Table 3.
Prediction of transcription factors (TF) binding sites with the context of novel SNPs [in brackets] identified in silico in the promoter of the pPAG2-L gene with the use of Lasagne-Search 2.0, Cluster Buster, and MatInspector
| TF motif | Localization | Strand | Score | TF sequence |
|---|---|---|---|---|
| Lasagne-Search 2.0 | ||||
| AP-2rep | 23–29 | − | 8.14 | CAGTGGG b |
| NF-Y | 93–103 | + | 13.05 | TGACCAA[T/C][G/A]TG |
| MoyD | 188–199 | + | 11.99 | ACACAGGTGCTT |
| CHOP:C/EBPalpha | 275–297 | − | 13.2 | ATGTGAAATC[C/T] CC |
| HNF-1 | 404–420 | − | 14.2 | AGTCAATGAATGGCCTG |
| FAC1 | 574–587 | − | 10.21 | ATCCAAAACATGTT |
| AREB6 | 667–678 | − | 11.89 | TGACACCTGGGG |
| MRF-2 | 995–1005 | − | 18.64 | CAGAAT[A/C]CAGA |
| GATA-2 | 1051–1060 | − | 11.32 | CCTGATAAGA |
| GATA-2 | 1070–1079 | − | 11.32 | CCTGATAAGA |
| STAT5A | 1158–1165 | − | 8.85 | GAGTTCTG |
| Cluster Buster | ||||
| GATA | 11–23 | − | 6.87 | GACAGATAAGCCA |
| CCAAT | 37–52 | + | 6.16 | CTTGACAAATGGAAGG |
| Ets | 47–57 | + | 8.18 | GGAAGGAAAAG |
| AP-1 | 52–62 | − | 4.49 | TGTGACTTTTC |
| Myc | 57–66 | − | 7.12 | ACCATGTGAC |
| CCAAT a | 92–107 | + | 4.28 | TTTGACCAA[T/C][G/A]TGGCT |
| Myc | 97–106 | + | 4.58 | CCAA[T/C][G/A]TGGC |
| LSF | 101–115 | + | 5.26 | [T/C][A/G]TGGCTGGAACCTC |
| LSF | 102–116 | − | 5.85 | GGAGGTTCCAGCCA[T/C] |
| NF-1 | 128–145 | + | 4.65 | TCTTGACTCCCACCCCCA |
| AP-1 | 129–139 | + | 4.63 | CTTGA CTCCCA |
| Sp1 | 133–145 | − | 7.06 | TGGGGGTGGGAGT |
| LSF | 173–187 | + | 5.45 | [A/G]CAGG[T/C]TGAATCCAG |
| LSF | 174–188 | − | 8.86 | GCTGGATTCAACCTG |
| NF1 c | 100–117 | + | 5.25 | A[C/T][A/G]TGGCTGGAACCTCCT |
| AP-1 | 177–187 | + | 4.12 | GC[T/C]GAATCCAG |
| NF-1 | 812–829 | − | 7.85 | TCTTGGCAGCCACTTTGT |
| SRF | 838–850 | + | 5.33 | AACTATGAAATGC |
| TATA | 840–854 | + | 4.45 | CTATGAAATGCCAAG |
| SRF | 848–860 | + | 5.9 | TGCCAAGCATGGC |
| NF-1 | 854–871 | + | 5.03 | GCATGGCCCCCAGCACTT |
| Myf | 864–875 | − | 4.46 | AAATAAGTGCTG |
| Mef-2 | 868–879 | + | 7.84 | ACTTATTTTTAT |
| GATA | 872–884 | − | 6.1 | ATGTGATAAAAAT |
| GATA | 1050–1062 | − | 6.94 | TCCTGATAAGATC |
| GATA | 1069–1081 | − | 8.43 | ACCTGATAAGAAA |
| MatInspector | ||||
| MZF1.01 | 18–28 | − | 1.0 | GTGGGGACAGA |
| FOXP1 ES.01 a | 265–281 | + | 1.0 | ATTTGA[A/C]A[A/T]CAGG[G/A]GAT |
| SMAD3.01 | 293–303 | − | 1.0 | GAAGTCTGGAT |
| FOXP1 ES.01 | 568–584 | + | 1.0 | TGAATAAAACATGTTTT |
| FOXP1 ES.01 | 573–589 | − | 1.0 | CATCCAAAACATGTTTT |
| TBX20.01 | 797–819 | − | 1.0 | CACTTTGTGAGGTGTGCCTTTCT |
| GATA.01 | 1069–1081 | − | 1.0 | ACCTGATAAGAAA |
| TGIF.01 d | 1106–1122 | + | 1.0 | A[C/G]AGG[C/T]ATGTCAGAGCA |
aUnderlined motifs are the TFBS with SNPs in the core sequence
bBolded letters are the core nucleotides
cBolded and underlined motifs are the new TFBS that appeared as a result of SNP occurrence
dUnderlined and italic motifs are the TFBS with SNP outside the core sequence