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 | Klf15 | 959 | 980 | + | 15.80 | GCCACCACACCCCCTTCCCCGG |
| LTR78 | blmp-1 | 943 | 953 | + | 15.76 | GAAAGAGAAAA |
| LTR78 | DOF3.6 | 940 | 960 | - | 15.76 | GCTTCTTTTTTCTCTTTCCCT |
| LTR78 | KLF16 | 962 | 972 | + | 15.74 | ACCACACCCCC |
| LTR78 | PK10344.1 | 312 | 319 | + | 15.74 | GGGACCAC |
| LTR78 | KLF4 | 242 | 249 | + | 15.48 | CCCCACCC |
| LTR78 | Wt1 | 1012 | 1021 | - | 15.43 | CCTCCCCCAG |
| LTR78 | TFCP2 | 113 | 121 | + | 15.35 | AAACCGGTT |
| LTR78 | ZNF281 | 926 | 935 | + | 15.27 | GGGGGAGGAG |
| LTR78 | EBF1 | 638 | 648 | + | 15.23 | TTCCCAGGGGC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
