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Table 1 Transcription factors binding sites identified in noncoding regions of coexpressed genes in three fish species

From: Transcriptional dynamics of a conserved gene expression network associated with craniofacial divergence in Arctic charr

Transcription factor

Transcription factor family

Motifs (coverage) and species

Matrix ID

D. rerio

O. latipes

T. nigroviridis

E-value

E-value

E-value

Ap1

Basic region leucine zipper

 

M00925

3.40E-05

2.98E-03

2.98E-03

AACTCA (82%)_D.re

M00174

1.00E-04

–

–

CCTCA (94%)_O.la

M00199

1.40E-04

–

–

CCTCA (88%)_T.ni

M00924

1.70E-04

–

–

Ets2

E-26 transformation specific

CTTCA (94%)_D.re

M00340

–

1.40E-08

9.18E-05

ACAGGAA (75%);

CTTCA (100%)_O.la

M00771

1.00E-04

7.38E-06

–

ACAGG (94%)_T.ni

Lmaf

Basic region leucine zipper

GTTGAC (71%)_D.re

M01139

5.80E-04

1.91E-03

2.06E-03

AGCAA (88%); CCAGC (88%)_O.la

CCTGA (88%)_T.ni

Lyf1

Zinc finger DNA binding

CTCTCC (77%)_D.re

M00141

3.20E-04

5.27E-06

5.08E-05

CTCCC (81%)_O.la

GGAGA (100%)_T.ni

Maz

RGGKANNGA (77%); CTCTCC (77%); CTCHNTCC (71%)_D.re

M00649

2.50E-05

8.92E-07

1.18E-03

CCTCA (94%); CTCCC (81%)_O.la

CAGGG (88%); GGAGA (100%); CCTCA (88%); AAGGG (88%)_T.ni

Nfkb

Rel homology domain

 

M00051

–

8.21E-03

–

CTCTCC (77%)_D.re

M00052

–

–

4.49E-06

DGRADB (100%)_O.la

M00054

–

–

7.14E-05

GGAAA (88%)_T.ni

M00194

3.80E-03

–

3.87E-05

 

M00208

3.30E-04

–

3.49E-05

Sf1

Nuclear hormone receptor

CAAGC (100%)_D.re

M00727

1.00E-03

2.15E-06

1.00E-03

AGGTC (100%)_O.lat

M01132

2.02E-03

4.56E-06

1.32E-03

CATGG (77%); AAGGG (88%); AGGCC (71%)_T.ni

Smad3

Mothers against decapentaplegic

CAGAC (94%); TCTGG (88%); TCTGT (88%)_D.re

M00701

2.60E-06

6.00E-06

2.32E-03

TCTGT (100%)_O.la

CAGAG (94%); CAGAA_T.ni

Smad4

CAGAC (94%)_D.re

M00733

1.38E-03

8.52E-04

8.52E-04

GCAGC (81%)_O.la

GCAGC (88%)_T.ni

  1. Conserved noncoding regions of 17 genes, with differential expression between morphs and positive expression correlation were analysed in three fish species (D. rerio, T. nigroviridis and O. latipes). Motifs present in at least 12 of 17 genes (70% coverage) were identified by SCOPE and run against position weight matrices in the TRANSFAC database to identify known transcription factor binding sites.