Open Access Research article

Patterns and evolution of ACGT repeat cis-element landscape across four plant genomes

Rajesh Mehrotra*, Sachin Sethi, Ipshita Zutshi, Purva Bhalothia and Sandhya Mehrotra

Author Affiliations

Biological Sciences Department, Birla Institute of Technology and Science, Pilani, RJ, India

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BMC Genomics 2013, 14:203  doi:10.1186/1471-2164-14-203

Published: 25 March 2013

Additional files

Additional file 1: Table S2:

Frequency analysis of control cis-elements across four plant species. A comparison of the frequency of occurrence of each of the 4 palindromic and 4 non-palindromic control elements used for N=(0-30) in -1000 bp regions of Arabidopsis, Soybean, Sorghum and Rice.

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Additional file 2: Table S3:

Functional analysis of Arabidopsis and Rice genes containing ACGT cis-elements. The (A) total number of ACGT(N)ACGT (0<=N<=30) containing promoters in Arabidopsis that are also regulated by certain conditions, with a spacer-length wise frequency analysis, (B) likelihood of occurrence to contain ACGT(N)ACGT, calculated for each of these conditions, (C) identical analysis conducted for each of the eight control elements used previously (Additional file 1), (D) comparison of the likelihoods for ACGT and each of the controls, with conditions highlighted in green being those for which the likelihood of ACGT is significant in the Grubbs’ test for outliers (E) total number of ACGT(N)ACGT (0<=N<=30) containing promoters in Rice that are up-regulated by salt and drought stress, with a spacer length wise analysis and a similar analysis for control elements and (F) comparison of the likelihoods for ACGT and for each of the controls in Rice with both conditions emerging significant in Grubbs’ test for outliers.

Format: XLSX Size: 189KB Download file

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