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 | lin-54 | 97 | 109 | - | 14.07 | AGAAATTTAAATA |
| EutTc1-N1 | sex-1 | 279 | 286 | + | 13.79 | GAGGTCAC |
| EutTc1-N1 | DMRTC2 | 303 | 313 | - | 13.77 | TTTTGATACAT |
| EutTc1-N1 | TSO1 | 476 | 490 | - | 13.74 | ATTTAAATTTTTAAA |
| EutTc1-N1 | CREM | 277 | 286 | - | 13.67 | GTGACCTCAC |
| EutTc1-N1 | CREM | 277 | 286 | + | 13.66 | GTGAGGTCAC |
| EutTc1-N1 | TCX6 | 98 | 112 | + | 13.64 | ATTTAAATTTCTTTT |
| EutTc1-N1 | SREBP | 244 | 253 | - | 13.53 | ATCAGGTGAC |
| EutTc1-N1 | Ddit3::Cebpa | 351 | 360 | + | 13.49 | ATGCAATCCT |
| EutTc1-N1 | ERF012 | 434 | 441 | - | 13.42 | CCACCGTC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
