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 | ZNF281 | 1014 | 1023 | + | 20.07 | GGGGGAGGGG |
| LTR78 | Klf15 | 957 | 978 | + | 19.06 | AAGCCACCACACCCCCTTCCCC |
| LTR78 | ZNF148 | 1014 | 1023 | - | 18.97 | CCCCTCCCCC |
| LTR78 | ERF9 | 419 | 437 | + | 18.65 | AGCTGCTCTGACGGCGGAG |
| LTR78 | Wt1 | 924 | 933 | - | 18.54 | CCTCCCCCAC |
| LTR78 | ZNF740 | 731 | 740 | - | 17.57 | CCCCCCCCCC |
| LTR78 | CTCF | 581 | 613 | - | 17.18 | CTGCTGAGGTCCCTTCGCCCCTCCAGGCGGCCC |
| LTR78 | ZNF281 | 242 | 251 | - | 17.16 | GGGGGTGGGG |
| LTR78 | ARF10 | 1233 | 1243 | + | 17.10 | AGTGGGAGACA |
| LTR78 | ERF8 | 427 | 437 | + | 17.06 | TGACGGCGGAG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
