LTR8A
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000616 |
|---|---|
| TE superfamily | ERV1 |
| TE class | LTR |
| Species | Haplorrhini |
| Length | 727 |
| Kimura value | 15.23 |
| Tau index | 1.0000 |
| Description | LTR8A (Long Terminal Repeat) for ERV1 endogenous retrovirus |
| Comment | LTR8A is a subfamily of LTR8. Solo LTRs are flanked by 4 bp TSDs, characteristic of MER4-int group. Internal sequence HERV8-int is also related to the MER4-int group. HUERS-P1 LTR. |
| Sequence |
TGAAACCGCCTTTGCAAAAATTATAACAGTGAGAAAATTATGACAGTGAAAGAGATCTGATCTAACCAACCCCCATCTTGCCTTTAACCTCCAAACTGCCCTTAATCATTCCTGGGCTTGGGCCAAGCTAACTTTGGGAGANATTTAGTTTATAGTTTAAATGATAATAGCCCTTCCCCAAAACTNAACCGCCTTTGTAAAGCTAATGAAAGGCCACCAGGTTAGGAGGATGAGAGGAGCCTGAATTCTGCTAAGGTGTAGACATAAACGATTACCAGCCATTATTCCGGAGGTCACAAGATTTGCAACTTCCCCAATTACTCCTGCAGATAACATCACTATTGTAGAACCTAAGATTGGCCTTTTGAGATGTCTTTTCAGGTTTTTTCGCATTTCTGACACCGATGGCTCCACCTGGACCCGCCAACCGCTCCTGTGGCCCCACCCAGAAGCGACTCAGCACGCANGAGGACCATTTTCCACACCCCTATGATTGCATCCCCAACCAATCAGCAGCAAGCACCCATTNCCTAGCCACCCCCACCCCCTGCCCGCCAAACTATCTTTGAAAAACCCTAGCCTCCGAATTTTCGGGGAGACTGATTTGAGTAATAACTCCGTCTCCCACGTGGCGTGGCCGGCCTCGCGTCAATTAAACTCTTTCTCTACTGCAATGCCGTGGTCTTTGTCTGTGCAGCGGGCAGGAAGAACCCATCGGGCGGTTACA
|
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 |
|---|---|---|---|---|---|---|
| LTR8A | MYCN | 625 | 632 | - | 15.35 | CCACGTGG |
| LTR8A | Creb3l2 | 625 | 633 | - | 15.25 | GCCACGTGG |
| LTR8A | KLF10 | 539 | 547 | - | 15.20 | GGGGTGGGG |
| LTR8A | BZIP16 | 625 | 634 | + | 15.20 | CCACGTGGCG |
| LTR8A | Plagl1 | 437 | 444 | - | 15.15 | TGGGGCCA |
| LTR8A | Usf | 624 | 633 | + | 14.87 | CCCACGTGGC |
| LTR8A | PIF4 | 626 | 633 | + | 14.80 | CACGTGGC |
| LTR8A | KLF5 | 538 | 547 | + | 14.78 | CCCCCACCCC |
| LTR8A | AT1G72740 | 571 | 581 | - | 14.77 | GGCTAGGGTTT |
| LTR8A | TRB1 | 571 | 579 | + | 14.70 | AAACCCTAG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
