LTR40c
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000516 |
|---|---|
| TE superfamily | ERV3 |
| TE class | LTR |
| Species | Eutheria |
| Length | 465 |
| Kimura value | 24.54 |
| Tau index | 0.8479 |
| Description | LTR40b (Long Terminal Repeat) for HERVL40 endogenous retrovirus |
| Comment | 5 bp TSDs. |
| Sequence |
TGTTGGGAGACAATCCTCCATGGGCCCCTNGCGCTCCTGCACGTCTTGCTGGGTATGCCAAGAATGCAAGGCCCTGACCGCTCTTTACCTCGGGCCATTTCTCAGGGTTGTGTTTGCAGCGAGCAACCTTGAGGGATGAGGTAATGTCTCCCTCCGGGACAAAGAGCAGGCTTGCTTACTGCTTGCTATAAAAGCGGTGGATTCCCCAAGCTCAGTGTTCCTCNGCTGTAACGCAAACCCACTGCGTGCGCAGCATCCATCTGGGCCCTCCGCGTCGCCCCCGTGGGACTTGGGGGGNCANGGGGAACCGACGCAAACATGCTGATGCTCATGCTGCTTGCTGTGCCGTGAGTAATAAAGTCCTTTGTCTCTGACCCAGGAGTCTCGTGTCTTCTGCCAGCATCCATGAAACAGTAACAGGCTAACTTATTAGCTTGTAAGTAGGGTAAAATCCCAGACCTGACA
|
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 |
|---|---|---|---|---|---|---|
| LTR40c | Rel | 197 | 207 | + | 3.87 | GTGGATTCCCC |
| LTR40c | NFKB1 | 195 | 207 | + | 3.31 | CGGTGGATTCCCC |
| LTR40c | ZAP1 | 126 | 140 | + | 3.28 | ACCTTGAGGGATGAG |
| LTR40c | Zm00001d020595 | 276 | 285 | - | 2.62 | CACGGGGGCG |
| LTR40c | IXR1 | 170 | 184 | - | -0.29 | AAGCAGTAAGCAAGC |
| LTR40c | BPC1 | 80 | 103 | - | -1.67 | GAGAAATGGCCCGAGGTAAAGAGC |
| LTR40c | ZAP1 | 122 | 136 | - | -5.00 | TCCCTCAAGGTTGCT |
| LTR40c | GLIS1 | 263 | 277 | + | -5.51 | GGGCCCTCCGCGTCG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
