LTR12D
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000403 |
|---|---|
| TE superfamily | ERV1 |
| TE order | 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 | EWSR1-FLI1 | 1002 | 1019 | + | -5.74 | GGACGGAAGGAACGAACA |
| LTR12D | GLIS1 | 1050 | 1064 | + | -6.65 | ACACTCACCGCGAAG |
| LTR12D | GLIS1 | 924 | 938 | + | -6.65 | ACACTCACCGCGAAG |
| LTR12D | DAL81 | 176 | 194 | + | -25.74 | GAGAGGCGCGGGCGGGAGC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
