LTR17
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000427 |
|---|---|
| TE superfamily | ERV1 |
| TE class | LTR |
| Species | Catarrhini |
| Length | 780 |
| Kimura value | 4.64 |
| Tau index | 0.9806 |
| Description | LTR17 (Long Terminal Repeat) for HERV17 endogenous retrovirus |
| Comment | LTR17/HERV17 elements are flanked by 4 bp direct repeats. |
| Sequence |
TGAGAGACAGGACTAGCTGGATTTCCTAGGCCGACTAAGAATCCCTAAGCCTAGCTGGGAAGGTGACCGCATCCACCTTTAAACACGGGGCTTGCAACTTAGCTCACACCCGACCAATCAGGTAGTAAAGAGAGCTCACTAAAATGCTAATTAGGCAAAAACAGGAGGTAAAGAAATAGCCAATCATCTATCGCCTGAGAGCACAGCGGGAGGGACAATGATCGGGATATAAACCCAGGCATTCGAGCCGGCAACGGCNACCCCCTTTGGGTCCCCTCCCTTTGTATGGGAGCTCTGTTTTCACTCTATTAAATCTTGCAACTGCACTCTTCTGGTCCGTGTTTGTTACGGCTCGAGCTGAGCTTTCGCTCGCCGTCCACCACTGCTGTTTGCCGCCGTCGCAGACCCGCCGCTGACTTCCATCCCTCCGGATCCGGCAGGGTGTCCGCTGTGCTCCTGATCCAGCGAGGCGCCCATTGCCGCTCCCGATCGGGCTAAAGGCTTGCCATTGTTCCTGCACGGCTAAGTGCCCGGGTTCGTCCTAATCGAGCTGAACACTAGTCACTGGGTTCCACGGTTCTCTTCCGTGACCCACGGCTTCTAATAGAGCTATAACACTCACCGCATGGCCCAAGATTCCATTCCTTGGAATCCGTGAGGCCAAGAACCCCAGGTCAGAGAACACGAGGCTTGCCACCATCTTGGAAGCGGCCCGCCGCCATTTTGGAAGCGGCCCGCCACCATCTTGGGAGCTCTGGGAGCAAGGACCCCCCGGTAACA
|
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 |
|---|---|---|---|---|---|---|
| LTR17 | PLAG1 | 261 | 274 | - | 4.72 | GGACCCAAAGGGGG |
| LTR17 | Zm00001d020595 | 394 | 403 | - | 3.75 | TGCGACGGCG |
| LTR17 | phol | 695 | 704 | + | 3.00 | CACCATCTTG |
| LTR17 | phol | 739 | 748 | + | 3.00 | CACCATCTTG |
| LTR17 | Zm00001d020595 | 405 | 414 | - | 2.65 | AGCGGCGGGT |
| LTR17 | GLIS3 | 742 | 755 | - | 2.33 | GAGCTCCCAAGATG |
| LTR17 | EWSR1-FLI1 | 412 | 429 | - | -4.47 | GGAGGGATGGAAGTCAGC |
| LTR17 | ZSCAN16 | 289 | 306 | - | -15.30 | GAGTGAAAACAGAGCTCC |
| LTR17 | DAL81 | 705 | 723 | - | -52.00 | AATGGCGGCGGGCCGCTTC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
