2009
05/27/2009
A new track for RFLP and SSR markers was created. The data was placed in the downlaod page.
Pack-MULE data was updated, and Pack-MULE sequences without nested transposons are available at the download page.
05/01/2009
New annotation of IRGSP build 5 is available on RAP-DB Alpha Version. RAP-DB Alpha also displays genome-wide comparisons between japonica rice and indica/Sorghum. Please note that RAP-DB Alpha is provisional, and will frequently be changed.
Gene family data were updated, and can be downloaded.
04/03/2009
We added Pack-MULEs in the Transposable Elements track. The data set was provided by Drs. Hanada and Jiang. For details, see their paper published in Plant Cell.
02/10/2009
Gene family information is now available! Descriptions of gene families were added to the detailed viewer.
We fixed some problems about O. rufipogon cDNAs that were accidentally missing in our dataset.
01/08/2009
New tracks for indica & O. rufipogon FLcDNAs, and Sorghum genes were added in GBrowse.
2008
12/25/2008
IRGSP genome build 5 has just been released. A repeat-masked version is available from our download page.
12/02/2008
A new track for the PLUG data on the IRGSP build 4.0 assembly was added to GBrowse.
11/05/2008
IRGSP genome build 5 will be released this year.
10/22/2008
Organelle genome data were added.
08/18/2008
The POSTECH FST data were updated.
06/04/2008
The track of the curated RetrOryza data was reorganized and updated.
05/12/2008
A conserved domain database 'SALAD' has been released! Domain organizations and dendrograms are displayed. At the moment, some contents are written in Japanese. Their English versions will be coming soon.
01/25/2008
The FASTA files of "All sequences" on the Download page contained sequences without evidence of expression. The sequences were removed from the files.
2007
12/17/2007
RAP-DB paper was published in Nucleic Acids Research Database Issue.
11/22/2007
The GFF file of the Download page contained erroneous functional descriptions of unrelated proteins. This problem was fixed.
10/17/2007
Genome assembly information was added in the SITE CONTENTS with details on the positions of BAC/PAC clones and gaps in the Download page. The RAP-DB statistics page was updated.
GFF files for RNA genes (rRNA and tRNA) and for each chromosomes can be accessed from the Download page.
ID converter system has been upgraded and includes Os IDs, LOC_Os IDs, and UniProtKB/Swiss-Prot accessions and entries. Any ID or entry can be used as query.
10/09/2007
An overview of RAP-DB statistics was added.
10/01/2007
The interface of the BLAST search service was improved. Mapping of your DNA sequence can be viewed by GBrowse.
09/14/2007
The top page design was changed.
Our new annotation (RAP2) on the IRGSP genome assembly build 4 was released. This release includes the positions of BAC/PAC clones, FSTs determined by 10 groups, MPSS data, miRNA predictions, transposable elements, and NCBI's annotation.
The keyword search system was upgraded. Enter your keyword(s) in the 'Search for' window on the upper right corner and click on 'GO'! In addition, a search engine for IE7/Fx2 is availabe. The gene identifiers of RAP and TIGR can be converted by the 'ID Converter' function.
The results of BLAT can be displayed directly on GBrowse. Click on '[viewer]' and see how your sequence was mapped to the genome.
03/06/2007
The track for the RetrOryza data on the IRGSP build 4.0 assembly was added to GBrowse.
Flanking sequence tags (FSTs) of Ds and T-DNA insertion mutants were added to GBrowse for the IRGSP build 4.0 assembly. The FSTs were determined and released by the following research groups: CGT, UCD, GSNU, NUS, CSIRO, TRIM, RMD and Genoplante.
02/27/2007
The track for TIGR transcripts (Release 5) on the IRGSP build 3 and 4.0 assembly have been released.
02/01/2007
The link to the UniProt from the GBrowse detail viewer has been set.
RAP1 paper was published in Genome Research (Freely available from [Genome Res]).
01/13-17/2007
The RAP-DB was demonstrated and introduced in the poster session in the Plant and Animal Genome XV Conference at San Diego, CA.
2006
08/30/2006
The track for the positions of the flanking sequences of the T-DNA inserted regions (by POSTECH, Korea) on the IRGSP build 4.0 assembly have been released. Please select build 4.0 from the schematic view of chromosomes or the 'Data Source' pull-down menu in GBrowse.
Two new GFF files, predicted_loci.gff.gz and predicted_transcript.gff.gz are now included in the GFF_forDL directory. It is available from Download site.
08/08/2006
The table for OsIDs corresponding to the TIGR LOC_OsIDs on the IRGSP genome sequence (build 3) is now available from Download site.
07/31/2006
The RAP-DB was presented in the poster session of the SwissProt20th in Fortaleza, Brazil. For details, please visit SP20's web site.
07/07/2006
We are pleased to open a mirror server at NIAS to the public. The URLs are listed on the top page.
06/22/2006
The tracks for the OMAP BAC end sequences (BESs) of 13 Oryza species on the IRGSP build 4.0 assembly have been released. Please select build 4.0 from the schematic view of chromosomes or the 'Data Source' pull-down menu in GBrowse.
03/08/2006
The track for TIGR transcripts (Release 4) on the IRGSP build 4.0 assembly have been released. Please select build 4.0 from the schematic view of chromosomes or the 'Data Source' pull-down menu in GBrowse.
02/28/2006
The track for TIGR transcripts on the IRGSP build 3 assembly have been updated with TIGR transcripts (Release 4). Please select build 3 from the schematic view of chromosomes or the 'Data Source' pull-down menu in GBrowse.
02/21/2006
The NCBI gene models on the IRGSP build 4.0 assembly have been released. Please select build 4.0 from the schematic view of chromosomes or the 'Data Source' pull-down menu in GBrowse.
01/13/2006
The RAP1 annotations on the IRGSP build 4.0 assembly have been released. Please select build 4.0 from the schematic view of chromosomes or the 'Data Source' pull-down menu in GBrowse.
2005
12/31/2005
The Nucleic Acids Research Database Issue with the RAP-DB article is now available.
12/27/2005
Some rows in the GBrowse annotation tables have been modified.
12/22/2005
The predicted loci have been added in GBrowse.
12/15/2005
The RAP-DB is now open to the public.
The gene IDs have been fixed based on the revised gene nomenclature for rice.