Ppdb: plant promoter database version 3.0

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Abstract: ppdb (http://ppdb.agr.gifu-u.ac.jp) is a plant promoter database that provides information on transcription start sites (TSSs), core promoter structure (TATA boxes, Initiators, Y Patches, GA and CA elements) and regulatory element groups (REGs) as putative and comprehensive transcriptional regulatory elements. Since the last report in this journal, the database has been updated in three areas to version 3.0. First, new genomes have been included in the database, and now ppdb provides information on Arabidopsis thaliana, rice, Physcomitrella patens and poplar. Second, new TSS tag data (34 million) from A. thaliana, determined by a high throughput sequencer, has been added to give a ∼200-fold increase in TSS data compared with version 1.0. This results in a much higher coverage of ∼27 000 A. thaliana genes and finer positioning of promoters even for genes with low expression levels. Third, microarray data-based predictions have been appended as REG annotations which inform their putative physiological roles

Standort
Deutsche Nationalbibliothek Frankfurt am Main
Umfang
Online-Ressource
Sprache
Englisch
Anmerkungen
Nucleic acids research. - 42, D1 (2014) , D1188-D1192, ISSN: 0305-1048

Klassifikation
Biowissenschaften, Biologie

Ereignis
Veröffentlichung
(wo)
Freiburg
(wer)
Universität
(wann)
2019
Urheber
Hieno, Ayaka
Naznin, Hushna Ara
Hyakumachi, Mitsuro
Sakurai, Tetsuya
Tokizawa, Mututomo
Koyama, Hiroyuki
Sato, Naoki
Nishiyama, Tomoaki
Hasebe, Mitsuyasu
Zimmer, Andreas D.
Lang, Daniel
Reski, Ralf
Rensing, Stefan A.
Obokata, Junichi
Yamamoto, Yoshiharu Y.
Beteiligte Personen und Organisationen
FRIAS School of Life Sciences - LifeNet

DOI
10.1093/nar/gkt1027
URN
urn:nbn:de:bsz:25-freidok-1225136
Rechteinformation
Open Access; Der Zugriff auf das Objekt ist unbeschränkt möglich.
Letzte Aktualisierung
08.08.2024, 16:44 MESZ

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Beteiligte

  • Hieno, Ayaka
  • Naznin, Hushna Ara
  • Hyakumachi, Mitsuro
  • Sakurai, Tetsuya
  • Tokizawa, Mututomo
  • Koyama, Hiroyuki
  • Sato, Naoki
  • Nishiyama, Tomoaki
  • Hasebe, Mitsuyasu
  • Zimmer, Andreas D.
  • Lang, Daniel
  • Reski, Ralf
  • Rensing, Stefan A.
  • Obokata, Junichi
  • Yamamoto, Yoshiharu Y.
  • FRIAS School of Life Sciences - LifeNet
  • Universität

Entstanden

  • 2019

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