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
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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 | RFX4 | 365 | 377 | + | 4.74 | GTCACTGAGCAGC |
| EutTc1-N1 | Rfx | 178 | 190 | - | 3.75 | GTCGCCCAGAAAC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
