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 | JUN::JUNB | 308 | 318 | - | 15.77 | CGTGACGTCAT |
| Charlie29a | Atf-2 | 307 | 317 | + | 15.75 | AATGACGTCAC |
| Charlie29a | FOSL2::JUN | 308 | 317 | + | 15.73 | ATGACGTCAC |
| Charlie29a | Atf3 | 308 | 317 | - | 15.70 | GTGACGTCAT |
| Charlie29a | TGA9 | 307 | 317 | + | 15.70 | AATGACGTCAC |
| Charlie29a | HOXB13 | 530 | 538 | - | 15.62 | CCAATAAAA |
| Charlie29a | FOSB::JUN | 307 | 317 | + | 15.61 | AATGACGTCAC |
| Charlie29a | FOS::JUN | 308 | 317 | - | 15.49 | GTGACGTCAT |
| Charlie29a | Fos-b | 308 | 317 | - | 15.47 | GTGACGTCAT |
| Charlie29a | Fos-b | 308 | 317 | + | 15.46 | 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.
