FordPrefect_a
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000146 |
|---|---|
| TE superfamily | Tip100 |
| TE class | DNA |
| Species | Eutheria |
| Length | 508 |
| Kimura value | 25.22 |
| Tau index | 0.0000 |
| Description | hAT-Tip100 DNA transposon, FordPrefect_a subfamily (non-autonomous) |
| Comment | FordPrefect_a is an internal deletion product of FordPrefect. It had (at least) 41 CpG dimers, basically representing a mobile CpG island. |
| Sequence |
CAGTACCGCCCTTAGACCCGGGCAAGCGGGGCCCCTGCCCCGGGCCCCGCGCCTCAGGGGACCCCGCGCTTTGGAGTGCCTTCCTCGAAATTTTCTAAGTCCCCCTCCGGTGCCTGGGACCGGCCGGGGCCGGCAGTGCCATCCGGGCGGGGCGCCCCGAGCCCGGACCGGGACCCGCGTGGGCCCCGGTCCCCGTTTCTCCCCTTCGGGGCGCTCTCCGACCCTCTACCCCATGCGTGGGGTCGACCAGATGCCCCGAGGAGCTCCGGGACTCGCGCCTATGGGGTCGTCCCGGGGCCCCGTGGCCGGGCCCCGGTTCCAGGAGGGCGGCCTGGCGAGCGGATCGCTCCCGCTGGCCGGCGCGGTATTTCTTTCGCGGGATCGCGTGAGATTGGGCCGCCAGAATGGTGCTGACACGCTGATTTNGGGTGACTCAAATTGTTTATATAGACAGGGGCCCCGCAAAAAATATTTGCCCGGGGCCCCGCACACCCTAGGGGCGGCCCTG
|
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 |
|---|---|---|---|---|---|---|
| FordPrefect_a | Glyma19g26560.1 | 179 | 186 | - | 14.75 | GGGCCCAC |
| FordPrefect_a | GLYMA19G26560 | 179 | 186 | - | 14.75 | GGGCCCAC |
| FordPrefect_a | Tfcp2l1 | 120 | 133 | - | 14.66 | CCGGCCCCGGCCGG |
| FordPrefect_a | ZNF454 | 105 | 121 | - | 14.63 | GGTCCCAGGCACCGGAG |
| FordPrefect_a | TCP16 | 179 | 186 | + | 14.51 | GTGGGCCC |
| FordPrefect_a | CHES-1-like | 438 | 447 | - | 14.27 | TATAAACAAT |
| FordPrefect_a | luna | 145 | 153 | - | 14.21 | GCCCCGCCC |
| FordPrefect_a | ZNF454 | 36 | 52 | + | 14.16 | TGCCCCGGGCCCCGCGC |
| FordPrefect_a | BAD1 | 178 | 189 | - | 14.13 | CCGGGGCCCACG |
| FordPrefect_a | TCP7 | 179 | 189 | + | 14.08 | GTGGGCCCCGG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
