MAIN


©1996-2019 All Rights Reserved. Online Journal of Bioinformatics . You may not store these pages in any form except for your own personal use. All other usage or distribution is illegal under international copyright treaties. Permission to use any of these pages in any other way besides the  before mentioned must be gained in writing from the publisher. This article is exclusively copyrighted in its entirety to OJB publications. This article may be copied once but may not be, reproduced or  re-transmitted without the express permission of the editors. This journal satisfies the refereeing requirements (DEST) for the Higher Education Research Data Collection (Australia). Linking:To link to this page or any pages linking to this page you must link directly to this page only here rather than put up your own page.


OJBTM
  
Online Journal of Bioinformatics© 

  

Volume 9 (2): 130-145, 2008.


In silico analysis of PCR amplified DOF (DNA binding with one finger) transcription factor domain

and cloned genes from cereals and millets

 

Kushwaha H, Gupta N, Singh VK, Kumar A, Yadav D.

 

Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar (UttaraKhand), India

 

ABSTRACT

 

Kushwaha H, Gupta N, Singh VK, Kumar A, Yadav D., In silico analysis of PCR amplified DOF (DNA binding with one finger) transcription factor domain and cloned genes from cereals and millets, On J Bioinform, 9 (2): 130, 2008. The PCR amplified DOF domain of different cereals and millets were gel eluted, sequenced and subjected to homology search, multiple sequence alignment, phylogenetic tree construction and motif analysis. The presence of four cysteine residues associated with a typical zinc like finger and a conserved motif with multilevel consensus sequence QPRHFCKSCQRYWTA was uniformly observed across different cereals and millets. The putative DOF genes of Eleusine coracana along with Oryza sativa, Triticum aestivum, Hordeum vulgare and Zea mays were PCR amplified, gel eluted, cloned and assigned accession numbers EU760631, EU586268, EU586269, EU586267 and EU586266 respectively after sequencing. The homology search confirmed their identity to PBF (Prolamin-box Binding Factor) DOF genes except for O. sativa. Multiple sequence alignment of these PBF DOF genes revealed the presence of conserved DOF domain with four cysteine residues in E. coracana while partial sequences were observed in other cloned genes. The presence of conserved motifs involved with regulation of seed storage protein genes further confirmed their identity to PBF DOF genes. Phylogenetic tree constructed based on protein sequences of cloned DOF genes resulted in distinct clusters for PBF DOF genes of monocots and dicots.

 

Keywords: DOF, Transcription factor, Cereals, Millets, PBF, Multiple sequence alignment, Motif, Domain.


MAIN

FULL-TEXT(SUBSCRIPTION OR PURCHASE TITLE $25USD)