LTR40c
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000516 |
|---|---|
| TE superfamily | ERV3 |
| TE order | 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 | Pparg::Rxra | 156 | 168 | + | 12.73 | GGGACAAAGAGCA |
| LTR40c | StBRC1 | 22 | 28 | + | 12.69 | GGGCCCC |
| LTR40c | Jra | 347 | 356 | - | 12.67 | ATTACTCACG |
| LTR40c | ZNF692 | 20 | 27 | - | 12.65 | GGGCCCAT |
| LTR40c | TWIST1 | 257 | 264 | - | 12.63 | CCAGATGG |
| LTR40c | dl | 197 | 206 | + | 12.49 | GTGGATTCCC |
| LTR40c | ZNF416 | 258 | 267 | + | 12.47 | CATCTGGGCC |
| LTR40c | Sox6 | 156 | 165 | - | 12.27 | TCTTTGTCCC |
| LTR40c | klu-1 | 276 | 282 | + | 12.23 | CGCCCCC |
| LTR40c | ARF36 | 5 | 16 | + | 12.20 | GGGAGACAATCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
