|REG Octamer (All REG List)
|GO Slim form UniProt KB
|Tissue of references form UniProt KB
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
-Genome sequence and annotation from
-659 LDSS-positive octamer elements identified by our analysis
Yamamoto et al, BMC Genomics 8: 67, 2007
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analysis (unpublished data).
Source tissues of RNA are green and
etiolated seedlings, roots, flowers, flower buds, stems, and cauline
-Selected 62,108 fl-cDNA sequences from
for additional TSS information
-Additional 34 million TSS tags (unpublished data).
Rice (Oriza sativa)
-Genome sequence and annotation from RAP2
-Selected 17,286 fl-cDNA sequences from
for TSS information
-660 LDSS-positive octamer elements identified by our analysis
et al, BMC Genomics 8: 67, 2007
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 Tomoaki Nishiyama (Kanazawa Univ) (unpublished data)
-198 LDSS-positive octamer elements identified by our analysis (unpublished data)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)
-Genome sequence and annotation (v 3.1) from JGI(###)
-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
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Yoshiharu Y Yamamoto
Faculty of Applied Biological Sciences, Gifu University
Yanagido 1-1, Gifu City, Gifu 501-1193, Japan
Graduate School of Life and Environmental Sciences, Kyoto Prefectural University
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.