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 | ZNF740 | 729 | 738 | - | 17.04 | CCCCCCCCAT |
| LTR78 | CG7928 | 888 | 899 | + | 16.93 | TCCAACCCTGGA |
| LTR78 | DOF4.5 | 1247 | 1259 | + | 16.91 | ATAAAGTTGCTTT |
| LTR78 | SUT2 | 1047 | 1056 | - | 16.90 | AAACTCCGAA |
| LTR78 | ERF4 | 427 | 435 | - | 16.74 | CCGCCGTCA |
| LTR78 | ERF087 | 428 | 437 | + | 16.58 | GACGGCGGAG |
| LTR78 | ARALYDRAFT_496250 | 312 | 319 | + | 16.55 | GGGACCAC |
| LTR78 | LEP | 428 | 437 | - | 16.30 | CTCCGCCGTC |
| LTR78 | TCP3 | 312 | 319 | + | 16.23 | GGGACCAC |
| LTR78 | TCP24 | 312 | 319 | + | 16.21 | GGGACCAC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
