The PlantProm DB: Recent updates

Ilham Shahmuradov*, Amina Abdulazimova, Farah Zaib Khan, Victor Solovyev, Nurmamed Mustafayev, Yagut Akbarova, Raheel Qamar, Jalal Aliyev

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

3 Scopus citations

Abstract

We present the second release of the Plant Prom DB (initially lunched in 2003), an annotated, non-redundant collection of proximal promoter sequences for RNA polymerase II (Pol II) with experimentally determined transcription start site(s) (TSS) from 86 plant species. It contains 576 entries including 150, 403 and 23 promoters of monocot, dicot and other plants genes, respectively. The database provides DNA sequences and nucleotide composition characteristics of the promoters upstream and downstream of TSS (-200:+51), taxonomic/promoter type classification of promoters and Nucleotide Frequency Matrices (NFMs) for important promoter elements such as TATA-box, INR-motif, Y-patch and DPE. We demonstrated a difference in general nucleotide composition of promoter sequences between monocots and dicots. The database also contains information on statistically significant motifs of known regulatory elements found in the described promoters. The Plant Prom DB is available at http://cub.comsats.edu. pk.

Original languageEnglish (US)
Title of host publicationProceedings - 2012 International Conference on Biomedical Engineering and Biotechnology, iCBEB 2012
Pages612-614
Number of pages3
DOIs
StatePublished - 2012
Externally publishedYes
Event2012 International Conference on Biomedical Engineering and Biotechnology, iCBEB 2012 - Macau, China
Duration: May 28 2012May 30 2012

Other

Other2012 International Conference on Biomedical Engineering and Biotechnology, iCBEB 2012
CountryChina
CityMacau
Period05/28/1205/30/12

Keywords

  • database
  • Nucleotide Frequency Matrices
  • promoter
  • RNA polymerase II

ASJC Scopus subject areas

  • Biotechnology
  • Biomedical Engineering

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