EutTc1-N2
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001231 |
|---|---|
| TE superfamily | Tc1 |
| TE class | DNA |
| Species | Eutheria |
| Length | 378 |
| Kimura value | 20.04 |
| Tau index | 0.0000 |
| Description | TcMar-Tc2 DNA transposon, EutTc1-N2 subfamily |
| Comment | Hairpin with just pos 177-204 as a unique loop (the first/final 168 bp are basically the same as in EutTc1-N1). Present at orthologous sites in all eutheria, absent from marsupials. |
| Sequence |
CAGGGTGTCCCAAAAGTCTTAGTGCAGTTTTAAGCTTTAATAACTTCAGAAGTATAAATGCTACAAACTTACAAAAAACATCATTTGAAAGTTTAATTATTTAAATTTCTTTTACACTTATTTAGTTTTGTGAATTTTGAATAATAAATTTTTAATTTTAATTTTTTTGTTTCAGTCCCTCTGATTGAAGATGGCAAACGTTGACTGAAACAAAAAATTAAAATTAAAAATTTATTATTCAAAATTCACAAAACTAAATAAGTGTAAAAGAAATTTAAATAATTAAACTTTCAAATGATGTTTTTTGTAAGTTTGTAGCATTTATACTTCTGAAGTTATTAAAGCTTAAAACTGCACTAAGACTTTTGGGACACCCTG
|
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-N2 | TCX6 | 99 | 113 | + | 13.64 | ATTTAAATTTCTTTT |
| EutTc1-N2 | WRKY55 | 199 | 207 | + | 13.55 | CGTTGACTG |
| EutTc1-N2 | Lhx3 | 140 | 151 | - | 13.45 | AAATTTATTATT |
| EutTc1-N2 | Lhx3 | 228 | 239 | + | 13.45 | AAATTTATTATT |
| EutTc1-N2 | D1 | 275 | 282 | + | 13.38 | TTAAATAA |
| EutTc1-N2 | D1 | 97 | 104 | - | 13.38 | TTAAATAA |
| EutTc1-N2 | ZHD1 | 278 | 286 | + | 13.26 | AATAATTAA |
| EutTc1-N2 | ZHD1 | 93 | 101 | - | 13.26 | AATAATTAA |
| EutTc1-N2 | WRKY38 | 199 | 206 | + | 13.02 | CGTTGACT |
| EutTc1-N2 | Hmga1 | 148 | 155 | + | 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.
