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 | KLF16 | 538 | 548 | + | 14.67 | CCCCCACCCCC |
| LTR8A | BZIP68 | 625 | 634 | - | 14.65 | CGCCACGTGG |
| LTR8A | ARALYDRAFT_493022 | 438 | 445 | + | 14.64 | GGCCCCAC |
| LTR8A | KLF1 | 440 | 447 | - | 14.64 | GGGTGGGG |
| LTR8A | KLF1 | 539 | 546 | - | 14.64 | GGGTGGGG |
| LTR8A | PK24205.1 | 626 | 633 | + | 14.62 | CACGTGGC |
| LTR8A | mxl-3 | 625 | 632 | + | 14.59 | CCACGTGG |
| LTR8A | mxl-3 | 625 | 632 | - | 14.59 | CCACGTGG |
| LTR8A | NFYA | 506 | 513 | + | 14.54 | CCAATCAG |
| LTR8A | SREBP | 629 | 638 | - | 14.46 | GCCACGCCAC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
