©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.