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 | EREB138 | 211 | 220 | + | 17.53 | CCGCCGCCAT |
| THE1A | Zm00001d020267 | 209 | 218 | + | 17.04 | TGCCGCCGCC |
| THE1A | ERF105 | 211 | 220 | - | 16.95 | ATGGCGGCGG |
| THE1A | ERF073 | 209 | 219 | + | 16.95 | TGCCGCCGCCA |
| THE1A | ERF091 | 208 | 220 | - | 16.71 | ATGGCGGCGGCAA |
| THE1A | ABR1 | 209 | 220 | - | 16.65 | ATGGCGGCGGCA |
| THE1A | Zm00001d020595 | 209 | 218 | - | 16.42 | GGCGGCGGCA |
| THE1A | ERF082 | 211 | 219 | + | 16.26 | CCGCCGCCA |
| THE1A | SPIC | 190 | 202 | - | 16.25 | AAATGAGGAAGAA |
| THE1A | EREB29 | 210 | 219 | + | 16.22 | GCCGCCGCCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
