LTR78
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000583 |
|---|---|
| TE superfamily | ERV1 |
| TE order | 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 | RARA | 1117 | 1134 | - | -11.58 | AAAGTCCTACGGTCACTT |
| LTR78 | BPC5 | 1217 | 1246 | + | -42.18 | ATAAATTTAAAGGGACAGTGGGAGACAAAA |
| LTR78 | BPC5 | 1225 | 1254 | + | -44.89 | AAAGGGACAGTGGGAGACAAAAATAAAGTT |
| LTR78 | BPC5 | 1215 | 1244 | + | -45.98 | GAATAAATTTAAAGGGACAGTGGGAGACAA |
| LTR78 | BPC5 | 1219 | 1248 | + | -48.68 | AAATTTAAAGGGACAGTGGGAGACAAAAAT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
