Eutr18
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001266 |
|---|---|
| TE superfamily | Long_Terminal_Repeat_Element |
| TE class | LTR |
| Species | Eutheria |
| Length | 636 |
| Kimura value | 33.25 |
| Tau index | 0.8527 |
| Description | Ancient interspersed repetitive sequence from eutherian mammals. |
| Comment | Still incomplete, at least on on 5'end. LTR classification is not entirely sure. |
| Sequence |
GTATTTGTGAGGAAGGGTTCTNNNNTTTGTATTTGNAGAGGAACAAGCTGGGCAGGAGACCAGCTCCCNGGGGNGGGANGGNAAGATGGCGCCCGCCACGCGGAGACAGGCCGGGAGCTGGGAGGGAAGGAAGCCAGGCAAGGTGCCTGCGAAGTTGTGCCAGCCCTTTGGGGCTAGAGCGTAACTNTCCTGGGGAATAGAACAGGGCCTGCGAGCCTGGNAAGCGAGTTAGCTATNGTAGGATCAGAAACCTGTACTTTGNAAGCCGGACTGTTTTTATGCTTCTTGTATTTTCTGTGTTTATTTCCTTTTTGTTCTCCCTTAGTATTTAGTAAAGTTCTTTTTGAAAATNCCAGCCTGTCTCAGCTGTGCTAAGGGGAACCAAGGAAAGGGGTTTTTGTCCACGCTTGGGCCGGAGTTTTAAAGGGGGAGCGGCGCACCCCTGGGGCCTGGGAGTGGTGGCGGCAGGAACAGGCCAGAGAGGGAGGCCCCAAGGGGAAGGTGAAACTCAGGGAGACAGAGTCGGGGTGCCTGGTTACCCCCTCCCCTACGGAGATTCTCCTTCCAGAGCTCTTCTCTGCTCAAACCTTGGAGGGTTCTGTGTTTTGTTTTAATAAGGGAGGCCGTTCCCTTACA
|
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 |
|---|---|---|---|---|---|---|
| Eutr18 | Zfp961 | 87 | 94 | - | 15.99 | GGGCGCCA |
| Eutr18 | SP4 | 540 | 548 | - | 15.85 | GGGGAGGGG |
| Eutr18 | Klf15 | 444 | 465 | - | 15.80 | CCGCCACCACTCCCAGGCCCCA |
| Eutr18 | CRF4 | 459 | 468 | - | 15.22 | CTGCCGCCAC |
| Eutr18 | TFAP2B | 487 | 499 | - | 15.20 | TCCCCTTGGGGCC |
| Eutr18 | pita | 393 | 410 | - | 15.12 | CAAGCGTGGACAAAAACC |
| Eutr18 | DOF3.6 | 304 | 324 | + | 15.11 | TTTCCTTTTTGTTCTCCCTTA |
| Eutr18 | ERF076 | 459 | 468 | - | 15.06 | CTGCCGCCAC |
| Eutr18 | CTCF | 83 | 92 | + | 14.97 | AAGATGGCGC |
| Eutr18 | DOF1.5 | 303 | 318 | - | 14.92 | AGAACAAAAAGGAAAT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
