THE1A
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000005 |
|---|---|
| TE superfamily | MaLR |
| TE class | LTR |
| Species | Haplorrhini |
| Length | 355 |
| Kimura value | 7.51 |
| Tau index | 0.8500 |
| Description | Long terminal repeat (THE1A subfamily) |
| Comment | The LTR of THE1A retrovirus-like MaLR element. Has 5bp TSDs. This entry shows ~90% full-length similarity to THE1B. |
| Sequence |
TGATATGGTTTGGCTGTGTCCCCACCCAAATCTCAACTTGAATTGTATCTCCCAGAATTCCCACGTGTTGTGGGAGGGACCCAGGGGGAGGTAATTGAATCATGGGGGCCGGTCTTTCCCGTGCTATTCTCGTGATAGTGAATAAGTCTCACGAGATCTGATGGGTTTATCAGGGGTTTCCGCTTTTGCTTCTTCCTCATTTTCCTCTTGCCGCCGCCATGTAAGAAGTGCCTTTCGCCTCCCGCCATGATTCTGAGGCCTCCCCAGCCATGTGGAACTGTAAGTCCAATTAAACCTCTTTTTCTTCCCAGTCTCGGGTATGTCTTTATCAGCAGCGTGAAAACGGACTAATACA
|
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 |
|---|---|---|---|---|---|---|
| THE1A | KLF4 | 20 | 27 | + | 15.48 | CCCCACCC |
| THE1A | ERF076 | 211 | 220 | + | 15.48 | CCGCCGCCAT |
| THE1A | DUX4 | 92 | 102 | + | 15.43 | TAATTGAATCA |
| THE1A | RAP2-6 | 205 | 219 | - | 15.39 | TGGCGGCGGCAAGAG |
| THE1A | Os05g0497200 | 212 | 219 | + | 15.23 | CGCCGCCA |
| THE1A | CRF2 | 211 | 218 | + | 15.20 | CCGCCGCC |
| THE1A | Zm00001d049364 | 208 | 218 | + | 15.17 | TTGCCGCCGCC |
| THE1A | PK17878.1 | 212 | 219 | + | 15.11 | CGCCGCCA |
| THE1A | ERF1B | 212 | 219 | + | 14.91 | CGCCGCCA |
| THE1A | BZR2 | 59 | 68 | - | 14.84 | ACACGTGGGA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
