Keyword Search

Select organism species.

Arabidopsis thaliana Oryza sativa
Physcomitrella patens Poplar

Input a gene name or a keyword to search.

ex) AT1G67090, fgenesh1_kg.scaffold_1000002, Rubisco, POPTR_1006s00200.1  

Homologue Gene Search

Input a gene ID (Locus or Gene Model).

ex) AT1G67090.1, Os01g0974600 , AK101721 

Index of Genes

Organism	Arabidopsis thaliana	Oryza sativa	Physcomitrella patens	Chlamydomonas reinhardtii	Poplar
REG Octamer (All REG List)	308	242	23	-	-
PPDB Motif	12	12	-	-	-
PLACE Motif	21	5	-	-	-
GO Slim form UniProt KB	64	64	-	-	-
Tissue of references form UniProt KB	88	69	-	-	-

Basis of this database

News

2020/05/22 InternetExplorer (~v10) is not accepted. Please use other browsers. 2018/9/12 Survice will stop on Sept 30 due to planned power cut. 2018/9/12 Survice stopped from Sept 9 to 12 due to network construction of the university. 2015/09/12 Data server had stopped for maintenance from 2015/08/28 to 2015/09/12. We are sorry for inconvenience. 2014/01/01 An article discribing ppdb 3.0 has been published: Hieno et al Nucleic Acids Res 42: D1188-1192, 2014. 2013/06/05 ppdb ver 3.0 release. Previdous version is available at http://ppdb.agr.gifu-u.ac.jp/ppdb2.1/ major change. 1) Arabidopsis: 34 millions of TSS tag info are included. Now 25k genes have their TSS info. 2) Arabidopsis: New annotations of 53 REGs. Predicted phytohormone responses are now included (Yamamoto et al, BMC Plant Biol, 11: 39, 2011). 3) Poplar genome is included. 2013/02/14 Email address changed to ppdb@gifu-u.ac.jp 2011/03/14 Address changed to http://ppdb.agr.gifu-u.ac.jp 2010/11/09 ppdb ver 2.1 release. change. 1) new annotation (Arabidopsis: TAIR9, rice: RAP2, Physco: ver 1.6), 2) Arabidopsis & rice: new core elements (Inr & GA) included, 3) Data link to TAIR & NCBI. 2008/06/04 Rice gene name translation from TIGR ID to RAP ID: Please check Oryzabase http://www.shigen.nig.ac.jp/rice/oryzabase/genes/genesTop.jsp 2008/04/23 ppdb ver 2.0 release (previous version is available at http://ppdb2.gene.nagoya-u.ac.jp) added feature: Physcomitrella data, promoter comparison page, GO search page Notes on Physco gene models. Gene models are not currently associated with biological description, so key word search is not available. Please refer other web sites (JGI: http'//genome.jgi.org/Phypa1_1/, PHYSCObase: http://moss.nibb.ac.jp/, or COSMOSS: http://www.cosmoss.org/) to know gene models of your interest. Or if you know Gene Model of Arabidopsis or rice homologue, you can use the Promoter Comparison page for selecting Physco genes. Currently, considerable Physco gene models appear to be mapped inappropriately. This problem would be fixed after update of Physco annotation at JGI. 2007/06/27 ppdb ver 1.0 release Arabidopsis & rice data

Reference

ppdb: Plant Promoter Database vwer 3.0
Hieno A, Naznin HA, Hyakumachi M, Sakurai T, Tokizawa M, Koyama H, Sato N, Nishiyama T, Hasebe M, Zimmer AD, Dang D, Reski R, Rensing S, Obokata J, Yamamoto YY. (2014) Nucleic Acids Res 42, D1188-D1192
ppdb, a plant promoter database
Yamamoto YY, Obokata J. (2008) Nucleic Acids Res 36, D977-D981

Arabidopsis thaliana

-Genome sequence and annotation from TAIR9
-659 LDSS-positive octamer elements identified by our analysis
     Yamamoto et al, BMC Genomics 8: 67, 2007
-PLACE   motifs that match LDSS-positive REG elements (only matched motifs)
-Annotation to 53 REGs with predicted phytohormone responses
     Yamamoto et al (2011) BMC Plant Biol 11: 39.
-158,237 TSS tags containing Cap-Signature determined by our CT-MPSS analysis.
     Yamamoto et al, Plant J 60: 350-362, 2009
    Source tissues of RNA are green and etiolated seedlings, roots, flowers, flower buds, stems, and cauline leaves.
-Selected 62,108 fl-cDNA sequences from RARGE for additional TSS information 
-Additional 34 million TSS tags .
     Tokizawa et al, Plant J 90: 587-605, 2017

Rice (Oriza sativa)

-Genome sequence and annotation from RAP2
-Selected 17,286 fl-cDNA sequences from KOME for TSS information
-660 LDSS-positive octamer elements identified by our analysis
     Yamamoto et al, BMC Genomics 8: 67, 2007
-PLACE  motifs that- match LDSS-positive REG elements (only matched motifs)

Moss (Physcomitrella patens)

-Genome sequence and annotation (v 1.1) from JGI
-5A1C7SAGE tag data (1,122,382 tags in 7 libraries) from Dr. Mitsuyasu Hasebe (NIBB) and Dr. Tomoaki Nishiyama (Kanazawa Univ) (unpublished data)
-198 LDSS-positive octamer elements identified by our analysis (unpublished data)

Poplar (Populus trichocarpa)

-Genome sequence and annotation from JGI
-FL-cDNA info from GenBank (BP921855-937111(15,256 clones) & DB874873-910976 (36,103 clones))
-LDSS elements from Arabidopsis (core elements & REG)

Chlamydomonas reinhardtii

-Genome sequence and annotation (v 3.1) from JGI(###)

Promoter Comparison

-Ortholog data from Gclust established by Dr. Naoki Sato (Tokyo Univ).

memo

TPM: Tag Per Million. an indicator of relative expression in the MPSS tag library.

Peak TSS: the highest TSS in a TSS cluster

REG, TATA, Y, Inr: detected according to the position relative to a Peak TSS. REG: -300 to -40, TATA: -45 to -18, Y: -50 to +50. Global detection without any positional restriction can be achieved by selecting the ALL switch (ALL <-> Reliable).

Genes without any TSS in the database do not show any information unless selecting ALL. REGs appeared after selecting ALL are not linked. For more information, please consult the ALL REG List page (link in this page).

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This database is run by

Yoshiharu Y Yamamoto
Faculty of Applied Biological Sciences, Gifu University
Yanagido 1-1, Gifu City, Gifu 501-1193, Japan
yamamoto.yoshiharu.h5<at>f.gifu-u.ac.jp

Acknowledgements

We would like to thank Dr. Naoki Sato (Tokyo University) for supporting development of the Promoter Comparison pages, Dr. Mitsuyasu Hasebe (NIBB) and Dr. Tomoaki Nishiyama (Kanazawa University) for providing a large set of 5' SAGE data of Physcomitrella patens.

This work is in part supported by Grant-in-Aids for Scientific Research on Priority Areas "Comparative Genomics" and Publication of Scientific Research Results from Ministry of Education, Culture, Sports, Science and Technology, and by Gifu University.