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 | TCP22 | 179 | 189 | + | 15.38 | GTGGGCCCCGG |
| FordPrefect_a | Foxq1 | 438 | 447 | + | 15.29 | ATTGTTTATA |
| FordPrefect_a | ZNF454 | 147 | 163 | - | 15.28 | GGCTCGGGGCGCCCCGC |
| FordPrefect_a | GLIS2 | 231 | 244 | - | 15.25 | GACCCCACGCATGG |
| FordPrefect_a | TFAP2A | 51 | 59 | + | 15.22 | GCCTCAGGG |
| FordPrefect_a | TFAP2C | 51 | 59 | - | 15.20 | CCCTGAGGC |
| FordPrefect_a | VIT_15s0048g01150 | 179 | 186 | - | 15.13 | GGGCCCAC |
| FordPrefect_a | PLAG1 | 174 | 187 | - | 15.03 | GGGGCCCACGCGGG |
| FordPrefect_a | ZNF692 | 179 | 186 | - | 15.00 | GGGCCCAC |
| FordPrefect_a | ARALYDRAFT_897773 | 179 | 187 | - | 14.87 | GGGGCCCAC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
