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Table 2 Hexamers with potential regulatory function as evidenced by increased conservation, positional preferences, and co-expression of genes harboring respective motifs in their first introns. ‘Cohen’s d correlation’ is the effect size of difference in the distribution of correlation coefficients between the expression levels of genes harboring the respective motif relative to a gene set containing frequency-matched random hexamer motifs across all experimental conditions present in the expression dataset. ‘Cohen’s d expression level’ refers to the effect size related to expression level of genes containing the respective motif in the first intron relative to all other intron-harboring genes. Listed also are the numbers of genes, in which the respective intron motif was found. Listed are all motifs with ‘Cohen’s d expression’>0.05. For a complete listing of all 81 candidate motifs, identified based on conservation and positional preference alone, see Supplementary Table 1

From: Identification of cis-regulatory motifs in first introns and the prediction of intron-mediated enhancement of gene expression in Arabidopsis thaliana

Hexamer

Cohen’s d, Correlation, comparable, random hexamer

Cohen’s d, Expression level

Number of genes

AGATCG

1.45E-01

0.46

1807

ACCCTA

9.82E-02

0.18

2964

TCGATC

9.16E-02

0.34

2014

TCGGAG

8.58E-02

0.27

857

TCTCGC

8.13E-02

0.19

785

GATTCG

7.68E-02

0.32

2516

ATCGAA

7.07E-02

0.31

4188

AAATCG

7.00E-02

0.28

4086

AATCGA

6.88E-02

0.31

4406

TTAGGG

6.76E-02

0.19

2896

ATCGAG

6.20E-02

0.28

1773

TCTCGA

5.79E-02

0.22

2044

CTCTCG

5.77E-02

0.23

1124

AAACCC

5.33E-02

0.18

4970

TTCTCG

5.27E-02

0.19

2188

TTTCGA

5.20E-02

0.21

3866