FordPrefect
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000145 |
|---|---|
| TE superfamily | Tip100 |
| TE class | DNA |
| Species | Eutheria |
| Length | 1683 |
| Kimura value | 23.98 |
| Tau index | 0.8502 |
| Description | hAT-Tip100 DNA transposon, FordPrefect subfamily (non-autonomous) |
| Comment | Has 8bp TSDs. The first 66 bp of FordPrefect are 90% ID, and the last 36 bp are 80% ID to those of Zaphod. FordPrefect does not seem to have had coding capacity and perhaps hitchhiked with Zaphod. |
| Sequence |
CAGTACCGCCCTTAGACCCGGGCAAGCGGGGCCCCTGCCCCGGGCCCCGCGCCTCAGGGGACCCCGTGCTTTGGAGTGCCTTCCTCGAAATTTTCTAAGTCCCCCTCCGGTGCCTGGGACCGGCCGGGGCCGGCAGTGCCATCCGGGCGGGGCGCCCCGAGCCCGGACCGGGACCCGCGTGGGCCCTGGTCCCCGTTTCTCCCCTTCGGGGCGCTCTCCGACCCTCTACCCCGCGCGTGGGGTCGACCAGATGCCCCGAGGAGCTCCGGGACTCGCGCCTATGGGGTCGTCCCGGGGCCCCGTGGCCGGGCCCCGGTTCCAGGAGGGCGGCCTGGCGAGCGGATCGCTCCCGCTGGCCGGCGCGGTATTTCTTTCGCGGGATCGCGCGAGATTGGGCCGCCAGAATGGTGCTGACACGCTGATTTGGGGTGACTCTCACTCACGTCGGACACAGGACGAGTTCAGGGCTCTGGGCTACCGACGGTCCACCGCCGACCCTTGGGCTTGAGCCGCATGTGTGGGCCCATGCGTCGGCTCTCGCCCGTCCGTGTTCCGACCGCGGTGCCGCCTCCGGTCTACAGCACCCGAGGGCGGCGGGGGTGGCGGCAGGCATCCTTTACCCTGTGCGCCTCCCACCGCTGGCACCCAGGGCGGTCACCCCACCCCCTCCGCAGGCTCCGCGCCACGTGTCAGGCAGTCCTCCGGGGGTGGCCGCGCCTATCTCCTCCGAGGGCTTTCGAGACCGTTGCTCCGCAACGCCAACGGGCCCTTCCGATCGATGTCCTCTCTTGCCTCCGATCGATGTGGTGACGTCGTGCTCTCCCGGGTCGGTCTTAAGCCGTGCCGGACGAGGGACGGACATTCCTTGCGCGAATGGGACCGCTCTTCTCGCTCCGCCCACGGGCCCCTCGCCTATCCTCCCCGCTGTGGCGGTGTGTGGAAGGCAGGGGTGCGGTCAACATTGAAAGAGATCACATTCTAGGAATGCAGTGATTACGGCCTAAAGAGTTCAAGAGAAGACATGGTTGGAAGATGTGTTGTTCTACGTTTATGCTATAAAATTCCGAACGGTAAATTTAACATGACCAGAAAACGAATTATCGTTCACATTTTCCTGCATACTCTGGGTAAGACTTGCATTTGTGGTCATCATCAACGAAGCACAGTAACAACCTTTGAGAGAGTCATTGGAAGCCAGTATTCACGGGCGGCACGATGGATGATGCAGCGTCATGAGTAATGATGTAACCAGCATTAAATAAATGGTATTAGGGAACTGCAGAGGCAAGAAGATCTATATTGTTTCAATACAAACAGGTTCCGAAGAGCCATGGCATTGTGAGTAATAACAGCGTTGCTACCTTTTTCTCGCGGTGGGAGATATGAAATTAGCCAGGAACGGCGCATTTGACAATAAAGAACACGAAGAGATGGTTCCTGGACCTGAACAGGAAGAGATGGTGCCTGGACACTACGAAGAATCTTCACGTGCACTGATTGGACAATAAACAAATACGTAAGTACCTCTTCTCTACCCATTATTCTAAATCTTCATCGATAAATCACTATACCTCACATGGGCCCATGAATTTTGTAATACATTTTTAATCAAATTGTTTATATAGACAGGGGCCCCGCAAAAAATATTTGCCCGGGGCCCCGCACACCCTAGGGGCGGCCCTG
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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 |
|---|---|---|---|---|---|---|
| FordPrefect | PATZ1 | 143 | 153 | + | 16.65 | CCGGGCGGGGC |
| FordPrefect | ZmbZIP96 | 682 | 692 | + | 16.63 | GCCACGTGTCA |
| FordPrefect | ZNF257 | 786 | 795 | - | 16.56 | GAGGCAAGAG |
| FordPrefect | Zm00001d002364 | 590 | 599 | - | 16.53 | CCCCGCCGCC |
| FordPrefect | FOXE1 | 1614 | 1625 | - | 16.52 | CTATATAAACAA |
| FordPrefect | Zm00001d052229 | 590 | 599 | - | 16.50 | CCCCGCCGCC |
| FordPrefect | PATZ1 | 590 | 600 | + | 16.36 | GGCGGCGGGGG |
| FordPrefect | TCP23 | 179 | 186 | - | 16.36 | GGGCCCAC |
| FordPrefect | TCP23 | 518 | 525 | - | 16.36 | GGGCCCAC |
| FordPrefect | klu | 593 | 603 | - | 16.33 | CCACCCCCGCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
