EutTc1-N1
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001170 |
|---|---|
| TE superfamily | Tc1 |
| TE class | DNA |
| Species | Eutheria |
| Length | 588 |
| Kimura value | 17.33 |
| Tau index | 0.0000 |
| Description | Ancient Mariner/Tc1 DNA transposon from eutherian mammals. |
| Comment | Almost identical to Tc1-N1_MD in marsupials. No evidence for orthologous copies between marsupials and eutheria. A more common related element is EutTc1-N2, that is more or less a hairpin loop of the first 166 bp of EutTc1-N1. |
| Sequence |
CAGGGTGTCCCAAAAGTCTTAGTGCAATTTTAAGCTTTAATAACTTCAGAAGTATAAATGCTACAAACTTACAAAAACATCATTTGAAAGTTTANTTATTTAAATTTCTTTTACACTTATTTAGTTTTGCGAATTTTGAATAGTAAGTTTTAATTTTAATTTTTTNCGTGTGCAACAGTTTCTGGGCGACACTTTCTCAGACCGGTGGATTGGTAGAGNAGNTCCTNNTNCTTGGCCACCTCGGTCACCTGATCTATCTCNATTAGACTNNTTCTTGTGAGGTCACATCAAAANCGTTGTGTATGTATCAAAACCTCGTTCTTTGGATGATCTTAAAGCTAGGATTACAAATGCAATCCTTTCAGTCACTGAGCAGCAGCCGATGAAAGTTTTTGCAAAGTTCGAAAATCGACTAGAGCNATATATAGCACNAGACGGTGGTTATGTTGAATTTTAATAAGAAACATNTCANTATTTTAAAAATTTAAATAATTNNNCTTTCAAATGTCGTTTTTTGTAAGTTTGTAGCATTTATACTTCTGAGGTTATTAAAGCTTAAAACTGCACCAAGACTTTTGGGACACCCTG
|
TF motifs of the concenus sequence
Use FIMO to detect transcription factor motifs in the concenus sequence of the TE family.
| TE_family | TFBS | Start | End | Strand | Score | Matched sequence |
|---|---|---|---|---|---|---|
| EutTc1-N1 | D1 | 485 | 492 | + | 13.38 | TTAAATAA |
| EutTc1-N1 | D1 | 96 | 103 | - | 13.38 | TTAAATAA |
| EutTc1-N1 | SREBP | 244 | 253 | + | 13.29 | GTCACCTGAT |
| EutTc1-N1 | PRDM1 | 192 | 198 | + | 13.28 | CTTTCTC |
| EutTc1-N1 | ATF2 | 277 | 286 | + | 13.21 | GTGAGGTCAC |
| EutTc1-N1 | ERF054 | 434 | 441 | + | 13.14 | GACGGTGG |
| EutTc1-N1 | SREBF1 | 244 | 253 | - | 13.10 | ATCAGGTGAC |
| EutTc1-N1 | SOL1 | 127 | 141 | - | 13.09 | ATTCAAAATTCGCAA |
| EutTc1-N1 | E2FC | 181 | 195 | - | 13.03 | AAAGTGTCGCCCAGA |
| EutTc1-N1 | Hmga1 | 477 | 484 | - | 12.99 | ATTTTTAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
