LTR85b
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000604 |
|---|---|
| TE superfamily | Gypsy |
| TE order | 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
|
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 | TFAP2B | 152 | 162 | + | 15.02 | CCCCCAGGGCA |
| LTR85b | Fer1 | 761 | 773 | + | 14.98 | ACCTCAGCTGACA |
| LTR85b | Tbx6 | 135 | 143 | + | 14.98 | GGGTGTGAA |
| LTR85b | ERF014 | 357 | 371 | - | 14.95 | CCACCTCCGCCACCG |
| LTR85b | TFAP2C | 152 | 162 | + | 14.83 | CCCCCAGGGCA |
| LTR85b | ERF2 | 356 | 368 | - | 14.65 | CCTCCGCCACCGG |
| LTR85b | NAC69 | 488 | 495 | - | 14.59 | ACAAGGCA |
| LTR85b | ERF077 | 359 | 368 | - | 14.58 | CCTCCGCCAC |
| LTR85b | ZNF341 | 570 | 577 | + | 14.55 | GAACAGCC |
| LTR85b | TWIST1 | 771 | 778 | - | 14.54 | CCAGATGT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
