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 | IDD6 | 62 | 77 | - | 8.44 | TTTTTGTAAGTTTGTA |
| EutTc1-N2 | IRF3 | 163 | 179 | - | 6.34 | GGGACTGAAACAAAAAA |
| EutTc1-N2 | ZNF558 | 285 | 313 | - | 3.85 | AACTTACAAAAAACATCATTTGAAAGTTT |
| EutTc1-N2 | ZNF558 | 66 | 94 | + | 3.85 | AACTTACAAAAAACATCATTTGAAAGTTT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
