MLT1O
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001026 |
|---|---|
| TE superfamily | MaLR |
| TE class | LTR |
| Species | Theria_mammals |
| Length | 542 |
| Kimura value | 31.69 |
| Tau index | 0.9071 |
| Description | MLT1O Long Terminal Repeat for ERVL-MaLR retrotransposon |
| Comment | MLT10 has 5 bp TSDs. There are ~1000 about copies in the reconstructed Laurasiatherian genome (with substitution levels of ~35%). Note that a full-length ERV-MaLR (Mammalian apparent LTR retrotransposon) element is derived from an ERV (Endogenous Retrovirus), but only contains the Gag gene (that is, no Pol or Env). |
| Sequence |
TGTAGTGGACACCTTTTGGGGTGTCTGCCCAGCCCCCCTTCTCTGGGAACCGCCCCCCCACCCACAGGGGTGGGCCCCCGGCAGCCATGTTTGTACTACGTGACCCCGCCCCCCTGGCCACAGCTGATTGGACCAGGGGTGGACACCTGACCCAAGCTGGGCCAATCAGATTCTCTCTCCCGGGAATTTGGAATTGGGACTNAGAGATNCTAGTCAGTCTCTGCTGGTCGCTTGAACTGGGGANATGTAAACTCGGGAGCTGTGGGGCGGCCATNTTCCGCCATGTGNACGGAGAAGCAGAGAAAGCCGGTCTGCAGAGAGAGGAGAATGAAGCAGACGCGCAGAGAGAAGCAGAGACGAGAGACCGGGTGGCCTCAGAGACAGAGAAAGATGGAGCCGATTCTCTCCTGAGGCCCGGCTGCATTCCTGCCCTTGGGTTCCGTGAGACACCCCTGTATCCTTATAATAAATTCCCCTTTTTTGCTTAAGCTAGCTCGAGTGGGTTTCTGTTACTTGCAACCAAAAGAGCCTTGACTAAGACA
|
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 |
|---|---|---|---|---|---|---|
| MLT1O | SP9 | 104 | 113 | + | 16.33 | CCCCGCCCCC |
| MLT1O | KLF15 | 104 | 111 | + | 16.27 | CCCCGCCC |
| MLT1O | cassava45561.m1 | 70 | 78 | - | 16.09 | GGGGCCCAC |
| MLT1O | LjSGA_053525.1 | 70 | 77 | - | 16.05 | GGGCCCAC |
| MLT1O | ZNF148 | 104 | 113 | + | 15.95 | CCCCGCCCCC |
| MLT1O | SP8 | 104 | 114 | + | 15.89 | CCCCGCCCCCC |
| MLT1O | PK19717.1 | 70 | 78 | - | 15.77 | GGGGCCCAC |
| MLT1O | KLF7 | 104 | 111 | - | 15.72 | GGGCGGGG |
| MLT1O | OsI_08196 | 70 | 77 | - | 15.69 | GGGCCCAC |
| MLT1O | PLAGL2 | 72 | 79 | + | 15.67 | GGGCCCCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
