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 | klu | 535 | 545 | + | 15.89 | CCACCCCCACC |
| LTR8A | KLF5 | 439 | 448 | + | 15.88 | GCCCCACCCA |
| LTR8A | BHLH72 | 624 | 632 | + | 15.53 | CCCACGTGG |
| LTR8A | KLF4 | 440 | 447 | + | 15.48 | CCCCACCC |
| LTR8A | KLF4 | 539 | 546 | + | 15.48 | CCCCACCC |
| LTR8A | ARALYDRAFT_495258 | 438 | 445 | + | 15.43 | GGCCCCAC |
| LTR8A | ARALYDRAFT_484486 | 438 | 445 | + | 15.43 | GGCCCCAC |
| LTR8A | NFIB | 111 | 127 | + | 15.42 | CCTGGGCTTGGGCCAAG |
| LTR8A | SP8 | 535 | 545 | + | 15.38 | CCACCCCCACC |
| LTR8A | MYCN | 625 | 632 | + | 15.35 | CCACGTGG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
