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
|
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 | Mad | 50 | 64 | - | 16.50 | CGGACGCCGAGGCCG |
| LTR12D | GSM1 | 1118 | 1127 | + | 16.41 | AAACTCCGGA |
| LTR12D | GSM1 | 1151 | 1160 | + | 16.41 | AAACTCCGGA |
| LTR12D | Mad | 33 | 47 | - | 16.12 | GAGGCGCCGAGAGCG |
| LTR12D | ZNF768 | 115 | 123 | + | 16.08 | CCCTCTCTG |
| LTR12D | IME1 | 247 | 254 | - | 15.91 | CCGCCGAG |
| LTR12D | KLF5 | 764 | 773 | - | 15.88 | GCCCCACCCA |
| LTR12D | PLAGL2 | 109 | 116 | - | 15.67 | GGGCCCCC |
| LTR12D | ERF109 | 1029 | 1036 | + | 15.56 | GCGCCGCC |
| LTR12D | ERF109 | 903 | 910 | + | 15.56 | GCGCCGCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
