Charlie17b
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000094 |
|---|---|
| TE superfamily | Charlie |
| TE class | DNA |
| Species | Eutheria |
| Length | 1204 |
| Kimura value | 26.22 |
| Tau index | 0.9500 |
| Description | hAT-Charlie DNA transposon, Charlie17b subfamily |
| Comment | Charlie17b TSD is 'CTCTAGAG' |
| Sequence |
CAGAGCTTCCCAACCGGTGTGCCGCGAATGGGTTACAGGTGTGCCGNGAGATACTGATCCCCTCAGCCCTCGGGGCGGCCGGGCGGGGCCTGGGGCGGCCGGAGCCCCCGGGCCGGTCGCCTCCGGCCGCGAGCAGCCTCGTCCGGGGCTCCTCGGAGGGCGGCCCGAGCGGAGCGGGGTCTGACGGCGCGCCCCGCGGTCCCCGCAGGCGGCGAGCACGATGAGCGACATCCGGCACTCGCTGCTCCGCCGCGACGCGCTGAGCGCGGCCAAGGAGGTGCTCTACCACCTGGACATCTACTTCAGCAGCCAGCTGCAGAGCGCGCCGCTGCCCATCGTGGACAAGGGGCCCGCGGAGCTGCTGGAGGAGTTCGTGTTCCAGGTGCCCAAGGAGCACGGCGCGCAGCCCAAGGTGCGGCCAGTTGGGGNCGGAGAGGCTGGGAGAGCCGGCAGGGGCTCCTGGCGGGCGCAGCTCCAGGCGGCGGCCCCGAATCTCTGTCTTCACATATATCGGATACTTCTGTCCGTTTGCGGCTGATGTGCCCTTTTAGTGGCGTCCAAGCTAGCTGCAGGGTGACTGCTCTAACAATGCATGCGCGTTCTGCAAATTAGAGCTTCATCATTATTTTGAAATACTTGATATGAAAAAGTTCGATTGGATTCGAAATCCATTCGCATTATCACAAGAAATTTCAACATTACATTTGTCAATGAAAGAAAAGGAAGAGCTGTTAGATTCTTTAAATATAATTTCAACTGTTGTAAATTTTTGAATGGTTGTAAAAATGGTTTTAAATTTTTTATCACCTACTTGTGCGAACAAAGTTTCTCGTCGATGGTGACTATCAAGAATTTGAAGAGATCATCATTAAAAAGTCTTGATCAGGAATTGCGTGTAGCCATTTCAAGCATAAAACCTGATATNAAAAAGTTATGTTCACGGAAGCAAGCTCAAGTTTCTCATTAAAAATTTTGAAAAGATTTTATTTGGAAGTTTTATACAAATTCAATATTTAATATCTTCCCTAATACTTTGTATTTTATTTTTCTTATCATAATTATATAATATAAAGAAAATGTAATGAATTTTTTCACCAAGCCCCATATAGACGCCCCCAAATCCCCTCCAGTTTACCCCAGTGTGCCGTACAAATATTATCATTTTCTATGTGTGCCATGACGTGAAAAAGGTTGGGAAGCACTG
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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 |
|---|---|---|---|---|---|---|
| Charlie17b | Zm00001d052229 | 478 | 487 | - | 16.96 | GGCCGCCGCC |
| Charlie17b | Zm00001d002364 | 478 | 487 | - | 16.92 | GGCCGCCGCC |
| Charlie17b | TFAP2A | 65 | 77 | + | 16.85 | AGCCCTCGGGGCG |
| Charlie17b | TFAP2C | 65 | 77 | - | 16.69 | CGCCCCGAGGGCT |
| Charlie17b | Zm00001d049364 | 478 | 488 | - | 16.68 | GGGCCGCCGCC |
| Charlie17b | PATZ1 | 79 | 89 | + | 16.65 | CCGGGCGGGGC |
| Charlie17b | TCX6 | 964 | 978 | - | 16.64 | TTTCAAAATTTTTAA |
| Charlie17b | TFAP2B | 65 | 77 | + | 16.49 | AGCCCTCGGGGCG |
| Charlie17b | TFAP2B | 65 | 77 | - | 16.39 | CGCCCCGAGGGCT |
| Charlie17b | TFAP2A | 65 | 77 | - | 16.33 | CGCCCCGAGGGCT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
