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 | ERF076 | 713 | 722 | + | 15.48 | CCGCCGCCAT |
| LTR17 | ZIC4 | 202 | 215 | - | 15.35 | TCCCTCCCGCTGTG |
| LTR17 | Zm00001d052229 | 711 | 720 | + | 15.25 | GCCCGCCGCC |
| LTR17 | Os05g0497200 | 714 | 721 | + | 15.23 | CGCCGCCA |
| LTR17 | CRF2 | 713 | 720 | + | 15.20 | CCGCCGCC |
| LTR17 | opa | 766 | 777 | + | 15.15 | GACCCCCCGGTA |
| LTR17 | PK17878.1 | 714 | 721 | + | 15.11 | CGCCGCCA |
| LTR17 | HAP3 | 178 | 186 | - | 15.11 | TGATTGGCT |
| LTR17 | ZIC5 | 201 | 215 | - | 15.06 | TCCCTCCCGCTGTGC |
| LTR17 | POU3F3 | 141 | 153 | + | 14.96 | AAAATGCTAATTA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
