Charlie29a
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000104 |
|---|---|
| TE superfamily | Charlie |
| TE class | DNA |
| Species | Eutheria |
| Length | 748 |
| Kimura value | 28.49 |
| Tau index | 0.0000 |
| Description | hAT-Charlie DNA transposon, Charlie29a subfamily (non-autonomous) |
| Comment | Over 1000 copies in the reconstructed laurasiatherian genome. |
| Sequence |
CAGTGTTTCTCAAACTGGGGTCCGCGGACGTATTCTCGGGGGTCCGCGAGTTCTCTACGAGAATTTTTTAATTTTGTGTTTTCATTTCGATGATAATCTAAAAAAATTAATATAAGCATATTCTGGATCATCTGGATGACCACCTTATAACCGAGTACTGCCACGCGATTTCAGTGCCCGCGTTTGCGTTTGTGTTTACGATCGCGTTGGCGCCAAGTAGTACTACTTTAATTGTCGCGGGCTAATGAGAAAAGAACAGAGGCGGACTTAATACGTAAATGATGCGTTCGCGCCAAGTGAAGGCCAAATGACGTCACGGCGCGCTGTACGAACGAAGGTTTCGCAGTAGTTCGAATAGAGAAAAGTGGTGGGAGAATTGAGTCATCACACGGCACACGGTAGTATAGGCATGCCGAACTCAAAAGAACCTGCGCCGTAGCAGTCAGTACCATATTCACGTTGCGAGCGGCGATTTAGTTTCAGCAAAACAACATCATCCGTCACATTAAATTAATGTTGTTAATTTGAATTTTATTGGTTTTGTAGTTTTGTTTGTATTTAATTTGTAAATTTGTTTTGGTTTTATAGTTGTATAAGAGCTATAAGCATAAGGAGTTTATACCTAGTTTTATGTTTGTACATATTTAAGTAACATTATAATAAAAATAATTTAAGTCAACACTGGGGGTCCGCGAGAATTTTTTTCCTTAAAAGGGGTCCGTACATTACTCAAGTTTGAGAAACACTG
|
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 |
|---|---|---|---|---|---|---|
| Charlie29a | CrebB | 308 | 317 | - | 16.92 | GTGACGTCAT |
| Charlie29a | CrebB | 308 | 317 | + | 16.91 | ATGACGTCAC |
| Charlie29a | TGA7 | 308 | 317 | + | 16.89 | ATGACGTCAC |
| Charlie29a | PDR3 | 21 | 28 | + | 16.61 | TCCGCGGA |
| Charlie29a | PDR3 | 21 | 28 | - | 16.61 | TCCGCGGA |
| Charlie29a | TGA2 | 308 | 317 | - | 16.60 | GTGACGTCAT |
| Charlie29a | ATF7 | 308 | 317 | - | 16.57 | GTGACGTCAT |
| Charlie29a | zip-8 | 308 | 316 | + | 16.50 | ATGACGTCA |
| Charlie29a | FOSL2::JUND | 308 | 317 | - | 16.36 | GTGACGTCAT |
| Charlie29a | lin-54 | 522 | 534 | - | 16.34 | TAAAATTCAAATT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
