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Title: | Genome-wide Identification and Characterization of Transcription Factor Binding Motifs of NBS-LRR Genes in Rice and Arabidopsis |
Other Titles: | Not Available |
Authors: | Ramkumar G, Madhav MS, Biswal AK, Rama Devi SJS, Sakthivel K, Madhan Mohan K, Umakanth B, Mangrauthi SK, Sundaram RM and Viraktamath BC |
ICAR Data Use Licennce: | http://krishi.icar.gov.in/PDF/ICAR_Data_Use_Licence.pdf |
Author's Affiliated institute: | ICAR::Indian Institute of Rice Research |
Published/ Complete Date: | 2014-02-26 |
Project Code: | Not Available |
Keywords: | NBS-LRR transcription factor binding motifs cis-acting elements strong motif motif modules positional conservation |
Publisher: | Not Available |
Citation: | Ramkumar G, Madhav MS, Biswal AK, Rama Devi SJS, Sakthivel K, Madhan Mohan K, Umakanth B, Mangrauthi SK, Sundaram RM and Viraktamath BC (2014). Genome-wide Identification and Characterization of Transcription Factor Binding Motifs of NBS-LRR Genes in Rice and Arabidopsis. Journal of Genomes and Exomes 3: 1-9.http://dx.doi.org/10.4137/JGE.S13945 |
Series/Report no.: | Not Available; |
Abstract/Description: | Nucleotide binding site leucine rich repeat (NBS-LRR) gene encoding proteins are the major biotic stress resistance genes of rice and Arabidopsis thaliana. Upstream sequences of 206 entire NBS-LRR genes of Arabidopsis and 120 genes of rice were analyzed with three highly reliable motif prediction tools for enhanced accuracy of prediction and characterization of potential transcription factor binding motifs (TFBMs). A total of 36 and 30 novel, strong TFBMs were discovered from NBS-LRR genes of rice and A. thaliana, respectively. All the motifs identified in these sequences were analyzed for their positional conservation and the possible motif network associations were also identified. Further, the probability of the presence of motifs in these NBS-LRR genes were validated and statistically tested. Although Arabidopsis NBS-LRR sequences showed 76.3% similarity with rice sequences at motif level, the analysis revealed that rice sequences have many unique TFBMs and are more evolved in gene expression mechanisms. The study also provided a list of novel candidate motifs for these genes, which will be a good resource for experimental validation. A novel strategy of prediction of gene expression based on motif arrangement was also demonstrated in this study. The findings of this study, such as the motifs’ positional conservation, architecture, etc. offered new biological insights into the role of TFBMs in the regulation of resistance genes. |
Description: | Not Available |
ISSN: | Not Available |
Type(s) of content: | Research Paper |
Sponsors: | Not Available |
Language: | English |
Name of Journal: | Journal of Genomes and Exomes |
NAAS Rating: | Not Available |
Impact Factor: | 0 |
Volume No.: | 3 |
Page Number: | 1-9 |
Name of the Division/Regional Station: | Not Available |
Source, DOI or any other URL: | http://dx.doi.org/10.4137/JGE.S13945 |
URI: | http://krishi.icar.gov.in/jspui/handle/123456789/53165 |
Appears in Collections: | CS-IIRR-Publication |
Files in This Item:
File | Description | Size | Format | |
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f_4090-JGE-Genome-wide-Identification-and-Characterization-of-Transcription-Fact.pdf_5488.pdf | 1.69 MB | Adobe PDF | View/Open |
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