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 | TRP2 | 570 | 590 | - | 4.27 | AACTATAAAACCAAAACAAAT |
| Charlie29a | RREB1 | 536 | 554 | - | 3.78 | AAACAAAACTACAAAACCA |
| Charlie29a | RREB1 | 481 | 499 | + | 3.05 | CAGCAAAACAACATCATCC |
| Charlie29a | CG4360 | 488 | 500 | + | 3.03 | ACAACATCATCCG |
| Charlie29a | BACH2 | 303 | 321 | + | 2.51 | GCCAAATGACGTCACGGCG |
| Charlie29a | ZNF558 | 63 | 91 | - | 1.64 | ATCGAAATGAAAACACAAAATTAAAAAAT |
| Charlie29a | IRF4 | 572 | 585 | - | 0.85 | TAAAACCAAAACAA |
| Charlie29a | Rarg | 300 | 316 | + | -3.71 | AAGGCCAAATGACGTCA |
| Charlie29a | E2F7 | 285 | 298 | + | -4.74 | CGTTCGCGCCAAGT |
| Charlie29a | E2F7 | 363 | 376 | - | -6.07 | TTCTCCCACCACTT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
