ppdb version

Keyword Search

Select organism species.

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



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 Tomoaki Nishiyama (Kanazawa Univ) (unpublished data)
-198 LDSS-positive octamer elements identified by our analysis (unpublished data)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).


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


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.

Copyright(c) 2007- ppdb Stirring Committee. All Rights Reserved.