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 | Sox6 | 362 | 371 | + | 13.83 | CCTTTGTCTC |
| LTR40c | Hand1 | 453 | 461 | + | 13.64 | CCCAGACCT |
| LTR40c | Zfp809 | 451 | 459 | + | 13.62 | ATCCCAGAC |
| LTR40c | PLAGL2 | 22 | 29 | + | 13.61 | GGGCCCCT |
| LTR40c | ZNF547 | 326 | 338 | + | 13.59 | TGCTCATGCTGCT |
| LTR40c | NFIC | 56 | 62 | - | 13.37 | CTTGGCA |
| LTR40c | NEUROD1 | 257 | 264 | - | 13.36 | CCAGATGG |
| LTR40c | Atoh1 | 257 | 263 | - | 13.34 | CAGATGG |
| LTR40c | pal-1 | 352 | 359 | + | 13.31 | GTAATAAA |
| LTR40c | NAC035 | 344 | 350 | - | 13.30 | CACGGCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
