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 | ERF095 | 208 | 220 | - | 16.18 | ATGGCGGCGGCAA |
| THE1A | ERF4 | 211 | 219 | + | 16.16 | CCGCCGCCA |
| THE1A | ERF077 | 211 | 220 | + | 16.14 | CCGCCGCCAT |
| THE1A | ERF112 | 211 | 219 | + | 16.11 | CCGCCGCCA |
| THE1A | Zm00001d002364 | 209 | 218 | + | 16.04 | TGCCGCCGCC |
| THE1A | ERF2 | 208 | 220 | + | 15.98 | TTGCCGCCGCCAT |
| THE1A | Zm00001d052229 | 209 | 218 | + | 15.87 | TGCCGCCGCC |
| THE1A | ERF104 | 205 | 220 | + | 15.85 | CTCTTGCCGCCGCCAT |
| THE1A | ERF118 | 211 | 218 | + | 15.56 | CCGCCGCC |
| THE1A | IG1 | 211 | 219 | + | 15.50 | CCGCCGCCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
