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 | Lhx1 | 93 | 102 | + | 13.77 | CCTAATTAGC |
| Charlie13b | fos-1 | 357 | 363 | + | 13.76 | TGACTCA |
| Charlie13b | fos-1 | 368 | 374 | - | 13.76 | TGACTCA |
| Charlie13b | wor | 140 | 146 | + | 13.74 | CACCTGC |
| Charlie13b | sage | 136 | 146 | + | 13.70 | TAACCACCTGC |
| Charlie13b | ERF118 | 147 | 154 | + | 13.60 | CCGCCGCA |
| Charlie13b | MYB113 | 162 | 171 | - | 13.59 | AGTCAGTTAC |
| Charlie13b | ces-2 | 238 | 246 | + | 13.58 | ATTATATAA |
| Charlie13b | ces-2 | 239 | 247 | - | 13.58 | ATTATATAA |
| Charlie13b | MYB43 | 89 | 100 | + | 13.54 | TTTACCTAATTA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
