LTR85b
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000604 |
|---|---|
| TE superfamily | Gypsy |
| TE class | LTR |
| Species | Eutheria |
| Length | 784 |
| Kimura value | 33.12 |
| Tau index | 0.9939 |
| Description | LTR85b (Long Terminal Repeat) with unclear association (possibly Gypsy) |
| Comment | 4 bp TSDs. |
| Sequence |
TGTAACAGAGAGGAAAAAATTGCTATTTAAAACCANAACTGACTGCAGCCGCTTCTGCCTCCTAAGGGAGTGGCANAATTCCTCTCCGGAGNAGATGGCTCTTTGTTTAGGAAAATACCTTGATAGGCCNCTTTGGGTGTGAAAGGTGAGGCCCCCAGGGCATGGTCTGGAAGGAGACAGTGAAACAAAGAGANAGCTAAACTGCTCTGCATAANAAAATGAACAGAATTTNGGGGANNTGGAGGGNNGGNAGGAGAGGGGAGAGGGAGNTGAGAGAGGGGAGACAGGGGCAAGCAACTGAGAGAAGTCAGGAGATATGGGAAGCCTGTGGAGAAAGGTGGCCAGTGAGAAATTCCCGGTGGCGGAGGTGGCCGAAGGACTTTTAAGAACAGGGATGTCTAATATTCAATTTTAAGTTGTTTGCGTTGCTGTGATGTAACCCCCTCCGTCNCCCCAAACCTTCAGTAAAGTCTGCTACACACACAAATGCCTTGTGTGAGTGGTGTTTTGGGGAAATCAAGGAAAGGGGCTGNGTTCCACGTCTGGGTCGGCGCGGAGCAGAGAGAAGAGAACAGCCACGGGAGGTGAGACGCGAGTGAGATCGAGAGTTCAGCGGAAGCAGGAANTCGGAGCCAGAGGTGACCATGAGAACGTAAGCCCCCCGGGAATTCGCAGAAATCTTGGGGAGGGCATTGGACTTCCCACAGGATGTGGGATGGGGGTTTGAGCCAATTTTATTTAAATCTCAAAGGACAGGGTGACCTCAGCTGACATCTGGGTTACA
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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 |
|---|---|---|---|---|---|---|
| LTR85b | ERF104 | 356 | 371 | - | 16.76 | CCACCTCCGCCACCGG |
| LTR85b | PRDM9 | 358 | 377 | + | 16.69 | GGTGGCGGAGGTGGCCGAAG |
| LTR85b | RAP2-6 | 357 | 371 | + | 16.48 | CGGTGGCGGAGGTGG |
| LTR85b | ZKSCAN5 | 581 | 589 | + | 16.46 | GGAGGTGAG |
| LTR85b | DREB2D | 358 | 371 | - | 16.42 | CCACCTCCGCCACC |
| LTR85b | DREB2G | 358 | 371 | + | 16.41 | GGTGGCGGAGGTGG |
| LTR85b | ERF104 | 359 | 374 | - | 16.20 | CGGCCACCTCCGCCAC |
| LTR85b | cg | 477 | 487 | + | 15.88 | ACACACACAAA |
| LTR85b | ERF2 | 359 | 371 | - | 15.77 | CCACCTCCGCCAC |
| LTR85b | RREB1 | 495 | 513 | - | 15.11 | CCCCAAAACACCACTCACA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
