EUTREP16
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001153 |
|---|---|
| TE superfamily | Long_Terminal_Repeat_Element |
| TE class | LTR |
| Species | Eutheria |
| Length | 517 |
| Kimura value | 32.22 |
| Tau index | 0.0000 |
| Description | Conserved repetitive element present in placental mammals. |
| Comment | TG..CA termini and presence of AATAAA at appropriate place (pos 426-431) suggests LTR. |
| Sequence |
TGTTGGGATTTTAGGAATGGATTTTTATATAGTTTGGTATAGTTCAGTAATTTTCCAGAAAGACAGATTACCTGGGCCAGATGGGTGGTTTCTCCAGCCATGCTGTCTGTCCTTTTGTATGTNAATGCATCTTTTACCCATCAAGGGGGCTGTGGGNTGGGCCAGGAGCANAGAGNCGCAGACTTGACCTTAAAAGGTCAAGAATCTAGGACCCAGAGAGGTAGATGAAATCTGACCAATGAAACACCTTAGCAACATCCAGGGACCTATGGGGGATGGGCACCATTGTTTCCTAGATGTACTGATGATGTAATTTGTAATATAAAAGAATGTGACCTCCATGAGCACGTGGCTGTTCTCCTGGGANTGTGAGTTGGGCAAACGGTCCTGTGCAGGNGTGCACGCCCGTATAGCAAAGGTGGCCGAATAAACTTGTGCTTGCTTCAATCTGTGTCTCTTCGGACCGGTCTGTTCTCAGTCACACTGGGGAAACTGAGGCAGCTTAGCAGACTCATCA
|
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 |
|---|---|---|---|---|---|---|
| EUTREP16 | BZIP43 | 342 | 353 | - | 5.18 | GCCACGTGCTCA |
| EUTREP16 | SRF | 185 | 200 | - | 4.59 | TGACCTTTTAAGGTCA |
| EUTREP16 | ZNF16 | 258 | 278 | + | 4.31 | TCCAGGGACCTATGGGGGATG |
| EUTREP16 | GLI3 | 77 | 91 | - | 2.31 | AAACCACCCATCTGG |
| EUTREP16 | ZNF558 | 24 | 52 | - | 0.55 | AATTACTGAACTATACCAAACTATATAAA |
| EUTREP16 | Rarb | 193 | 208 | + | -2.64 | AAAGGTCAAGAATCTA |
| EUTREP16 | Nr2F6 | 186 | 200 | + | -3.66 | GACCTTAAAAGGTCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
