Charlie29a
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000104 |
|---|---|
| TE superfamily | Charlie |
| TE order | 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 | JDP2 | 308 | 317 | + | 18.60 | ATGACGTCAC |
| Charlie29a | Creb5 | 308 | 317 | + | 18.09 | ATGACGTCAC |
| Charlie29a | TCX3 | 521 | 532 | - | 17.89 | AAATTCAAATTA |
| Charlie29a | ATF3 | 308 | 317 | - | 17.83 | GTGACGTCAT |
| Charlie29a | ATF3 | 308 | 317 | + | 17.81 | ATGACGTCAC |
| Charlie29a | JUNB | 308 | 318 | + | 17.57 | ATGACGTCACG |
| Charlie29a | Creb1 | 308 | 317 | + | 17.53 | ATGACGTCAC |
| Charlie29a | Creb1 | 308 | 317 | - | 17.53 | GTGACGTCAT |
| Charlie29a | ATF7 | 308 | 317 | + | 17.53 | ATGACGTCAC |
| Charlie29a | TGA2 | 308 | 317 | + | 17.05 | ATGACGTCAC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
