PlantPromoterDB

Keyword Search

Index of Genes

Organism	Arabidopsis thaliana	Oryza sativa	Physcomitrella patens
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	-

2009/11/15~23 Service accidentally stopped. Sorry for inconvenience. 2009/6/6 ~ 10, 6/12~15 Service accidentally stopped. Sorry for inconvenience. 2008/12/10 00:35PM - 2008/12/12 00:30PM Service accidentally stopped. Sorry for inconvenience. 2008/12/04 8:34AM - 0:28PM Service accidentally stopped. Sorry for inconvenience. 2008/11/10 Service will stop due to construction in the university 08/11/16 8AM - 6PM 2008/06/24 Service will stop due to construction in the university 08/06/29 9AM - 5PM 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 2008/05/07 Service will stop due to network construction in the university: 08/05/10 9AM - 08/05/11 5PM 08/05/24 9AM - 08/05/25 7PM 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, a plant promoter database
Yamamoto YY, Obokata J. (2008) Nucleic Acids Res 36, D977-D981

Arabidopsis thaliana

-Genome sequence and annotation from TAIR6
-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)
-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

Rice (Oriza sativa)

-Genome sequence and annotation from RAP-DB
-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)

Physcomitrella patens

-Genome sequence and annotation (v 1.1) from JGI
-5’SAGE 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)

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
Junichi Obokata
Center for Gene Research, Nagoya University
Nagoya 464-8602, Japan
yyy<at>gifu-u.ac.jp

Acknowledgements

We would like to thank Dr. Naoki Sato (University of Tokyo) 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, and also Dr. Stefan Rensing and Dr. Daniel Lang (University of Freiburg) for providing LTR information of Physcomitrella patens.

This work is supported in part by Grant-in-Aid for Scientific Research on Priority Areas "Comparative Genomics" from MEXT.

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