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
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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 |
|---|---|---|---|---|---|---|
| LTR17 | Znf423 | 260 | 274 | + | 14.92 | ACCCCCTTTGGGTCC |
| LTR17 | ERF1B | 714 | 721 | + | 14.91 | CGCCGCCA |
| LTR17 | ERF095 | 390 | 402 | - | 14.89 | GCGACGGCGGCAA |
| LTR17 | Sox17 | 506 | 515 | - | 14.82 | GGAACAATGG |
| LTR17 | ERF077 | 393 | 402 | + | 14.77 | CCGCCGTCGC |
| LTR17 | EREB29 | 712 | 721 | + | 14.76 | CCCGCCGCCA |
| LTR17 | Zm00001d002364 | 711 | 720 | + | 14.71 | GCCCGCCGCC |
| LTR17 | SPIC | 158 | 170 | + | 14.68 | AAAACAGGAGGTA |
| LTR17 | CRF4 | 713 | 722 | + | 14.67 | CCGCCGCCAT |
| LTR17 | ERF017 | 371 | 379 | - | 14.64 | TGGACGGCG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
