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 | KLF4 | 401 | 408 | - | 15.48 | CCCCACCC |
| LTR12D | KLF4 | 765 | 772 | - | 15.48 | CCCCACCC |
| LTR12D | ARALYDRAFT_495258 | 767 | 774 | - | 15.43 | GGCCCCAC |
| LTR12D | ARALYDRAFT_484486 | 767 | 774 | - | 15.43 | GGCCCCAC |
| LTR12D | Ets98B | 229 | 237 | - | 15.36 | ACCCGGAAC |
| LTR12D | PK19717.1 | 109 | 117 | - | 15.24 | GGGGCCCCC |
| LTR12D | GRF4 | 880 | 887 | - | 15.23 | GCAGCAGC |
| LTR12D | ZNF449 | 384 | 393 | - | 15.17 | AAGCCCAGCC |
| LTR12D | Plagl1 | 768 | 775 | + | 15.15 | TGGGGCCA |
| LTR12D | Zic2 | 283 | 291 | - | 15.14 | CCCAGCAGG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
