LTR86C
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000610 |
|---|---|
| TE superfamily | ERV3 |
| TE order | LTR |
| Species | Eutheria |
| Length | 621 |
| Kimura value | 33.83 |
| Tau index | 1.0000 |
| Description | LTR86C (Long Terminal Repeat) for ERVL endogenous retrovirus |
| Comment | 5 bp TSDs, with a bias for NNNNC. |
| Sequence |
TGCAGGATAGGCCCTATAGCTGGTCTAAGGGCCTGTTAGCATGACTCCCAGAGACGTCTGGGTAACTGACCCTTGTTCTAGTTCCGCAGCNCTGAGTTCAGGAATGTACTTGGACCAGGCTGTGTTAGCCTGGGGAGGCTGAGGGTGATAAATGAGGACTGTGTTCATGCCTGAGTGTACTGTACTGTACTGTGCTCTGCAGTCATATTGTATATTGTATAACTCCGAGATTGATGAGGTGCACCTGGCCCAGATGAGGTGGTCCCCGGCACATATCCAGACTAGCCTACGTGCAGAACTGCTCCAGCCTTATGTATATAAGGCTGGGCTTGGAGGGGGGCAGTTGAGCTTCCAGAAGGTCTGATGTGACCCTCACTCACTCAGACGTTATCATCCGCAACTGTGCGCCCCCTGGTGAGGATCTTGGGGTCCGGAAGCTTGCACCTCCGTCTGTCCTGGAGAATGTTGCTGATCTCTCTGCCGTGTATCCTGACTGCGCTGACTTCCTTCTGTATCCTTTAGATAAGTAAACCTTGTTTGATTTACCCAAGTGGTGTCTGTGTCTGGTCTTTCCGTCAATCTGAACCTACTATTGACATTTGTCAATACAGTGGTCGTGCA
|
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 |
|---|---|---|---|---|---|---|
| LTR86C | REST | 62 | 81 | - | 5.83 | CTAGAACAAGGGTCAGTTAC |
| LTR86C | PLAG1 | 398 | 411 | - | 4.81 | GGGGCGCACAGTTG |
| LTR86C | PKNOX2 | 594 | 605 | + | 4.21 | TGACATTTGTCA |
| LTR86C | Poxm | 163 | 177 | - | 0.11 | CACTCAGGCATGAAC |
| LTR86C | RFX1 | 34 | 49 | + | -1.78 | TGTTAGCATGACTCCC |
| LTR86C | ZSCAN16 | 116 | 133 | - | -24.21 | CCAGGCTAACACAGCCTG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
