LTR12D
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000403 |
|---|---|
| TE superfamily | ERV1 |
| TE class | LTR |
| Species | Catarrhini |
| Length | 1254 |
| Kimura value | 6.72 |
| Tau index | 0.9598 |
| Description | LTR12D (Long Terminal Repeat) for HERV9-like endogenous retrovirus |
| Comment | A variant of LTR12C with internal indels. |
| Sequence |
TGAGAGGTGACAACGTGCTAGCAGCCCTCGCTCGCTCTCGGCGCCTCCTCGGCCTCGGCGTCCGCTCTGGCCGCGCTCGAGGAGCCCTTCAGCCCGCCGCTGCGCTGTGGGGGCCCCTCTCTGGGGCTGGCCGAGGCCGGAGCCGGCTCCCTCTGCTCGCGGGGAGGTGTGGAGGGAGAGGCGCGGGCGGGAGCCGGGGCTGCGCGCGGCGCTCGCGGGCCGGCGCGGGTTCCGGGTGGGCGCGGGCTCGGCGGGCCCCGCACTCGGCGCGGCCGGCCGGCGCCTGCTGGGCTTGATCGGGGGACGAGCTCCCTCTGGGCTGCCGGAGTGCCCGGGCTAGGTGCCGCAAAGTCCCGCGGCGAGTGCCAGTGAGAGGTGAAGCCGGCTGGGCTTCTGGGTCGGGTGGGGACTTGGAGAACTTTTCTGTCTAGCTAAAGGATTGTAAACGCACCAATCAGCACTCTGTGTCTAGCTAAAGGTTTGTAAACGCACCAATCAGCACTCTGTGTCTAGCTAAAGGTTTGTAAACGCACCAATCAGCGCTCTGTGTCTAGCTAATCNGGTGGGGACTTGGAGAACTTTTGTGTCTAGCTAAAGGATTGTAAACGCACCAATCAGCACTCTGTGTCTAGCTAAAGGTTTGTAAACGCACCAATCAGCACTCTGTCAAAACGGACCAATCAGCTCTCTGTAAAACGGACCAATCAGCTCTCTGTAAAATGGACCAATCAGCTCTCTGTAAAATGGACCAATCAGCAGGATGTGGGTGGGGCCAGATAAGGGAATAAAAGCAGGCCACCCGAGCCAGCAGCGGCAACCCGCTCGGGTCCCCTTCCACGCTGTGGAAGCTTTGTTCTTTCGCTCTTCGCAATAAATCTTGCTGCTGCTCACTCTTTGGGTCCGCGCCGCCTTTATGAGCTGTAACACTCACCGCGAAGGTCTGCAGCTTCACTCCTGAAGCCAGCGAGACCACGAACCCACCGGGAGGAACGAACAACTCCGGACGGAAGGAACGAACAACTCCGGACGCGCCGCCTTTAAGAGCTGTAACACTCACCGCGAAGGTCTGCAGCTTCACTCCTGAAGTCAGCGAGACCACGAACCCACCAGAAGGAAGAAACTCCGGACACATCTGAACATCTGAAGGAACAAACTCCGGACACACCATCTTTAAGAACTGTAACACTCACCGCGAGGGTCCGCGGCTTCATTCTTGAAGTCAGCGAGACCAAGAACCCACCAATTCCGGACACA
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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 |
|---|---|---|---|---|---|---|
| LTR12D | ZNF574 | 59 | 72 | - | 18.12 | GGCCAGAGCGGACG |
| LTR12D | dar1 | 763 | 773 | - | 17.08 | GCCCCACCCAC |
| LTR12D | KLF9 | 763 | 773 | - | 17.03 | GCCCCACCCAC |
| LTR12D | Clamp | 24 | 37 | - | 17.02 | GAGCGAGCGAGGGC |
| LTR12D | KLF17 | 1095 | 1108 | + | 16.92 | ACCACGAACCCACC |
| LTR12D | KLF17 | 969 | 982 | + | 16.92 | ACCACGAACCCACC |
| LTR12D | nfya-1 | 675 | 684 | + | 16.78 | GACCAATCAG |
| LTR12D | nfya-1 | 699 | 708 | + | 16.78 | GACCAATCAG |
| LTR12D | nfya-1 | 723 | 732 | + | 16.78 | GACCAATCAG |
| LTR12D | nfya-1 | 747 | 756 | + | 16.78 | GACCAATCAG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
