What's New
12/Jul/2024
- We have updated CGSNL annotation and manual curation data (see update_2024-07-12.txt).
- QTL annotation in Q-TARO (QTL Annotation Rice Online database) is now available in the JBrowse ("Other rice annotations" -> "Q-TARO").
- We have updated CGSNL annotation and manual curation data (see update_2024-01-11.txt).
- TASUKE+ (685 varieties) has been updated to the latest version (TASUKE+ ver. 20231214).
- We have updated CGSNL annotation and manual curation data (see update_2023-09-07.txt).
- "Known functional alleles & mutations” data and RNA-Seq data have been updated.
- We have updated CGSNL annotation and manual curation data (see update_2023-03-15.txt).
- Protein alignments have been added in JBrowse.
- We have updated CGSNL annotation and manual curation data (see update_2022-09-01.txt).
- "ATAC-Seq", "ChIP-Seq" and "PLACE cis-regulatory elements" tracks were newly added in JBrowse.
- "Search and Retrieval", "ID Converter", "Agri. genes" and annotation pages have been updated.
- The list of “Curated genes” has been published (Documents > Curated genes).
- "Known functional alleles & mutations” data has been updated.
- 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.
- 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) ", "Expression (RiceXpro)" and "CoExp Network" section 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.
- 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”.
- We have updated CGSNL annotation and manual curation data (see update_2020-06-03.txt).
- We have updated CGSNL annotation and manual curation data (see update_2020-03-24.txt).
- We have updated CGSNL annotation and manual curation data (see update_2019-12-17.txt).
- "JBrowse" is now available. (Browser > JBrowse)
- 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).
- We have updated CGSNL annotation and manual curation data (see update_2019-06-26.txt).
- We have updated CGSNL annotation and manual curation data (see update_2019-03-22.txt).
- We have updated CGSNL annotation and manual curation data (see update_2018-11-26.txt).
- We have updated CGSNL annotation and manual curation data (see update_2018-03-29.txt).
- We’ve just started Twitter. Please follow @rapdb.
- 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 have updated CGSNL annotation and manual curation data (see update_2017-04-14.txt).
- We have updated CGSNL annotation and manual curation data (see update_2016-08-05.txt).
- We have updated CGSNL annotation and manual curation data (see update_2016-03-09.txt).
- Link to the TENOR database (Kawahara et al. 2016) was added to the "DB references" tab in the Gene details view.
- 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 manual curation data (see update_2015-03-31.txt).
- 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.
- We have updated the annotation (see update_2013-04-24.txt).
- We have updated CGSNL annotation and manual curation data (see update_2013-03-19.txt).
- New RAP-DB and related papers have been published!! When using the data obtained from the RAP-DB, kindly acknowledge the RAP project contribution by citing the following papers:
- 1. Sakai, H., et al. "Rice Annotation Project Database (RAP-DB): An integrative and interactive database for rice genomics"
- 2. Kawahara, Y., et al. "Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data"
The Rice Annotation Project (RAP)
was conceptualized in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project with the aim of providing the scientific community with an accurate and timely annotation of the rice genome sequence. One of the major objectives of this project is to facilitate a comprehensive analysis of the genome structure and function of rice on the basis of the annotation.
Here we provide 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.
