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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.