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 | NFIC | 123 | 137 | + | 0.78 | AGGGAAGGAAGCCAG |
| Eutr18 | IXR1 | 108 | 122 | + | 0.75 | AGGCCGGGAGCTGGG |
| Eutr18 | BPC1 | 300 | 323 | - | -0.33 | AAGGGAGAACAAAAAGGAAATAAA |
| Eutr18 | TRP1 | 591 | 611 | - | -1.26 | AAACAAAACACAGAACCCTCC |
| Eutr18 | EWSR1-FLI1 | 117 | 134 | + | -4.54 | GCTGGGAGGGAAGGAAGC |
| Eutr18 | EWSR1-FLI1 | 113 | 130 | + | -11.41 | GGGAGCTGGGAGGGAAGG |
| Eutr18 | EWSR1-FLI1 | 479 | 496 | + | -16.12 | GAGAGGGAGGCCCCAAGG |
| Eutr18 | BPC5 | 501 | 530 | + | -42.07 | GGTGAAACTCAGGGAGACAGAGTCGGGGTG |
| Eutr18 | BPC5 | 497 | 526 | + | -44.17 | GGAAGGTGAAACTCAGGGAGACAGAGTCGG |
| Eutr18 | BPC5 | 493 | 522 | + | -47.73 | AAGGGGAAGGTGAAACTCAGGGAGACAGAG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
