LTR78
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000583 |
|---|---|
| TE superfamily | ERV1 |
| TE class | LTR |
| Species | Eutheria |
| Length | 1304 |
| Kimura value | 33.80 |
| Tau index | 0.9631 |
| Description | LTR78 (Long Terminal Repeat) for ERV1 endogenous retrovirus |
| Comment | 4 bp TSDs. |
| Sequence |
TGTAACAGGATGTTAAANTGGAAGTTTCGGCTGAGGCACCAAGATACAATAGATACCANATTCCAAAGTGAGGTGCCAGACCACNATGCAGANTTTCAAAGGAGGTGGCCGAAAACCGGTTNNACGACTCTTAAACCCCTCACCCACATCGAGGGTATAAAAGGGTCGGGANGTTGGAGATGAGGGGAGATTTGTGAAGAGGATTTCTTTGGAGAGAGCTGTTGGTGTGCTGTGAGTCCCACCCCACCCCCAAGGAGAGAGGAGGGGGGGTGCTCCCCCTTCACCTCAAGCCNAGNGAGAGGGGCTTCAACGGGACCACTCGGAGAGCTTGATATGTGTCCCCTGCAGTTTGGGGGACACAGTGGACTGGTGTCTGACTCNCGCCTGGGAAATCTAAAGGGCGAGAGACGGGCTGGCCAGCTGCTCTGACGGCGGAGCAAAGGAGAGGTGGCTGCGCTGGGATCGGCCTGCACTCCCAGAGTTTGTCGGGGCAAAGGATGCGTGAGTGTTTCCCGTGGACCAGATGTGGGCCACGCGNGAGAGAGAGCCGGCGTGGGGTCGTCTTAGGTCCTGTCCAAGAGGGCCGCCTGGAGGGGCGAAGGGACCTCAGCAGAGAGAAGCTGGAGGTACCGCCGGATTCCCAGGGGCTGAGGAAGGAGTAAGCGACCAGCCGGAAGAGAGATGCATTCGCCCGCGTCAAGGGAACTGCAGGTGAGAGATCCCCAGCGATGGGGGGGGGGATCTCCGAAGAACCCACGAAAGCGCCCACGAGAGAAAGAGTCAGCTTTAAACACCTGCCAGGCCCAGAGAGCGCGAAGCCAGCTCACAGACAGTACCAGTCAAGTAAGAACTTTCCTGCTCCCCTTNCCTCTCCTCCCTCCCCNCGCTCCAACCCTGGAGGGGTCAGAAACCGCGGTTAGCAAGTGGGGGAGGAGGAGNAGGGAAAGAGAAAAAAGAAGCCACCACACCCCCTTCCCCGGCTGCAGGCTTCCNGCCTGCAGCAGGCCCGAGCTGGGGGAGGGGAGAAGCTTTAACTTTAAATCAAGTTCGGAGTTTTGATTATTACATGGGACTGGACATTTTAATTACTGAATTGAGACTGTGTTTTGTGACTTAAAGTGACCGTAGGACTTTTTATTACCTAAGAGTGACCAGAAAAGTCATGGGACCTGCCCGAGTTTTCATCCAGGGGCAGGGGAAGAACTANCCCCACTGAATAAATTTAAAGGGACAGTGGGAGACAAAAATAAAGTTGCTTTNTGATTACATCCCATGAGTCNTGCTTGTTCAACGTACCGGTTACA
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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 |
|---|---|---|---|---|---|---|
| LTR78 | TCP5 | 312 | 319 | + | 16.15 | GGGACCAC |
| LTR78 | dar1 | 962 | 972 | + | 16.10 | ACCACACCCCC |
| LTR78 | MAZ | 1016 | 1023 | - | 16.08 | CCCCTCCC |
| LTR78 | SP1 | 1015 | 1023 | + | 16.06 | GGGGAGGGG |
| LTR78 | ARF25 | 1233 | 1244 | + | 15.98 | AGTGGGAGACAA |
| LTR78 | TCP4 | 312 | 319 | + | 15.98 | GGGACCAC |
| LTR78 | KLF11 | 963 | 972 | + | 15.87 | CCACACCCCC |
| LTR78 | SP4 | 1015 | 1023 | + | 15.85 | GGGGAGGGG |
| LTR78 | Klf6-7-like | 958 | 977 | + | 15.83 | AGCCACCACACCCCCTTCCC |
| LTR78 | CDX1 | 1133 | 1142 | - | 15.81 | GGTAATAAAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
