Charlie13b
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000087 |
|---|---|
| TE superfamily | Charlie |
| TE class | DNA |
| Species | Mammalia |
| Length | 512 |
| Kimura value | 31.78 |
| Tau index | 1.0000 |
| Description | hAT-Charlie DNA transposon, Charlie13b subfamily (non-autonomous) |
| Comment | Vague 8bp TSDs flank the current ends. |
| Sequence |
CANGGGCATCCAACATGCGGCCCGCGGGCCAAATGCGGCCCGCCTGACCCCAGGGTGCGGCCCGCCTGAGATTTTTAGCAAAAATGTTTTTACCTAATTAGCTAGCACACATGAACTAGTAGGGCCAGNAGGGCCTAACCACCTGCCCGCCGCACCACTGTGTAACTGACTGCCGCCAGGTGTCATGCTAGCAGGCTTGGATCAATTAGTAATTGTAATTGAAGCTGAATGTAATTAATTATATAATTTTGAGCTGTTCAAGTTTAATTCCACTAAAATTACATCATGAAACTGGGGCATTATGAAGGATTACTGACAAAAGGAAAATAGGTATGAATAAAGCCTCCATATGCACTTGACTCACGTTTGAGTCACGTCCAATACTCGTACGCCAAGCGTGGACCCTCTCGACTCACCATTGTTATCAATAAAAAAATTCATGCGGCCCGCACACATATGGATTTCTGATCATGTGGCCCACTATTGAAAAAACNTGGACGCCCCTGCCCTAG
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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 |
|---|---|---|---|---|---|---|
| Charlie13b | THRB | 171 | 188 | + | 3.67 | TGCCGCCAGGTGTCATGC |
| Charlie13b | TFAP4::FLI1 | 132 | 145 | + | 2.50 | GGCCTAACCACCTG |
| Charlie13b | Fer1 | 174 | 186 | - | 2.46 | ATGACACCTGGCG |
| Charlie13b | TGIF1 | 174 | 185 | + | 1.08 | CGCCAGGTGTCA |
| Charlie13b | ZNF558 | 216 | 244 | - | 0.47 | ATATAATTAATTACATTCAGCTTCAATTA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
