRGSP-1.0 assemblies.
- New tracks, "Minimal Tiling Path" and "Centromere", have been added to GBrowse.
- New tool, "Build5 -> IRGSP-1.0 History (Search)", is now available. Users can search
with Os-ID and check whether exon/intron structure or sequences changed or
not between Build5 and IRGSP-1.0 assemblies.
- Sequence files for download were updated. Locus ID was added to the header line (>Osxxtxxxxxxx-xx|Osxxgxxxxxxx [Description]).
- Table of transcript-IDs and corresponding accession number and species name of transcript evidences is available on "Download" site (IRGSP-1.0_transcript-evidence_2012-04-11.txt.gz).
- New tracks for EST mapping data, "ESTs (Oryza)" and "ESTs (Other Poaceae)",
were added to GBrowse.
- List of RAP Os-IDs and corresponding MSU's LOC_Os-IDs is available on "Download" site (RAP-MSU.txt.gz).
- "BLAT" is now available.
- "Batch Retrieval" is now available.
- "ID Converter" is now available.
- Annotation data has been updated. Manually curated annotation information was added to 97 genes (105 transcripts). In addition, we corrected some errors including ORF mis-prediction and incorrect locus coordinates, and discarded five loci (see update_2012-03-15.txt).
- A new track for SSR sequences is available.
- New tracks for flanking sequence tag (FST) sequences from eight sources were added to GBrowse.
- Short-read Assembly Browser has been opened. New track for Illumina sequences of Guangluai-4 was added to GBrowse and links to the Short-read Assembly Browser.
- BLAST search is now available.
- GFF & sequence files of gene sets were updated.
- New tracks for OMAP BAC-end sequences were added to GBrowse.
- RNA-seq reads from 20 abiotic stress conditions and 7 tissues were mapped to the Os-Nipponbare-Reference-IRGSP-1.0.
- Here we provide a beta version of our updated annotation using the Os-Nipponbare-Reference-IRGSP-1.0 (IRGSP-1.0), a new genome assembly constructed as a joint collaboration of RAP and the MSU Rice Genome Annotation Project. The IRGSP sequences were re-examined using ~44X coverage sequence reads obtained by next-generation sequencers, so that many sequencing errors have been thoroughly corrected. In the present era of massive genome sequencing, the high-quality reference sequence of the rice genome will be more valuable to meet the demands of biodiversity studies and to enhance our understanding of major cereal crops.