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 | nfya-1 | 449 | 458 | + | 15.13 | CACCAATCAG |
| LTR12D | nfya-1 | 490 | 499 | + | 15.13 | CACCAATCAG |
| LTR12D | nfya-1 | 531 | 540 | + | 15.13 | CACCAATCAG |
| LTR12D | nfya-1 | 609 | 618 | + | 15.13 | CACCAATCAG |
| LTR12D | nfya-1 | 650 | 659 | + | 15.13 | CACCAATCAG |
| LTR12D | Clamp | 28 | 41 | - | 15.12 | CCGAGAGCGAGCGA |
| LTR12D | NDT80 | 580 | 588 | - | 15.06 | GACACAAAA |
| LTR12D | SUT2 | 1118 | 1127 | + | 14.95 | AAACTCCGGA |
| LTR12D | SUT2 | 1151 | 1160 | + | 14.95 | AAACTCCGGA |
| LTR12D | TB1 | 108 | 116 | - | 14.92 | GGGCCCCCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
